# Date 2007-10-25 Time 11:36:50 PDT -0700
#phil __OFF__

Command line arguments: "example.pdb" "example.mtz" "params" "--overwrite"

HOST = rosie.lbl.gov
HOSTTYPE = x86_64-linux
USER = afonine
PID = 17065

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: afonine
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Working crystal symmetry after inspecting all inputs:
  Unit cell: (125.959, 125.959, 118.438, 90, 90, 120)
  Space group: P 62 2 2 (No. 180)

example.pdb
  Monomer Library directory:
    "/net/rosie/scratch1/afonine/sources/mon_lib"
  Total number of atoms: 2195
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 2195
      Number of chains: 2
        Number of residues, atoms: 275, 2186
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 257, 'PCIS': 1}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
        Number of residues, atoms: 5, 9
          Unusual residues: {'MG ': 4, 'SO4': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 1.40, per 1000 atoms: 0.64


================================== X-ray data =================================

F-obs:
  example.mtz:F-obs(+),SIGF-obs(+),F-obs(-),SIGF-obs(-)

R-free flags:
  example.mtz:R-free-flags(+),R-free-flags(-)

Miller array info: example.mtz:F-obs(+),SIGF-obs(+),F-obs(-),SIGF-obs(-)
Observation type: xray.amplitude
Type of data: double, size=16371
Type of sigmas: double, size=16371
Number of Miller indices: 16371
Anomalous flag: True
Unit cell: (125.959, 125.959, 118.438, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
Systematic absences: 0
Centric reflections: 1651
Resolution range: 49.5412 3.20045
Completeness in resolution range: 0.94341
Completeness with d_max=infinity: 0.943084
Bijvoet pairs: 7360
Lone Bijvoet mates: 0
Anomalous signal: 0.0000

Number of F-obs in resolution range:                   16371
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  49.5412
                             d_min =   3.2004

Miller array info: example.mtz:R-free-flags(+),R-free-flags(-)
Observation type: None
Type of data: int, size=16869
Type of sigmas: None
Number of Miller indices: 16869
Anomalous flag: True
Unit cell: (125.959, 125.959, 118.438, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
Systematic absences: 0
Centric reflections: 1776
Resolution range: 49.5412 3.20045
Completeness in resolution range: 0.972109
Completeness with d_max=infinity: 0.971773
Bijvoet pairs: 7519
Lone Bijvoet mates: 55

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 49.5471 -  6.8896 [1715/1751]  1532   183  10.7%
  bin  2:  6.8896 -  5.4707 [1699/1730]  1528   171  10.1%
  bin  3:  5.4707 -  4.7798 [1698/1730]  1531   167   9.8%
  bin  4:  4.7798 -  4.3431 [1689/1731]  1510   179  10.6%
  bin  5:  4.3431 -  4.0319 [1668/1741]  1510   158   9.5%
  bin  6:  4.0319 -  3.7943 [1669/1747]  1502   167  10.0%
  bin  7:  3.7943 -  3.6044 [1602/1710]  1441   161  10.0%
  bin  8:  3.6044 -  3.4475 [1571/1752]  1412   159  10.1%
  bin  9:  3.4475 -  3.3148 [1537/1710]  1381   156  10.1%
  bin 10:  3.3148 -  3.2004 [1523/1751]  1371   152  10.0%
                                overall 14718  1653  10.1%

No array of experimental phases found.


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        0.63 -     0.96: 29
        0.96 -     1.28: 417
        1.28 -     1.61: 1352
        1.61 -     1.94: 394
        1.94 -     2.26: 49
  Bond restraints sorted by residual:
                          atom i - atom j                         ideal  model  delta   weight residual
  " C   LEU A 430 " segID="A   " - " N   GLY A 431 " segID="A   " 1.329  0.639  0.690 5.10e+03 2.43e+03
  " C   TRP A 548 " segID="A   " - " N   ALA A 549 " segID="A   " 1.329  0.671  0.658 5.10e+03 2.21e+03
  " C   SER A 475 " segID="A   " - " N   GLU A 476 " segID="A   " 1.329  0.687  0.642 5.10e+03 2.10e+03
  " C   ASP A 460 " segID="A   " - " N   LEU A 461 " segID="A   " 1.329  1.919 -0.590 5.10e+03 1.78e+03
  " CD  GLU A 510 " segID="A   " - " OE1 GLU A 510 " segID="A   " 1.249  2.009 -0.760 2.77e+03 1.60e+03
  ... (remaining 2236 not shown)
  Histogram of nonbonded interaction distances:
        0.74 -     1.57: 7
        1.57 -     2.40: 89
        2.40 -     3.23: 2528
        3.23 -     4.07: 5587
        4.07 -     4.90: 9881
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
                          atom i - atom j                          model   vdw sym.op. j
  " OD2 ASP A 460 " segID="A   " - " MG  MG    593 "               0.737 3.250
  " NH1 ARG A 389 " segID="A   " - " CD1 ILE A 524 " segID="A   "  0.841 3.540 x,x-y,-z+1/3
  " O   ARG A 389 " segID="A   " - " CD1 LEU A 461 " segID="A   "  0.920 3.460
  " NZ  LYS A 489 " segID="A   " - " N   ASN A 527 " segID="A   "  1.070 3.200 -x+2,-x+y+1,-z+1/3
  " CZ  ARG A 389 " segID="A   " - " CD1 ILE A 524 " segID="A   "  1.099 3.690 x,x-y,-z+1/3
  ... (remaining 18087 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.02 -    17.79: 536
       17.79 -    35.57: 179
       35.57 -    53.35: 72
       53.35 -    71.12: 32
       71.12 -    88.90: 12
  Dihedral angle restraints sorted by residual:
  " CA  TYR A 439 " segID="A   "
  " C   TYR A 439 " segID="A   "
  " N   LEU A 440 " segID="A   "
  " CA  LEU A 440 " segID="A   "
      ideal   model   delta periodicty    weight residual
     180.00  127.22   52.78     1       4.00e-02 1.11e+02
  " CA  LEU A 480 " segID="A   "
  " C   LEU A 480 " segID="A   "
  " N   LYS A 481 " segID="A   "
  " CA  LYS A 481 " segID="A   "
      ideal   model   delta periodicty    weight residual
     180.00  130.01   49.99     1       4.00e-02 9.99e+01
  " CA  PRO A 506 " segID="A   "
  " C   PRO A 506 " segID="A   "
  " N   GLU A 507 " segID="A   "
  " CA  GLU A 507 " segID="A   "
      ideal   model   delta periodicty    weight residual
     180.00 -133.27  -46.73     1       4.00e-02 8.74e+01
  ... (remaining 828 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 5
  Type Number    sf(0)   Gaussians
   S       7     15.96       2
   Mg      4     11.95       2
   O     404      7.97       1
   N     381      6.97       1
   C    1399      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = True
individual_adp         = True
group_adp              = True
tls                    = True
individual_occupancies = True
group_occupancies      = True
group_anomalous        = False
size = 2195

n_use            =  2195
n_use_u_iso      =  2195
n_use_u_aniso    =  2186
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2195

================= Automatic adjustment due to TLS refinement. =================

Automatic adjustment due to TLS refinement. 
  adp_restraints.iso.use_u_local_only   = True
  adp_restraints.iso.sphere_radius      = 1.55
  adp_restraints.iso.distance_power     = 0.0 
  adp_restraints.iso.average_power      = 0.0 
  adp_restraints.iso.plain_pairs_radius = 5   
  target_weights.wxu_scale              = 3.0 
  target_weights.wxu_scale              = 0.50

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/home/afonine/public_html/multiple_strategies_example/example_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/afonine/public_html/multiple_strategies_example/example_refine_001.geo

CPU time processing inputs: 4.51


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 125.9589996 125.9589996 118.4380035 90 90 120
    space_group = "P 62 2 2"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/home/afonine/public_html/multiple_strategies_example/example.pdb"
    }
    xray_data {
      file_name = "example.mtz"
      labels = "F-obs(+),SIGF-obs(+),F-obs(-),SIGF-obs(-)"
      r_free_flags {
        file_name = "example.mtz"
        label = "R-free-flags(+),R-free-flags(-)"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "example_refine"
    serial = 1
  }
  refine {
    strategy = *individual_sites *rigid_body *individual_adp *group_adp *tls \
               *individual_occupancies *group_occupancies group_anomalous
    sites {
      individual = "all"
      rigid_body = "(chain A and resid :421)"
      rigid_body = "(chain A and resid 422:)"
    }
    adp {
      individual {
        isotropic = "not (resname SO4 and resid 594)"
      }
      group = "resname SO4 and resid 594"
      one_adp_group_per_residue = False
      tls = "(chain A and resid :421)"
      tls = "(chain A and resid 422:430)"
      tls = "(chain A and resid 431:)"
    }
    occupancies {
      individual = "element Mg"
      group = "resname SO4 and resid 594"
    }
  }
  adp_restraints {
    iso {
      use_u_local_only = True
      sphere_radius = 1.55
      distance_power = 0
      average_power = 0
    }
  }
  target_weights {
    wxu_scale = 0.5
  }
}
#phil __OFF__


============================= ml refinement start =============================


|-Information about rigid groups----------------------------------------------|
| Total number of atoms = 2195    Number of rigid groups = 2                  |
| group: start point:                        end point:                       |
|               x      B  atom   residue <>        x      B  atom   residue   |
|     1:   74.015  10.00   C    GLY  295 <>   78.136  10.00   O    LEU  421   |
|     2:   77.621  20.00   N    GLU  422 <>   86.411  30.00   O    LYS  569   |
|-----------------------------------------------------------------------------|


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.5302   r_free= 0.5312   ksol= 0.00   Bsol= 0.00   scale= 0.029    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.39 A                  |
| x-ray target function (ml) for work reflections: 3.750057                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 49.5471 -  7.3200 0.98   1267  152 0.5397 0.4708      4.8242       4.818|
|  2:  7.3200 -  5.8130 0.99   1293  143 0.4927 0.4149      4.2116      4.2058|
|  3:  5.8130 -  5.0790 0.98   1262  142 0.4583 0.4853      4.1105      4.0518|
|  4:  5.0790 -  4.6150 0.98   1281  147 0.4848 0.5230      4.1502      4.0633|
|  5:  4.6150 -  4.2844 0.98   1272  144 0.4769 0.5451      4.0911      3.8942|
|  6:  4.2844 -  4.0319 0.95   1236  130 0.5055 0.5108      3.8028      3.8347|
|  7:  4.0319 -  3.8301 0.96   1234  139 0.5209 0.5777      3.6471      3.6868|
|  8:  3.8301 -  3.6634 0.94   1245  132 0.5259 0.4314      3.4939      3.3103|
|  9:  3.6634 -  3.5224 0.90   1162  132 0.5223 0.5408      3.3018      3.2121|
| 10:  3.5224 -  3.4009 0.91   1157  135 0.5196 0.5144      3.1512      3.1556|
| 11:  3.4009 -  3.2946 0.90   1198  135 0.5174 0.5209      3.0339      3.0181|
| 12:  3.2946 -  3.2004 0.86   1111  122 0.5017 0.3863      2.9342      2.7602|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error    Alpha        Beta  |
|  #        range        work  test        work    test                       |
|  1: 49.5471 -  7.3200  1267   152  0.48  52.81  50.56     0.03       2735.87|
|  2:  7.3200 -  5.8130  1293   143  0.35  63.32  59.64     0.02       1475.61|
|  3:  5.8130 -  5.0790  1262   142  0.45  55.68  56.11     0.02        837.50|
|  4:  5.0790 -  4.6150  1281   147  0.41  58.92  60.15     0.02        740.41|
|  5:  4.6150 -  4.2844  1272   144  0.35  63.45  67.74     0.01        680.22|
|  6:  4.2844 -  4.0319  1236   130  0.34  64.51  65.41     0.01        517.36|
|  7:  4.0319 -  3.8301  1234   139  0.36  63.22  62.77     0.01        358.26|
|  8:  3.8301 -  3.6634  1245   132  0.38  61.42  59.76     0.01        241.83|
|  9:  3.6634 -  3.5224  1162   132  0.30  67.45  68.38     0.01        189.50|
| 10:  3.5224 -  3.4009  1157   135  0.33  65.57  66.31     0.01        142.16|
| 11:  3.4009 -  3.2946  1198   135  0.38  61.22  61.47     0.01        105.23|
| 12:  3.2946 -  3.2004  1111   122  0.64  41.28  40.84     0.02         48.32|
|alpha:            min =        0.01 max =            0.03 mean =         0.02|
|beta:             min =       48.32 max =         2735.87 mean =       692.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.95 mean =        59.99|
|phase err.(test): min =        0.00 max =           89.92 mean =        59.98|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 9
total                    = 9

             ----------Target weights (before refinement)----------            


|-target weights and weight scales -------------------------------------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =           24.369020 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            1.278238 | wxu_scale =          0.500 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   89.426 (deg)            |
| angle between Xray and ADP gradient vectors:        89.621 (deg)            |
|-----------------------------------------------------------------------------|

        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.076:   946 |   0.002 -   5.373:  1387 |  0.737 -  1.154:        6 |
| 0.076 - 0.152:   596 |   5.373 -  10.745:   811 |  1.154 -  1.570:        1 |
| 0.152 - 0.228:   242 |  10.745 -  16.117:   364 |  1.570 -  1.986:       22 |
| 0.228 - 0.304:   203 |  16.117 -  21.489:   218 |  1.986 -  2.402:       67 |
| 0.304 - 0.380:   107 |  21.489 -  26.861:   133 |  2.402 -  2.819:      750 |
| 0.380 - 0.456:    72 |  26.861 -  32.233:    77 |  2.819 -  3.235:     1778 |
| 0.456 - 0.532:    45 |  32.233 -  37.605:    36 |  3.235 -  3.651:     2318 |
| 0.532 - 0.608:    19 |  37.605 -  42.977:     9 |  3.651 -  4.067:     3269 |
| 0.608 - 0.684:     6 |  42.977 -  48.349:     2 |  4.067 -  4.484:     4252 |
| 0.684 - 0.760:     5 |  48.349 -  53.720:     3 |  4.484 -  4.900:     5629 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2241 |   0.188    0.760  0.000 |      96.812 |              |
|     angle |     3040 |  11.665   53.720  0.002 |      42.524 |              |
| chirality |      337 |   0.932    3.229  0.003 |      21.715 |       15.517 |
| planarity |      394 |   0.067    0.249  0.000 |      50.968 |              |
|  dihedral |      831 |  24.175   88.901  0.017 |       3.790 |              |
| nonbonded |     2241 |   4.083    4.900  0.737 |       4.529 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   10.00   40.00   20.18    1.00  1.00   1.00       |
|    all(noH): 2195   2186   10.00   40.00   20.18    1.00  1.00   1.00       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   10.00   40.00   20.18    1.00  1.00   1.00       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  13.000: 1047   |   5:    25.000 -  28.000:    5        |
|      1:    13.000 -  16.000:    0   |   6:    28.000 -  31.000: 1077        |
|      2:    16.000 -  19.000:    0   |   7:    31.000 -  34.000:    0        |
|      3:    19.000 -  22.000:   62   |   8:    34.000 -  37.000:    0        |
|      4:    22.000 -  25.000:    0   |   9:    37.000 -  40.000:    4        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.000 -   1.000: 2186   |   5:     1.000 -   1.000:    0        |
|      1:     1.000 -   1.000:    0   |   6:     1.000 -   1.000:    0        |
|      2:     1.000 -   1.000:    0   |   7:     1.000 -   1.000:    0        |
|      3:     1.000 -   1.000:    0   |   8:     1.000 -   1.000:    0        |
|      4:     1.000 -   1.000:    0   |   9:     1.000 -   1.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 1.00   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.5302   r_free= 0.5312   ksol= 0.00   Bsol= 0.00   scale= 0.029    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.39 A                  |
| x-ray target function (ml) for work reflections: 3.750057                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.4755   r_free= 0.4677   ksol= 0.34   Bsol= 20.00   scale= 0.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.11 A                  |
| x-ray target function (ml) for work reflections: 3.705985                   |
|-----------------------------------------------------------------------------|

============================ rigid body refinement ============================

|-Geometry statistics: Before rigid body refinement---------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.076:   946 |   0.002 -   5.373:  1387 |  0.737 -  1.154:        6 |
| 0.076 - 0.152:   596 |   5.373 -  10.745:   811 |  1.154 -  1.570:        1 |
| 0.152 - 0.228:   242 |  10.745 -  16.117:   364 |  1.570 -  1.986:       22 |
| 0.228 - 0.304:   203 |  16.117 -  21.489:   218 |  1.986 -  2.402:       67 |
| 0.304 - 0.380:   107 |  21.489 -  26.861:   133 |  2.402 -  2.819:      750 |
| 0.380 - 0.456:    72 |  26.861 -  32.233:    77 |  2.819 -  3.235:     1778 |
| 0.456 - 0.532:    45 |  32.233 -  37.605:    36 |  3.235 -  3.651:     2318 |
| 0.532 - 0.608:    19 |  37.605 -  42.977:     9 |  3.651 -  4.067:     3269 |
| 0.608 - 0.684:     6 |  42.977 -  48.349:     2 |  4.067 -  4.484:     4252 |
| 0.684 - 0.760:     5 |  48.349 -  53.720:     3 |  4.484 -  4.900:     5629 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: Before rigid body refinement---------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2241 |   0.188    0.760  0.000 |      96.812 |              |
|     angle |     3040 |  11.665   53.720  0.002 |      42.524 |              |
| chirality |      337 |   0.932    3.229  0.003 |      21.715 |       15.517 |
| planarity |      394 |   0.067    0.249  0.000 |      50.968 |              |
|  dihedral |      831 |  24.175   88.901  0.017 |       3.790 |              |
| nonbonded |     2241 |   4.083    4.900  0.737 |       4.529 |              |
|-----------------------------------------------------------------------------|

|-Information about rigid groups----------------------------------------------|
| Total number of atoms = 2195    Number of rigid groups = 2                  |
| group: start point:                        end point:                       |
|               x      B  atom   residue <>        x      B  atom   residue   |
|     1:   74.015  10.00   C    GLY  295 <>   78.136  10.00   O    LEU  421   |
|     2:   77.621  20.00   N    GLU  422 <>   86.411  30.00   O    LYS  569   |
|-----------------------------------------------------------------------------|

Information about resolution zones and data for rigid body refinement:
  Data resolution: 41.23 - 3.20
  Resolution for rigid body refinement: 41.23 - 3.20
  Number of zones for Multi-Zone (MZ) protocol: 5
  Requested number of reflections for first low resolution zone: 250
  High resolution cutoffs for MZ protocol: 
    zone  resolution  number of reflections
     1:   41.23-8.00                  971
     2:   41.23-6.80                  1595
     3:   41.23-5.60                  2853
     4:   41.23-4.40                  5883
     5:   41.23-3.20                  14716

|-Start-(resolution: 3.20 - 49.54 A; n_refl. = 16371)-------------------------|
|                                                                             |
| r_work= 0.4755   r_free= 0.4677   ksol= 0.34   Bsol= 20.00   scale= 0.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
| group    2:    0.000    0.000    0.000    0.00    0.00   0.00   0.00   0.00 |
|-----------------------------------------------------------------------------|

           ----------Refinement at resolution: 41.23 - 8.00----------          

|-Rigid body refinement-(resolution: 3.20 - 49.54 A; n_refl. = 16371)---------|
|                                                                             |
| r_work= 0.3828   r_free= 0.3803   ksol= 0.32   Bsol= 20.00   scale= 0.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -2.279   -1.418   -1.334    2.98   -0.19  -0.14  -0.35   0.42 |
| group    2:   -2.088   -1.870   -1.473    3.15   -0.21  -0.40  -0.60   0.75 |
|-----------------------------------------------------------------------------|

           ----------Refinement at resolution: 41.23 - 6.80----------          

|-Rigid body refinement-(resolution: 3.20 - 49.54 A; n_refl. = 16371)---------|
|                                                                             |
| r_work= 0.3783   r_free= 0.3734   ksol= 0.32   Bsol= 20.00   scale= 0.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -2.405   -1.394   -1.452    3.12   -0.18  -0.19  -0.39   0.47 |
| group    2:   -2.312   -1.687   -1.496    3.21   -0.29  -0.43  -0.66   0.84 |
|-----------------------------------------------------------------------------|

           ----------Refinement at resolution: 41.23 - 5.60----------          

|-Rigid body refinement-(resolution: 3.20 - 49.54 A; n_refl. = 16371)---------|
|                                                                             |
| r_work= 0.3755   r_free= 0.3675   ksol= 0.32   Bsol= 20.00   scale= 0.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -2.540   -1.738   -0.996    3.22   -0.20  -0.25  -0.37   0.49 |
| group    2:   -2.813   -1.453   -1.231    3.38   -0.42  -0.47  -0.72   0.95 |
|-----------------------------------------------------------------------------|

           ----------Refinement at resolution: 41.23 - 4.40----------          

|-Rigid body refinement-(resolution: 3.20 - 49.54 A; n_refl. = 16371)---------|
|                                                                             |
| r_work= 0.3700   r_free= 0.3592   ksol= 0.32   Bsol= 0.00   scale= 0.083    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -2.882   -1.843   -1.104    3.58   -0.19  -0.23  -0.36   0.47 |
| group    2:   -3.183   -1.516   -1.744    3.91   -0.40  -0.52  -0.65   0.93 |
|-----------------------------------------------------------------------------|

           ----------Refinement at resolution: 41.23 - 3.20----------          

|-Rigid body refinement-(resolution: 3.20 - 49.54 A; n_refl. = 16371)---------|
|                                                                             |
| r_work= 0.3700   r_free= 0.3590   ksol= 0.32   Bsol= 0.00   scale= 0.083    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -2.930   -1.972   -0.917    3.64   -0.21  -0.23  -0.34   0.47 |
| group    2:   -3.262   -1.646   -1.651    3.99   -0.40  -0.53  -0.67   0.94 |
|-----------------------------------------------------------------------------|

|-Rigid body end-(resolution: 3.20 - 49.54 A; n_refl. = 16371)----------------|
|                                                                             |
| r_work= 0.3700   r_free= 0.3590   ksol= 0.32   Bsol= 0.00   scale= 0.083    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| Rigid body shift (Euler angles xyz):                                        |
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -2.930   -1.972   -0.917    3.64   -0.21  -0.23  -0.34   0.47 |
| group    2:   -3.262   -1.646   -1.651    3.99   -0.40  -0.53  -0.67   0.94 |
|-----------------------------------------------------------------------------|

|-rigid body shift (total)----------------------------------------------------|
|                            rotation (deg)                 translation (A)   |
|                         xyz              total           xyz          total |
| group    1:   -2.930   -1.972   -0.917    3.64   -0.21  -0.23  -0.34   0.47 |
| group    2:   -3.262   -1.646   -1.651    3.99   -0.40  -0.53  -0.67   0.94 |
|-----------------------------------------------------------------------------|


====================== bulk solvent modeling and scaling ======================

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.3695   r_free= 0.3589   ksol= 0.31   Bsol= 0.00   scale= 0.082    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 3.542661                   |
|-----------------------------------------------------------------------------|
|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.3695   r_free= 0.3589   ksol= 0.31   Bsol= 0.00   scale= 0.082    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 3.542661                   |
|-----------------------------------------------------------------------------|
|-Geometry statistics: After rigid body refinement----------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.122:  1346 |   0.002 -   5.373:  1388 |  1.628 -  1.955:        3 |
| 0.122 - 0.244:   473 |   5.373 -  10.745:   810 |  1.955 -  2.282:       22 |
| 0.244 - 0.366:   256 |  10.745 -  16.117:   365 |  2.282 -  2.609:      178 |
| 0.366 - 0.488:   115 |  16.117 -  21.489:   218 |  2.609 -  2.937:      998 |
| 0.488 - 0.610:    39 |  21.489 -  26.861:   132 |  2.937 -  3.264:     1419 |
| 0.610 - 0.732:    10 |  26.861 -  32.233:    77 |  3.264 -  3.591:     1751 |
| 0.732 - 0.854:     1 |  32.233 -  37.605:    36 |  3.591 -  3.918:     2404 |
| 0.854 - 0.976:     0 |  37.605 -  42.977:     9 |  3.918 -  4.246:     2674 |
| 0.976 - 1.098:     0 |  42.977 -  48.349:     2 |  4.246 -  4.573:     3704 |
| 1.098 - 1.219:     1 |  48.349 -  53.720:     3 |  4.573 -  4.900:     4434 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: After rigid body refinement----------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2241 |   0.190    1.219  0.000 |      99.563 |              |
|     angle |     3040 |  11.657   53.720  0.002 |      42.452 |              |
| chirality |      337 |   0.932    3.229  0.003 |      21.715 |       15.741 |
| planarity |      394 |   0.067    0.249  0.000 |      50.702 |              |
|  dihedral |      831 |  24.168   88.901  0.017 |       3.778 |              |
| nonbonded |     2241 |   4.090    4.900  1.628 |       0.862 |              |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================


|-target weights and weight scales -------------------------------------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            9.132583 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.437432 | wxu_scale =          0.500 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:   88.291 (deg)            |
| angle between Xray and ADP gradient vectors:        89.952 (deg)            |
|-----------------------------------------------------------------------------|

========================== group occupancy refinement =========================

|-group occupancy refinement (macro cycle = 0; iterations = 0)----------------|
| r_work = 0.3695 r_free = 0.3589 target = 3.542661 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 1; iterations = 6)----------------|
| r_work = 0.3686 r_free = 0.3587 target = 3.542171 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 2; iterations = 4)----------------|
| r_work = 0.3686 r_free = 0.3587 target = 3.542171 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 3; iterations = 4)----------------|
| r_work = 0.3686 r_free = 0.3587 target = 3.542171 convergence test = off    |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3686      final r-factor (work) = 0.3407          |
| start r-factor (free) = 0.3587      final r-factor (free) = 0.3609          |
|-----------------------------------------------------------------------------|
| T_start   = wxc      * Exray    + wc       * Echem                          |
| 31.915190 = 4.566292 * 3.542171 + 1.000000 * 15.740604                      |
|-----------------------------------------------------------------------------|
| T_final   = wxc      * Exray    + wc       * Echem                          |
| 16.068021 = 4.566292 * 3.471131 + 1.000000 * 0.217824                       |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   27   |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                       ----------TLS refinement----------                      

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3609 target = 3.472171 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3394 r_free = 0.3596 target = 3.469724 convergence test = off    |
|-----------------------------------------------------------------------------|

|-Information about rigid groups----------------------------------------------|
| Total number of atoms = 2195    Number of rigid groups = 3                  |
| group: start point:                        end point:                       |
|               x      B  atom   residue <>        x      B  atom   residue   |
|     1:   73.542  10.00   C    GLY  295 <>   77.782  10.00   O    LEU  421   |
|     2:   77.683  22.27   N    GLU  422 <>   97.467  22.27   O    LEU  430   |
|     3:   98.230  32.97   N    GLY  431 <>   86.303  32.97   O    LYS  569   |
|-----------------------------------------------------------------------------|

|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 0.135254  r_work = 0.3394  r_free = 0.3596       |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 10.00    max = 40.00    mean = 21.70   |
| Isotropic B only:              min = 5.00     max = 40.00    mean = 5.11    |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      5.000 -    8.500:    2186      |       10.000 -   13.000:    1047      |
|      8.500 -   12.000:       0      |       13.000 -   16.000:       0      |
|     12.000 -   15.500:       0      |       16.000 -   19.000:       0      |
|     15.500 -   19.000:       0      |       19.000 -   22.000:       0      |
|     19.000 -   22.500:       0      |       22.000 -   25.000:      67      |
|     22.500 -   26.000:       5      |       25.000 -   28.000:       0      |
|     26.000 -   29.500:       0      |       28.000 -   31.000:       0      |
|     29.500 -   33.000:       0      |       31.000 -   34.000:    1077      |
|     33.000 -   36.500:       0      |       34.000 -   37.000:       0      |
|     36.500 -   40.000:       4      |       37.000 -   40.000:       4      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7316   57.1008   -3.8786                |
|T11=  0.0633 T22=  0.0633 T33=  0.0633 T12=  0.0000 T13=  0.0000 T23=  0.0000|
|L11=  0.0000 L22= -0.0000 L33= -0.0000 L12= -0.0000 L13=  0.0000 L23=  0.0000|
|S11=  0.0000 S22= -0.0000 S33= -0.0000 S12= -0.0000 S13= -0.0000 S21= -0.0000|
|S23= -0.0000 S31=  0.0000 S32= -0.0000                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2597   37.6441   -3.7929                |
|T11=  0.2187 T22=  0.2187 T33=  0.2187 T12=  0.0000 T13= -0.0000 T23= -0.0000|
|L11=  0.0000 L22= -0.0001 L33= -0.0001 L12=  0.0000 L13= -0.0001 L23= -0.0002|
|S11= -0.0000 S22=  0.0000 S33=  0.0000 S12= -0.0000 S13=  0.0000 S21= -0.0000|
|S23= -0.0000 S31=  0.0000 S32= -0.0000                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7666   27.3236    7.7170                |
|T11=  0.3542 T22=  0.3542 T33=  0.3542 T12=  0.0000 T13= -0.0000 T23=  0.0000|
|L11= -0.0000 L22= -0.0000 L33= -0.0000 L12=  0.0000 L13= -0.0000 L23=  0.0000|
|S11= -0.0000 S22= -0.0000 S33=  0.0000 S12= -0.0000 S13= -0.0000 S21= -0.0000|
|S23=  0.0000 S31= -0.0000 S32= -0.0000                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 5.00     max = 208.91   mean = 60.85   |
| Isotropic B only:              min = 5.00     max = 40.00    mean = 5.11    |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      5.000 -    8.500:    2186      |        5.000 -   25.391:     576      |
|      8.500 -   12.000:       0      |       25.391 -   45.781:     501      |
|     12.000 -   15.500:       0      |       45.781 -   66.172:     311      |
|     15.500 -   19.000:       0      |       66.172 -   86.563:     202      |
|     19.000 -   22.500:       0      |       86.563 -  106.954:     217      |
|     22.500 -   26.000:       5      |      106.954 -  127.344:     145      |
|     26.000 -   29.500:       0      |      127.344 -  147.735:     136      |
|     29.500 -   33.000:       0      |      147.735 -  168.126:      75      |
|     33.000 -   36.500:       0      |      168.126 -  188.516:      24      |
|     36.500 -   40.000:       4      |      188.516 -  208.907:       8      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7316   57.1008   -3.8786                |
|T11= -1.9756 T22=  0.7849 T33= -0.1389 T12=  0.1133 T13= -0.2535 T23=  0.1060|
|L11=  0.2332 L22=  0.1649 L33=  0.2962 L12=  0.0596 L13=  0.0464 L23=  0.1295|
|S11= -0.4770 S22=  0.2198 S33= -0.0000 S12=  1.6187 S13=  0.4149 S21= -4.3700|
|S23= -0.6401 S31= -1.4201 S32=  0.0932                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2597   37.6441   -3.7929                |
|T11=  0.8859 T22=  1.3231 T33=  1.5210 T12=  0.0340 T13=  0.1189 T23=  0.1096|
|L11=  0.0050 L22=  0.0083 L33=  0.0165 L12= -0.0008 L13=  0.0010 L23=  0.0064|
|S11= -0.0033 S22=  0.0857 S33=  0.0000 S12=  0.0101 S13= -0.0729 S21=  0.0036|
|S23=  0.0877 S31=  0.0036 S32=  0.0312                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7666   27.3236    7.7170                |
|T11=  0.9755 T22=  0.5727 T33=  1.0538 T12= -0.1289 T13=  0.5756 T23= -0.1285|
|L11= -0.0924 L22=  0.1521 L33= -0.0400 L12= -0.0149 L13=  0.1123 L23= -0.0339|
|S11= -0.5774 S22=  0.4591 S33=  0.0000 S12=  0.1705 S13= -2.8569 S21= -0.3176|
|S23=  0.1777 S31=  2.8946 S32= -0.4850                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 0.106165  r_work = 0.2965  r_free = 0.3094       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 2------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 7.19     max = 197.78   mean = 58.20   |
| Isotropic B only:              min = 5.00     max = 40.00    mean = 5.11    |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      5.000 -    8.500:    2186      |        7.194 -   26.253:     604      |
|      8.500 -   12.000:       0      |       26.253 -   45.312:     534      |
|     12.000 -   15.500:       0      |       45.312 -   64.371:     308      |
|     15.500 -   19.000:       0      |       64.371 -   83.429:     171      |
|     19.000 -   22.500:       0      |       83.429 -  102.488:     183      |
|     22.500 -   26.000:       5      |      102.488 -  121.547:     141      |
|     26.000 -   29.500:       0      |      121.547 -  140.606:     147      |
|     29.500 -   33.000:       0      |      140.606 -  159.665:      73      |
|     33.000 -   36.500:       0      |      159.665 -  178.724:      26      |
|     36.500 -   40.000:       4      |      178.724 -  197.783:       8      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7316   57.1008   -3.8786                |
|T11= -2.5989 T22=  0.5631 T33=  0.0785 T12=  0.1253 T13= -0.2974 T23=  0.1366|
|L11=  0.3541 L22=  0.2149 L33=  0.4004 L12=  0.0738 L13=  0.0282 L23=  0.1426|
|S11= -0.4816 S22=  0.3574 S33= -0.0000 S12=  1.0657 S13=  0.2273 S21= -5.0832|
|S23= -0.7676 S31= -1.5044 S32=  0.1406                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2597   37.6441   -3.7929                |
|T11=  0.8661 T22=  1.2178 T33=  1.5293 T12= -0.0394 T13=  0.1120 T23=  0.0216|
|L11=  0.0047 L22=  0.0061 L33=  0.0156 L12= -0.0019 L13=  0.0030 L23=  0.0103|
|S11= -0.0114 S22=  0.1013 S33=  0.0000 S12=  0.0122 S13= -0.0948 S21= -0.0009|
|S23=  0.1080 S31=  0.0082 S32=  0.0169                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7666   27.3236    7.7170                |
|T11=  0.9303 T22=  0.6816 T33=  1.0132 T12= -0.0698 T13=  0.5611 T23= -0.1437|
|L11= -0.1204 L22=  0.2094 L33= -0.0554 L12= -0.0025 L13=  0.1214 L23= -0.1015|
|S11= -0.8007 S22=  0.4947 S33=  0.0000 S12=  0.2097 S13= -2.7740 S21= -0.1814|
|S23=  0.3917 S31=  2.4440 S32= -0.6580                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
| target_work(ls_wunit_k1) = 0.105426  r_work = 0.2971  r_free = 0.3120       |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7316   57.1008   -3.8786                |
|T11= -2.5989 T22=  0.5631 T33=  0.0785 T12=  0.1253 T13= -0.2974 T23=  0.1366|
|L11=  0.3541 L22=  0.2149 L33=  0.4004 L12=  0.0738 L13=  0.0282 L23=  0.1426|
|S11= -0.4816 S22=  0.3574 S33= -0.0000 S12=  1.0657 S13=  0.2273 S21= -5.0832|
|S23= -0.7676 S31= -1.5044 S32=  0.1406                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2597   37.6441   -3.7929                |
|T11=  0.8661 T22=  1.2178 T33=  1.5293 T12= -0.0394 T13=  0.1120 T23=  0.0216|
|L11=  0.0047 L22=  0.0061 L33=  0.0156 L12= -0.0019 L13=  0.0030 L23=  0.0103|
|S11= -0.0114 S22=  0.1013 S33=  0.0000 S12=  0.0122 S13= -0.0948 S21= -0.0009|
|S23=  0.1080 S31=  0.0082 S32=  0.0169                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7666   27.3236    7.7170                |
|T11=  0.9303 T22=  0.6816 T33=  1.0132 T12= -0.0698 T13=  0.5611 T23= -0.1437|
|L11= -0.1204 L22=  0.2094 L33= -0.0554 L12= -0.0025 L13=  0.1214 L23= -0.1015|
|S11= -0.8007 S22=  0.4947 S33=  0.0000 S12=  0.2097 S13= -2.7740 S21= -0.1814|
|S23=  0.3917 S31=  2.4440 S32= -0.6580                                       |
|-----------------------------------------------------------------------------|

                 ----------Individual ADP refinement----------                 

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2971      final r-factor (work) = 0.2664          |
| start r-factor (free) = 0.3120      final r-factor (free) = 0.2913          |
|-----------------------------------------------------------------------------|
| T_start  = wxu      * Exray    + wu       * Eadp                            |
| 0.732054 = 0.218716 * 3.347050 + 1.000000 * undef                           |
|-----------------------------------------------------------------------------|
| T_final  = wxu      * Exray    + wu       * Eadp                            |
| 0.698327 = 0.218716 * 3.188043 + 1.000000 * undef                           |
|-----------------------------------------------------------------------------|
| number of iterations =   16    |    number of function evaluations =   27   |
|-----------------------------------------------------------------------------|

               ----------group isotropic ADP refinement----------              

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2664 r_free = 0.2913 target = 3.229990 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2663 r_free = 0.2908 target = 3.227312 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 5)-----------------|
| r_work = 0.2663 r_free = 0.2907 target = 3.227298 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 5)-----------------|
| r_work = 0.2663 r_free = 0.2907 target = 3.227298 convergence test = off    |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   2.43    192.78  69.23    0.00  0.56   0.06       |
|    all(noH): 2195   2186   2.43    192.78  69.23    0.00  0.56   0.06       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   2.43    192.78  69.23    0.00  0.56   0.06       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.425 -  21.461:  356   |   5:    97.604 - 116.640:  199        |
|      1:    21.461 -  40.497:  380   |   6:   116.640 - 135.676:  183        |
|      2:    40.497 -  59.532:  299   |   7:   135.676 - 154.712:  165        |
|      3:    59.532 -  78.568:  303   |   8:   154.712 - 173.747:   48        |
|      4:    78.568 -  97.604:  250   |   9:   173.747 - 192.783:   12        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   0.056: 1522   |   5:     0.279 -   0.335:    6        |
|      1:     0.056 -   0.112:  126   |   6:     0.335 -   0.391:    0        |
|      2:     0.112 -   0.168:  201   |   7:     0.391 -   0.447:    0        |
|      3:     0.168 -   0.224:  195   |   8:     0.447 -   0.503:    0        |
|      4:     0.224 -   0.279:   74   |   9:     0.503 -   0.559:   62        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= occupancy refinement ============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2663      final r-factor (work) = 0.2663          |
| start r-factor (free) = 0.2907      final r-factor (free) = 0.2907          |
|-----------------------------------------------------------------------------|
| T_start  =          * Exray                                                 |
| 3.227298 = 1.000000 * 3.227298 + 0.000000 * undef                           |
|-----------------------------------------------------------------------------|
| T_final  =          * Exray                                                 |
| 3.226805 = 1.000000 * 3.226805 + 0.000000 * undef                           |
|-----------------------------------------------------------------------------|
| number of iterations =    5    |    number of function evaluations =    7   |
|-----------------------------------------------------------------------------|
***
Occupancy refinement result is not accepted.
***

*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.2663   r_free= 0.2907   ksol= 0.31   Bsol= 0.00   scale= 0.109    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 3.227298                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.2640   r_free= 0.2880   ksol= 0.33   Bsol= 20.00   scale= 0.109   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 3.202076                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================


|-target weights and weight scales -------------------------------------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            4.358134 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.274161 | wxu_scale =          0.500 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:  107.507 (deg)            |
| angle between Xray and ADP gradient vectors:       104.041 (deg)            |
|-----------------------------------------------------------------------------|

========================== group occupancy refinement =========================

|-group occupancy refinement (macro cycle = 0; iterations = 0)----------------|
| r_work = 0.2640 r_free = 0.2880 target = 3.202076 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 1; iterations = 4)----------------|
| r_work = 0.2640 r_free = 0.2880 target = 3.202077 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 2; iterations = 4)----------------|
| r_work = 0.2640 r_free = 0.2880 target = 3.202077 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 3; iterations = 4)----------------|
| r_work = 0.2640 r_free = 0.2880 target = 3.202077 convergence test = off    |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2640      final r-factor (work) = 0.2467          |
| start r-factor (free) = 0.2880      final r-factor (free) = 0.2800          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wc       * Echem                           |
| 7.195365 = 2.179067 * 3.202077 + 1.000000 * 0.217824                        |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wc       * Echem                           |
| 7.013378 = 2.179067 * 3.152414 + 1.000000 * 0.144057                        |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   27   |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                       ----------TLS refinement----------                      

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2467 r_free = 0.2800 target = 3.147347 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2467 r_free = 0.2798 target = 3.147246 convergence test = off    |
|-----------------------------------------------------------------------------|

|-Information about rigid groups----------------------------------------------|
| Total number of atoms = 2195    Number of rigid groups = 3                  |
| group: start point:                        end point:                       |
|               x      B  atom   residue <>        x      B  atom   residue   |
|     1:   73.541  82.29   C    GLY  295 <>   77.710  15.67   O    LEU  421   |
|     2:   77.612 106.38   N    GLU  422 <>   97.447  94.10   O    LEU  430   |
|     3:   98.081  67.06   N    GLY  431 <>   86.426  93.63   O    LYS  569   |
|-----------------------------------------------------------------------------|

|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0770295  r_work = 0.2467  r_free = 0.2798      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 2.43     max = 192.78   mean = 69.25   |
| Isotropic B only:              min = 0.00     max = 88.39    mean = 16.16   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -    8.839:     917      |        2.425 -   21.461:     356      |
|      8.839 -   17.677:     453      |       21.461 -   40.497:     380      |
|     17.677 -   26.516:     334      |       40.497 -   59.532:     299      |
|     26.516 -   35.354:     199      |       59.532 -   78.568:     303      |
|     35.354 -   44.193:     134      |       78.568 -   97.604:     250      |
|     44.193 -   53.031:      56      |       97.604 -  116.640:     199      |
|     53.031 -   61.870:      52      |      116.640 -  135.676:     183      |
|     61.870 -   70.708:      31      |      135.676 -  154.712:     165      |
|     70.708 -   79.547:      15      |      154.712 -  173.747:      48      |
|     79.547 -   88.385:       4      |      173.747 -  192.783:      12      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7338   57.1056   -3.8878                |
|T11= -0.0391 T22=  0.5829 T33=  0.1851 T12=  0.0173 T13= -0.0019 T23=  0.1027|
|L11=  0.6350 L22=  4.0462 L33=  0.3746 L12=  0.9926 L13=  0.4230 L23=  1.2970|
|S11= -0.1976 S22=  0.0187 S33=  0.0547 S12=  0.9989 S13=  0.2829 S21= -0.5501|
|S23= -0.1094 S31= -0.1350 S32=  0.0823                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2513   37.6497   -3.7221                |
|T11=  0.8661 T22=  1.2178 T33=  1.5293 T12= -0.0394 T13=  0.1120 T23=  0.0216|
|L11=  0.0173 L22=  0.0027 L33=  0.0142 L12= -0.0055 L13=  0.0064 L23=  0.0126|
|S11= -0.0118 S22=  0.1016 S33=  0.0002 S12=  0.0117 S13= -0.0944 S21= -0.0008|
|S23=  0.1084 S31=  0.0080 S32=  0.0170                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7614   27.3124    7.7127                |
|T11=  0.9495 T22=  0.6071 T33=  1.0325 T12= -0.1010 T13=  0.5098 T23= -0.1375|
|L11=  3.2581 L22= -0.0792 L33=  2.7328 L12= -0.2713 L13=  0.3460 L23= -0.6259|
|S11= -0.9201 S22=  0.4463 S33=  0.1678 S12=  0.2495 S13= -2.2942 S21= -0.1173|
|S23=  0.3184 S31=  2.0375 S32= -0.5752                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 2.62     max = 201.50   mean = 67.14   |
| Isotropic B only:              min = 0.00     max = 88.39    mean = 16.16   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -    8.839:     917      |        2.620 -   22.507:     407      |
|      8.839 -   17.677:     453      |       22.507 -   42.395:     379      |
|     17.677 -   26.516:     334      |       42.395 -   62.282:     328      |
|     26.516 -   35.354:     199      |       62.282 -   82.170:     353      |
|     35.354 -   44.193:     134      |       82.170 -  102.057:     207      |
|     44.193 -   53.031:      56      |      102.057 -  121.945:     186      |
|     53.031 -   61.870:      52      |      121.945 -  141.833:     214      |
|     61.870 -   70.708:      31      |      141.833 -  161.720:      83      |
|     70.708 -   79.547:      15      |      161.720 -  181.608:      30      |
|     79.547 -   88.385:       4      |      181.608 -  201.495:       8      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7338   57.1056   -3.8878                |
|T11= -0.3105 T22=  0.5560 T33=  0.1063 T12=  0.0670 T13= -0.0355 T23=  0.0999|
|L11=  0.6364 L22=  4.0411 L33=  0.3750 L12=  0.9921 L13=  0.4238 L23=  1.2941|
|S11= -0.2073 S22=  0.0230 S33=  0.0547 S12=  1.0251 S13=  0.2922 S21= -0.6469|
|S23= -0.1074 S31= -0.1631 S32=  0.0837                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2513   37.6497   -3.7221                |
|T11=  0.8688 T22=  1.2236 T33=  1.5351 T12= -0.0352 T13=  0.1155 T23=  0.0231|
|L11=  0.0173 L22=  0.0026 L33=  0.0144 L12= -0.0056 L13=  0.0065 L23=  0.0127|
|S11= -0.0118 S22=  0.1038 S33=  0.0002 S12=  0.0122 S13= -0.0956 S21= -0.0012|
|S23=  0.1091 S31=  0.0071 S32=  0.0165                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7614   27.3124    7.7127                |
|T11=  0.8698 T22=  0.5777 T33=  1.0160 T12= -0.1014 T13=  0.5314 T23= -0.1555|
|L11=  3.2534 L22= -0.0781 L33=  2.7244 L12= -0.2730 L13=  0.3464 L23= -0.6268|
|S11= -0.9042 S22=  0.4584 S33=  0.1678 S12=  0.2480 S13= -2.3294 S21= -0.1187|
|S23=  0.3193 S31=  2.0885 S32= -0.5672                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 0.0771834  r_work = 0.2478  r_free = 0.2777      |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 2------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 2.61     max = 201.49   mean = 67.13   |
| Isotropic B only:              min = 0.00     max = 88.39    mean = 16.16   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -    8.839:     917      |        2.612 -   22.500:     407      |
|      8.839 -   17.677:     453      |       22.500 -   42.388:     379      |
|     17.677 -   26.516:     334      |       42.388 -   62.275:     329      |
|     26.516 -   35.354:     199      |       62.275 -   82.163:     352      |
|     35.354 -   44.193:     134      |       82.163 -  102.051:     207      |
|     44.193 -   53.031:      56      |      102.051 -  121.939:     186      |
|     53.031 -   61.870:      52      |      121.939 -  141.826:     214      |
|     61.870 -   70.708:      31      |      141.826 -  161.714:      83      |
|     70.708 -   79.547:      15      |      161.714 -  181.602:      30      |
|     79.547 -   88.385:       4      |      181.602 -  201.490:       8      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7338   57.1056   -3.8878                |
|T11= -0.3120 T22=  0.5559 T33=  0.1060 T12=  0.0672 T13= -0.0357 T23=  0.0999|
|L11=  0.6365 L22=  4.0411 L33=  0.3750 L12=  0.9921 L13=  0.4238 L23=  1.2941|
|S11= -0.2074 S22=  0.0230 S33=  0.0547 S12=  1.0252 S13=  0.2923 S21= -0.6476|
|S23= -0.1074 S31= -0.1633 S32=  0.0837                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2513   37.6497   -3.7221                |
|T11=  0.8689 T22=  1.2236 T33=  1.5351 T12= -0.0352 T13=  0.1156 T23=  0.0232|
|L11=  0.0173 L22=  0.0026 L33=  0.0144 L12= -0.0056 L13=  0.0065 L23=  0.0127|
|S11= -0.0118 S22=  0.1039 S33=  0.0002 S12=  0.0122 S13= -0.0957 S21= -0.0012|
|S23=  0.1091 S31=  0.0071 S32=  0.0165                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7614   27.3124    7.7127                |
|T11=  0.8693 T22=  0.5776 T33=  1.0159 T12= -0.1014 T13=  0.5315 T23= -0.1556|
|L11=  3.2533 L22= -0.0781 L33=  2.7244 L12= -0.2730 L13=  0.3464 L23= -0.6268|
|S11= -0.9041 S22=  0.4585 S33=  0.1678 S12=  0.2480 S13= -2.3296 S21= -0.1188|
|S23=  0.3193 S31=  2.0888 S32= -0.5671                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
| target_work(ls_wunit_k1) = 0.0771831  r_work = 0.2478  r_free = 0.2777      |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7338   57.1056   -3.8878                |
|T11= -0.3120 T22=  0.5559 T33=  0.1060 T12=  0.0672 T13= -0.0357 T23=  0.0999|
|L11=  0.6365 L22=  4.0411 L33=  0.3750 L12=  0.9921 L13=  0.4238 L23=  1.2941|
|S11= -0.2074 S22=  0.0230 S33=  0.0547 S12=  1.0252 S13=  0.2923 S21= -0.6476|
|S23= -0.1074 S31= -0.1633 S32=  0.0837                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2513   37.6497   -3.7221                |
|T11=  0.8689 T22=  1.2236 T33=  1.5351 T12= -0.0352 T13=  0.1156 T23=  0.0232|
|L11=  0.0173 L22=  0.0026 L33=  0.0144 L12= -0.0056 L13=  0.0065 L23=  0.0127|
|S11= -0.0118 S22=  0.1039 S33=  0.0002 S12=  0.0122 S13= -0.0957 S21= -0.0012|
|S23=  0.1091 S31=  0.0071 S32=  0.0165                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7614   27.3124    7.7127                |
|T11=  0.8693 T22=  0.5776 T33=  1.0159 T12= -0.1014 T13=  0.5315 T23= -0.1556|
|L11=  3.2533 L22= -0.0781 L33=  2.7244 L12= -0.2730 L13=  0.3464 L23= -0.6268|
|S11= -0.9041 S22=  0.4585 S33=  0.1678 S12=  0.2480 S13= -2.3296 S21= -0.1188|
|S23=  0.3193 S31=  2.0888 S32= -0.5671                                       |
|-----------------------------------------------------------------------------|

                 ----------Individual ADP refinement----------                 

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2478      final r-factor (work) = 0.2471          |
| start r-factor (free) = 0.2777      final r-factor (free) = 0.2736          |
|-----------------------------------------------------------------------------|
| T_start  = wxu      * Exray    + wu       * Eadp                            |
| 0.447034 = 0.137081 * 3.145873 + 1.000000 * undef                           |
|-----------------------------------------------------------------------------|
| T_final  = wxu      * Exray    + wu       * Eadp                            |
| 0.426359 = 0.137081 * 3.093704 + 1.000000 * undef                           |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   26   |
|-----------------------------------------------------------------------------|

               ----------group isotropic ADP refinement----------              

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2471 r_free = 0.2736 target = 3.132141 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2471 r_free = 0.2734 target = 3.132093 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2471 r_free = 0.2734 target = 3.132093 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2471 r_free = 0.2734 target = 3.132093 convergence test = off    |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   2.68    202.30  75.20    0.00  0.56   0.07       |
|    all(noH): 2195   2186   2.68    202.30  75.20    0.00  0.56   0.07       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   2.68    202.30  75.20    0.00  0.56   0.07       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.681 -  22.643:  322   |   5:   102.490 - 122.452:  199        |
|      1:    22.643 -  42.604:  413   |   6:   122.452 - 142.413:  162        |
|      2:    42.604 -  62.566:  308   |   7:   142.413 - 162.375:  215        |
|      3:    62.566 -  82.528:  276   |   8:   162.375 - 182.337:   73        |
|      4:    82.528 - 102.490:  213   |   9:   182.337 - 202.299:   14        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   0.056: 1357   |   5:     0.279 -   0.335:    2        |
|      1:     0.056 -   0.112:  210   |   6:     0.335 -   0.391:    0        |
|      2:     0.112 -   0.167:  317   |   7:     0.391 -   0.447:    0        |
|      3:     0.167 -   0.223:  189   |   8:     0.447 -   0.502:    0        |
|      4:     0.223 -   0.279:   49   |   9:     0.502 -   0.558:   62        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= occupancy refinement ============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2471      final r-factor (work) = 0.2471          |
| start r-factor (free) = 0.2734      final r-factor (free) = 0.2734          |
|-----------------------------------------------------------------------------|
| T_start  =          * Exray                                                 |
| 3.132093 = 1.000000 * 3.132093 + 0.000000 * undef                           |
|-----------------------------------------------------------------------------|
| T_final  =          * Exray                                                 |
| 3.131328 = 1.000000 * 3.131328 + 0.000000 * undef                           |
|-----------------------------------------------------------------------------|
| number of iterations =    5    |    number of function evaluations =    7   |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 3 *************************

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.2471   r_free= 0.2734   ksol= 0.33   Bsol= 20.00   scale= 0.115   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 3.132093                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.2511   r_free= 0.2738   ksol= 0.33   Bsol= 23.96   scale= 0.114   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 3.132243                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================


|-target weights and weight scales -------------------------------------------|
| target for coordinate refinement: T = Exray * wxc * wxc_scale + Echem * wc  |
| target for ADP refinement:        T = Exray * wxu * wxu_scale + Eadp * wu   |
| wxc =            5.025892 | wxc scale =          0.500 | wc =         1.000 |
| wxu =            0.257335 | wxu_scale =          0.500 | wu =         1.000 |
| angle between Xray and Geometry gradient vectors:  127.063 (deg)            |
| angle between Xray and ADP gradient vectors:       106.343 (deg)            |
|-----------------------------------------------------------------------------|

========================== group occupancy refinement =========================

|-group occupancy refinement (macro cycle = 0; iterations = 0)----------------|
| r_work = 0.2511 r_free = 0.2738 target = 3.132243 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 1; iterations = 5)----------------|
| r_work = 0.2510 r_free = 0.2738 target = 3.132189 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 2; iterations = 4)----------------|
| r_work = 0.2510 r_free = 0.2738 target = 3.132189 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group occupancy refinement (macro cycle = 3; iterations = 4)----------------|
| r_work = 0.2510 r_free = 0.2738 target = 3.132189 convergence test = off    |
|-----------------------------------------------------------------------------|

================================ xyz refinement ===============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2510      final r-factor (work) = 0.2365          |
| start r-factor (free) = 0.2738      final r-factor (free) = 0.2708          |
|-----------------------------------------------------------------------------|
| T_start  = wxc      * Exray    + wc       * Echem                           |
| 8.015132 = 2.512946 * 3.132189 + 1.000000 * 0.144110                        |
|-----------------------------------------------------------------------------|
| T_final  = wxc      * Exray    + wc       * Echem                           |
| 7.928340 = 2.512946 * 3.091007 + 1.000000 * 0.160806                        |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   28   |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                       ----------TLS refinement----------                      

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2365 r_free = 0.2708 target = 3.092948 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 5)-----------------|
| r_work = 0.2366 r_free = 0.2708 target = 3.092878 convergence test = off    |
|-----------------------------------------------------------------------------|

|-Information about rigid groups----------------------------------------------|
| Total number of atoms = 2195    Number of rigid groups = 3                  |
| group: start point:                        end point:                       |
|               x      B  atom   residue <>        x      B  atom   residue   |
|     1:   73.553  97.16   C    GLY  295 <>   77.697  27.22   O    LEU  421   |
|     2:   77.641 113.03   N    GLU  422 <>   97.303 102.86   O    LEU  430   |
|     3:   97.966  59.48   N    GLY  431 <>   86.524 109.22   O    LYS  569   |
|-----------------------------------------------------------------------------|

|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0702643  r_work = 0.2366  r_free = 0.2708      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 2.68     max = 202.30   mean = 75.21   |
| Isotropic B only:              min = 0.00     max = 103.19   mean = 24.24   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   10.319:     601      |        2.681 -   22.643:     322      |
|     10.319 -   20.639:     463      |       22.643 -   42.604:     413      |
|     20.639 -   30.958:     446      |       42.604 -   62.566:     308      |
|     30.958 -   41.277:     306      |       62.566 -   82.528:     276      |
|     41.277 -   51.596:     179      |       82.528 -  102.490:     213      |
|     51.596 -   61.916:      74      |      102.490 -  122.452:     199      |
|     61.916 -   72.235:      59      |      122.452 -  142.413:     162      |
|     72.235 -   82.554:      35      |      142.413 -  162.375:     215      |
|     82.554 -   92.874:      29      |      162.375 -  182.337:      73      |
|     92.874 -  103.193:       3      |      182.337 -  202.299:      14      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7359   57.1081   -3.8900                |
|T11= -0.0229 T22=  0.5542 T33=  0.1384 T12=  0.0416 T13= -0.0110 T23=  0.0858|
|L11=  1.0242 L22=  2.9169 L33=  0.4162 L12=  0.9567 L13=  0.5084 L23=  0.7484|
|S11= -0.1508 S22=  0.0019 S33=  0.0192 S12=  0.9821 S13=  0.2710 S21= -0.3544|
|S23= -0.0495 S31= -0.0925 S32=  0.0769                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2313   37.6583   -3.6175                |
|T11=  0.8689 T22=  1.2236 T33=  1.5352 T12= -0.0352 T13=  0.1156 T23=  0.0232|
|L11=  0.0383 L22= -0.0094 L33=  0.0139 L12= -0.0070 L13=  0.0108 L23=  0.0192|
|S11= -0.0122 S22=  0.1044 S33=  0.0000 S12=  0.0117 S13= -0.0943 S21= -0.0010|
|S23=  0.1100 S31=  0.0066 S32=  0.0166                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7624   27.2978    7.7096                |
|T11=  0.8700 T22=  0.5563 T33=  1.0149 T12= -0.1139 T13=  0.5160 T23= -0.1535|
|L11=  4.0048 L22= -0.1059 L33=  3.6649 L12= -0.3779 L13=  0.2740 L23= -0.7887|
|S11= -0.9191 S22=  0.4404 S33=  0.2009 S12=  0.2615 S13= -2.2338 S21= -0.0999|
|S23=  0.2956 S31=  1.9610 S32= -0.5359                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 2.25     max = 202.90   mean = 72.63   |
| Isotropic B only:              min = 0.00     max = 103.19   mean = 24.24   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   10.319:     601      |        2.250 -   22.316:     363      |
|     10.319 -   20.639:     463      |       22.316 -   42.381:     407      |
|     20.639 -   30.958:     446      |       42.381 -   62.446:     302      |
|     30.958 -   41.277:     306      |       62.446 -   82.511:     305      |
|     41.277 -   51.596:     179      |       82.511 -  102.577:     192      |
|     51.596 -   61.916:      74      |      102.577 -  122.642:     194      |
|     61.916 -   72.235:      59      |      122.642 -  142.707:     176      |
|     72.235 -   82.554:      35      |      142.707 -  162.773:     183      |
|     82.554 -   92.874:      29      |      162.773 -  182.838:      62      |
|     92.874 -  103.193:       3      |      182.838 -  202.903:      11      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7359   57.1081   -3.8900                |
|T11= -0.2288 T22=  0.5180 T33=  0.0600 T12=  0.0655 T13= -0.0353 T23=  0.0727|
|L11=  1.0243 L22=  2.9117 L33=  0.4154 L12=  0.9562 L13=  0.5087 L23=  0.7459|
|S11= -0.1567 S22=  0.0076 S33=  0.0192 S12=  0.9971 S13=  0.2807 S21= -0.4124|
|S23= -0.0480 S31= -0.1051 S32=  0.0828                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2313   37.6583   -3.6175                |
|T11=  0.8681 T22=  1.2233 T33=  1.5355 T12= -0.0335 T13=  0.1161 T23=  0.0231|
|L11=  0.0383 L22= -0.0095 L33=  0.0139 L12= -0.0070 L13=  0.0109 L23=  0.0193|
|S11= -0.0122 S22=  0.1053 S33=  0.0000 S12=  0.0121 S13= -0.0950 S21= -0.0015|
|S23=  0.1108 S31=  0.0062 S32=  0.0165                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7624   27.2978    7.7096                |
|T11=  0.8002 T22=  0.5157 T33=  1.0016 T12= -0.1126 T13=  0.5381 T23= -0.1656|
|L11=  4.0026 L22= -0.1057 L33=  3.6584 L12= -0.3784 L13=  0.2747 L23= -0.7889|
|S11= -0.9150 S22=  0.4451 S33=  0.2009 S12=  0.2623 S13= -2.2447 S21= -0.1016|
|S23=  0.2993 S31=  1.9928 S32= -0.5341                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 0.0698927  r_work = 0.2354  r_free = 0.2695      |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 2------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 1.09     max = 201.13   mean = 70.77   |
| Isotropic B only:              min = 0.00     max = 103.19   mean = 24.24   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   10.319:     601      |        1.087 -   21.091:     368      |
|     10.319 -   20.639:     463      |       21.091 -   41.096:     403      |
|     20.639 -   30.958:     446      |       41.096 -   61.100:     310      |
|     30.958 -   41.277:     306      |       61.100 -   81.105:     309      |
|     41.277 -   51.596:     179      |       81.105 -  101.109:     186      |
|     51.596 -   61.916:      74      |      101.109 -  121.114:     190      |
|     61.916 -   72.235:      59      |      121.114 -  141.118:     184      |
|     72.235 -   82.554:      35      |      141.118 -  161.123:     173      |
|     82.554 -   92.874:      29      |      161.123 -  181.128:      62      |
|     92.874 -  103.193:       3      |      181.128 -  201.132:      10      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7359   57.1081   -3.8900                |
|T11= -0.4038 T22=  0.4985 T33=  0.0102 T12=  0.0865 T13= -0.0560 T23=  0.0696|
|L11=  1.0253 L22=  2.9090 L33=  0.4155 L12=  0.9562 L13=  0.5092 L23=  0.7446|
|S11= -0.1599 S22=  0.0134 S33=  0.0192 S12=  1.0114 S13=  0.2896 S21= -0.4803|
|S23= -0.0482 S31= -0.1236 S32=  0.0887                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2313   37.6583   -3.6175                |
|T11=  0.8670 T22=  1.2226 T33=  1.5355 T12= -0.0320 T13=  0.1166 T23=  0.0228|
|L11=  0.0383 L22= -0.0096 L33=  0.0139 L12= -0.0071 L13=  0.0109 L23=  0.0194|
|S11= -0.0123 S22=  0.1062 S33=  0.0000 S12=  0.0124 S13= -0.0958 S21= -0.0020|
|S23=  0.1117 S31=  0.0058 S32=  0.0163                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7624   27.2978    7.7096                |
|T11=  0.7400 T22=  0.4855 T33=  0.9901 T12= -0.1112 T13=  0.5549 T23= -0.1724|
|L11=  4.0005 L22= -0.1054 L33=  3.6522 L12= -0.3791 L13=  0.2758 L23= -0.7891|
|S11= -0.9115 S22=  0.4506 S33=  0.2009 S12=  0.2638 S13= -2.2555 S21= -0.1038|
|S23=  0.3028 S31=  2.0226 S32= -0.5332                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
| target_work(ls_wunit_k1) = 0.0698805  r_work = 0.2348  r_free = 0.2699      |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7359   57.1081   -3.8900                |
|T11= -0.4038 T22=  0.4985 T33=  0.0102 T12=  0.0865 T13= -0.0560 T23=  0.0696|
|L11=  1.0253 L22=  2.9090 L33=  0.4155 L12=  0.9562 L13=  0.5092 L23=  0.7446|
|S11= -0.1599 S22=  0.0134 S33=  0.0192 S12=  1.0114 S13=  0.2896 S21= -0.4803|
|S23= -0.0482 S31= -0.1236 S32=  0.0887                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =   87.2313   37.6583   -3.6175                |
|T11=  0.8670 T22=  1.2226 T33=  1.5355 T12= -0.0320 T13=  0.1166 T23=  0.0228|
|L11=  0.0383 L22= -0.0096 L33=  0.0139 L12= -0.0071 L13=  0.0109 L23=  0.0194|
|S11= -0.0123 S22=  0.1062 S33=  0.0000 S12=  0.0124 S13= -0.0958 S21= -0.0020|
|S23=  0.1117 S31=  0.0058 S32=  0.0163                                       |
|TLS group number 3:                                                          |
|               Origin (x,y,z) =  101.7624   27.2978    7.7096                |
|T11=  0.7400 T22=  0.4855 T33=  0.9901 T12= -0.1112 T13=  0.5549 T23= -0.1724|
|L11=  4.0005 L22= -0.1054 L33=  3.6522 L12= -0.3791 L13=  0.2758 L23= -0.7891|
|S11= -0.9115 S22=  0.4506 S33=  0.2009 S12=  0.2638 S13= -2.2555 S21= -0.1038|
|S23=  0.3028 S31=  2.0226 S32= -0.5332                                       |
|-----------------------------------------------------------------------------|

                 ----------Individual ADP refinement----------                 

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2348      final r-factor (work) = 0.2335          |
| start r-factor (free) = 0.2699      final r-factor (free) = 0.2660          |
|-----------------------------------------------------------------------------|
| T_start  = wxu      * Exray    + wu       * Eadp                            |
| 0.407006 = 0.128667 * 3.096417 + 1.000000 * undef                           |
|-----------------------------------------------------------------------------|
| T_final  = wxu      * Exray    + wu       * Eadp                            |
| 0.396508 = 0.128667 * 3.062368 + 1.000000 * undef                           |
|-----------------------------------------------------------------------------|
| number of iterations =   25    |    number of function evaluations =   27   |
|-----------------------------------------------------------------------------|

               ----------group isotropic ADP refinement----------              

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2335 r_free = 0.2660 target = 3.084158 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2334 r_free = 0.2660 target = 3.084172 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 5)-----------------|
| r_work = 0.2334 r_free = 0.2660 target = 3.084175 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2334 r_free = 0.2660 target = 3.084175 convergence test = off    |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   1.09    208.36  74.59    0.00  0.56   0.05       |
|    all(noH): 2195   2186   1.09    208.36  74.59    0.00  0.56   0.05       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   1.09    208.36  74.59    0.00  0.56   0.05       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.087 -  21.814:  356   |   5:   104.725 - 125.452:  178        |
|      1:    21.814 -  42.542:  408   |   6:   125.452 - 146.180:  178        |
|      2:    42.542 -  63.269:  294   |   7:   146.180 - 166.907:  194        |
|      3:    63.269 -  83.997:  280   |   8:   166.907 - 187.635:   65        |
|      4:    83.997 - 104.725:  234   |   9:   187.635 - 208.362:    8        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   0.056: 1493   |   5:     0.279 -   0.334:    0        |
|      1:     0.056 -   0.111:  253   |   6:     0.334 -   0.390:    0        |
|      2:     0.111 -   0.167:  299   |   7:     0.390 -   0.446:    0        |
|      3:     0.167 -   0.223:   78   |   8:     0.446 -   0.501:    0        |
|      4:     0.223 -   0.279:    1   |   9:     0.501 -   0.557:   62        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= occupancy refinement ============================

| LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2334      final r-factor (work) = 0.2334          |
| start r-factor (free) = 0.2660      final r-factor (free) = 0.2660          |
|-----------------------------------------------------------------------------|
| T_start  =          * Exray                                                 |
| 3.084175 = 1.000000 * 3.084175 + 0.000000 * undef                           |
|-----------------------------------------------------------------------------|
| T_final  =          * Exray                                                 |
| 3.083250 = 1.000000 * 3.083250 + 0.000000 * undef                           |
|-----------------------------------------------------------------------------|
| number of iterations =    5    |    number of function evaluations =    7   |
|-----------------------------------------------------------------------------|
***
Occupancy refinement result is not accepted.
***

                         ----------X-ray data----------                        

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.2334   r_free= 0.2660   ksol= 0.33   Bsol= 23.96   scale= 0.114   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (62.09,62.09,92.16,-0.00,0.00,0.00); trace/3= 72.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 3.084175                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 49.5471 -  7.3200 0.98   1267  152 0.2606 0.2676      4.2595      4.3243|
|  2:  7.3200 -  5.8130 0.99   1293  143 0.2333 0.2586      3.6049      3.7504|
|  3:  5.8130 -  5.0790 0.98   1262  142 0.1920 0.2322      3.4103      3.5299|
|  4:  5.0790 -  4.6150 0.98   1281  147 0.1560 0.2235      3.2339      3.3913|
|  5:  4.6150 -  4.2844 0.98   1272  144 0.1641 0.2334      3.1775      3.3105|
|  6:  4.2844 -  4.0319 0.95   1236  130 0.1968 0.2285      3.0671      3.1219|
|  7:  4.0319 -  3.8301 0.96   1234  139 0.1964 0.2255      2.8795      3.0515|
|  8:  3.8301 -  3.6634 0.94   1245  132 0.1967 0.2135      2.7399      2.7307|
|  9:  3.6634 -  3.5224 0.90   1162  132 0.2360 0.2866      2.6884      2.7844|
| 10:  3.5224 -  3.4009 0.91   1157  135 0.2634 0.2953      2.6715      2.7826|
| 11:  3.4009 -  3.2946 0.90   1198  135 0.2712 0.3711      2.5913      2.7962|
| 12:  3.2946 -  3.2004 0.86   1111  122 0.3001 0.2862       2.495      2.5162|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error    Alpha        Beta  |
|  #        range        work  test        work    test                       |
|  1: 49.5471 -  7.3200  1267   152  0.81  24.40  25.33     0.12        672.99|
|  2:  7.3200 -  5.8130  1293   143  0.80  26.64  22.56     0.10        267.45|
|  3:  5.8130 -  5.0790  1262   142  0.84  22.36  20.73     0.10        169.84|
|  4:  5.0790 -  4.6150  1281   147  0.88  18.61  19.57     0.11        117.80|
|  5:  4.6150 -  4.2844  1272   144  0.88  18.07  22.19     0.11         99.70|
|  6:  4.2844 -  4.0319  1236   130  0.86  21.07  25.67     0.12         79.62|
|  7:  4.0319 -  3.8301  1234   139  0.86  20.72  20.33     0.12         55.77|
|  8:  3.8301 -  3.6634  1245   132  0.85  22.04  21.91     0.12         42.14|
|  9:  3.6634 -  3.5224  1162   132  0.80  27.24  25.81     0.12         38.04|
| 10:  3.5224 -  3.4009  1157   135  0.77  29.37  28.92     0.13         40.39|
| 11:  3.4009 -  3.2946  1198   135  0.77  30.05  33.08     0.14         35.83|
| 12:  3.2946 -  3.2004  1111   122  0.77  30.10  28.05     0.15         27.56|
|alpha:            min =        0.10 max =            0.15 mean =         0.12|
|beta:             min =       27.56 max =          672.99 mean =       140.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.93 mean =        24.09|
|phase err.(test): min =        0.00 max =           89.91 mean =        24.41|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.2378   r_free= 0.2679   ksol= 0.33   Bsol= 96.08   scale= 0.113   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-10.02,-10.02,20.05,-0.00,0.00,0.00); trace/3= 0.00                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 3.093009                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.2378   r_free= 0.2679   ksol= 0.33   Bsol= 96.08   scale= 0.113   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-10.02,-10.02,20.05,-0.00,0.00,0.00); trace/3= 0.00                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 3.093009                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 49.5471 -  7.3200 0.98   1267  152 0.2681 0.2737      4.2808      4.3401|
|  2:  7.3200 -  5.8130 0.99   1293  143 0.2410 0.2626      3.6191      3.7554|
|  3:  5.8130 -  5.0790 0.98   1262  142 0.1986 0.2279      3.4263      3.5114|
|  4:  5.0790 -  4.6150 0.98   1281  147 0.1604 0.2256      3.2422      3.3944|
|  5:  4.6150 -  4.2844 0.98   1272  144 0.1648 0.2293      3.1773      3.2868|
|  6:  4.2844 -  4.0319 0.95   1236  130 0.1967 0.2266      3.0728       3.111|
|  7:  4.0319 -  3.8301 0.96   1234  139 0.1981 0.2322      2.8878      3.0566|
|  8:  3.8301 -  3.6634 0.94   1245  132 0.1972 0.2116       2.745      2.7252|
|  9:  3.6634 -  3.5224 0.90   1162  132 0.2418 0.2921      2.7049      2.7857|
| 10:  3.5224 -  3.4009 0.91   1157  135 0.2629 0.2993      2.6753      2.7869|
| 11:  3.4009 -  3.2946 0.90   1198  135 0.2714 0.3780      2.5947      2.8073|
| 12:  3.2946 -  3.2004 0.86   1111  122 0.3021 0.2949      2.4976      2.5294|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM   Phase error    Alpha        Beta  |
|  #        range        work  test        work    test                       |
|  1: 49.5471 -  7.3200  1267   152  0.80  25.46  26.38     0.11        724.66|
|  2:  7.3200 -  5.8130  1293   143  0.80  26.29  22.98     0.10        263.60|
|  3:  5.8130 -  5.0790  1262   142  0.84  22.01  20.12     0.10        163.99|
|  4:  5.0790 -  4.6150  1281   147  0.88  18.14  19.17     0.11        112.18|
|  5:  4.6150 -  4.2844  1272   144  0.89  17.78  22.11     0.11         97.33|
|  6:  4.2844 -  4.0319  1236   130  0.86  20.88  25.50     0.12         78.55|
|  7:  4.0319 -  3.8301  1234   139  0.86  20.62  20.65     0.12         55.51|
|  8:  3.8301 -  3.6634  1245   132  0.85  22.03  21.67     0.12         42.41|
|  9:  3.6634 -  3.5224  1162   132  0.79  27.44  25.86     0.12         38.10|
| 10:  3.5224 -  3.4009  1157   135  0.77  29.90  29.52     0.13         41.66|
| 11:  3.4009 -  3.2946  1198   135  0.76  30.59  33.43     0.14         36.75|
| 12:  3.2946 -  3.2004  1111   122  0.76  30.58  28.35     0.15         28.19|
|alpha:            min =        0.10 max =            0.15 mean =         0.12|
|beta:             min =       28.19 max =          724.66 mean =       144.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.82|
|phase err.(work): min =        0.00 max =           89.97 mean =        24.16|
|phase err.(test): min =        0.00 max =           89.67 mean =        24.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.545)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   73.20   280.48  146.70   0.00  0.56   0.05       |
|    all(noH): 2195   2186   73.20   280.48  146.70   0.00  0.56   0.05       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   73.20   280.48  146.70   0.00  0.56   0.05       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    73.202 -  93.929:  356   |   5:   176.840 - 197.567:  178        |
|      1:    93.929 - 114.657:  408   |   6:   197.567 - 218.295:  178        |
|      2:   114.657 - 135.385:  294   |   7:   218.295 - 239.022:  194        |
|      3:   135.385 - 156.112:  280   |   8:   239.022 - 259.750:   65        |
|      4:   156.112 - 176.840:  234   |   9:   259.750 - 280.478:    8        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   0.056: 1493   |   5:     0.279 -   0.334:    0        |
|      1:     0.056 -   0.111:  253   |   6:     0.334 -   0.390:    0        |
|      2:     0.111 -   0.167:  299   |   7:     0.390 -   0.446:    0        |
|      3:     0.167 -   0.223:   78   |   8:     0.446 -   0.501:    0        |
|      4:     0.223 -   0.279:    1   |   9:     0.501 -   0.557:   62        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


================= overall refinement statistics: step by step =================

Information about total rigid body shift of selected groups:
                             rotation (deg)                 translation (A)
                          xyz              total           xyz          total
  group    1:   -2.930   -1.972   -0.917    3.64   -0.21  -0.23  -0.34   0.47
  group    2:   -3.262   -1.646   -1.651    3.99   -0.40  -0.53  -0.67   0.94
****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_rbr: rigid body refinement                                            
1_gbr: group B-factor refinement                                        
1_occ: refinement of individual occupancies                             
1_gor: refinement of grouped occupancies                                
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.5302 0.5312   3.750057e+00   3.695906e+00
   1_bss:  0.4755 0.4677   3.705985e+00   3.662358e+00
   1_rbr:  0.3700 0.3590   3.543197e+00   3.491334e+00
   1_bss:  0.3695 0.3589   3.542661e+00   3.491551e+00
   1_gor:  0.3686 0.3587   3.542171e+00   3.489376e+00
   1_xyz:  0.3407 0.3609   3.472171e+00   3.495911e+00
   1_adp:  0.2663 0.2907   3.227298e+00   3.286416e+00
   1_occ:  0.2663 0.2907   3.227298e+00   3.286416e+00
   2_bss:  0.2640 0.2880   3.202076e+00   3.253454e+00
   2_gor:  0.2640 0.2880   3.202077e+00   3.253452e+00
   2_xyz:  0.2467 0.2800   3.147347e+00   3.231682e+00
   2_adp:  0.2471 0.2734   3.132093e+00   3.214464e+00
   2_occ:  0.2471 0.2734   3.132093e+00   3.214464e+00
   3_bss:  0.2511 0.2738   3.132243e+00   3.204660e+00
   3_gor:  0.2510 0.2738   3.132189e+00   3.204799e+00
   3_xyz:  0.2365 0.2708   3.092948e+00   3.210594e+00
   3_adp:  0.2334 0.2660   3.084175e+00   3.199152e+00
   3_occ:  0.2334 0.2660   3.084175e+00   3.199152e+00
   3_bss:  0.2378 0.2679   3.093009e+00   3.199120e+00
------------------------------------------------------------------------
 Weights for target T = Exray * wxc * wxc_scale + Echem * wc and
 angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/d_sites)
 stage              wxc          wxu  wxc_sc  wxu_sc /_gxc,gc /_gxu,gu
   0    :    1.2185e+01   6.3912e-01   0.500   0.500   89.426   89.621
   1_bss:    1.2185e+01   6.3912e-01   0.500   0.500   89.426   89.621
   1_rbr:    1.2185e+01   6.3912e-01   0.500   0.500   89.426   89.621
   1_bss:    1.2185e+01   6.3912e-01   0.500   0.500   89.426   89.621
   1_gor:    4.5663e+00   2.1872e-01   0.500   0.500   88.291   89.952
   1_xyz:    4.5663e+00   2.1872e-01   0.500   0.500   88.291   89.952
   1_adp:    4.5663e+00   2.1872e-01   0.500   0.500   88.291   89.952
   1_occ:    4.5663e+00   2.1872e-01   0.500   0.500   88.291   89.952
   2_bss:    4.5663e+00   2.1872e-01   0.500   0.500   88.291   89.952
   2_gor:    2.1791e+00   1.3708e-01   0.500   0.500  107.507  104.041
   2_xyz:    2.1791e+00   1.3708e-01   0.500   0.500  107.507  104.041
   2_adp:    2.1791e+00   1.3708e-01   0.500   0.500  107.507  104.041
   2_occ:    2.1791e+00   1.3708e-01   0.500   0.500  107.507  104.041
   3_bss:    2.1791e+00   1.3708e-01   0.500   0.500  107.507  104.041
   3_gor:    2.5129e+00   1.2867e-01   0.500   0.500  127.063  106.343
   3_xyz:    2.5129e+00   1.2867e-01   0.500   0.500  127.063  106.343
   3_adp:    2.5129e+00   1.2867e-01   0.500   0.500  127.063  106.343
   3_occ:    2.5129e+00   1.2867e-01   0.500   0.500  127.063  106.343
   3_bss:    2.5129e+00   1.2867e-01   0.500   0.500  127.063  106.343
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.344  20.000  62.092  62.092  92.162  -0.000   0.000   0.000
   1_rbr:  0.315   0.000  62.092  62.092  92.162  -0.000   0.000   0.000
   1_bss:  0.314   0.000  62.092  62.092  92.162  -0.000   0.000   0.000
   1_gor:  0.314   0.000  62.092  62.092  92.162  -0.000   0.000   0.000
   1_xyz:  0.314   0.000  62.092  62.092  92.162  -0.000   0.000   0.000
   1_adp:  0.314   0.000  62.092  62.092  92.162  -0.000   0.000   0.000
   1_occ:  0.314   0.000  62.092  62.092  92.162  -0.000   0.000   0.000
   2_bss:  0.326  20.000  62.092  62.092  92.162  -0.000   0.000   0.000
   2_gor:  0.326  20.000  62.092  62.092  92.162  -0.000   0.000   0.000
   2_xyz:  0.326  20.000  62.092  62.092  92.162  -0.000   0.000   0.000
   2_adp:  0.326  20.000  62.092  62.092  92.162  -0.000   0.000   0.000
   2_occ:  0.326  20.000  62.092  62.092  92.162  -0.000   0.000   0.000
   3_bss:  0.326  23.963  62.092  62.092  92.162  -0.000   0.000   0.000
   3_gor:  0.326  23.963  62.092  62.092  92.162  -0.000   0.000   0.000
   3_xyz:  0.326  23.963  62.092  62.092  92.162  -0.000   0.000   0.000
   3_adp:  0.326  23.963  62.092  62.092  92.162  -0.000   0.000   0.000
   3_occ:  0.326  23.963  62.092  62.092  92.162  -0.000   0.000   0.000
   3_bss:  0.326  96.079 -10.023 -10.023  20.046  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.986 0.3974  0.0163      693.781
   1_bss:  54.096 0.4726  0.0538      497.053
   1_rbr:  36.980 0.6831  0.0732      267.587
   1_bss:  37.015 0.6827  0.0730      267.085
   1_gor:  36.900 0.6840  0.0733      265.284
   1_xyz:  37.237 0.6798  0.0715      263.177
   1_adp:  27.819 0.7851  0.1102      167.223
   1_occ:  27.819 0.7851  0.1102      167.223
   2_bss:  26.606 0.7982  0.1130      161.603
   2_gor:  26.606 0.7982  0.1130      161.634
   2_xyz:  25.260 0.8130  0.1153      153.028
   2_adp:  24.548 0.8206  0.1210      148.232
   2_occ:  24.548 0.8206  0.1210      148.232
   3_bss:  24.551 0.8203  0.1208      145.061
   3_gor:  24.547 0.8204  0.1207      144.469
   3_xyz:  24.543 0.8206  0.1206      142.076
   3_adp:  24.120 0.8250  0.1188      141.311
   3_occ:  24.120 0.8250  0.1188      141.311
   3_bss:  24.203 0.8240  0.1185      144.393
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target     wc
   0    :  11.665  0.188  0.932 24.175  0.067  4.083   1.5517e+01   1.00
   1_bss:  11.665  0.188  0.932 24.175  0.067  4.083   1.5517e+01   1.00
   1_rbr:  11.657  0.190  0.932 24.168  0.067  4.090   1.5741e+01   1.00
   1_bss:  11.657  0.190  0.932 24.168  0.067  4.090   1.5741e+01   1.00
   1_gor:  11.657  0.190  0.932 24.168  0.067  4.090   1.5741e+01   1.00
   1_xyz:   1.713  0.014  0.101 21.552  0.008  4.104   2.1782e-01   1.00
   1_adp:   1.713  0.014  0.101 21.552  0.008  4.104   2.1782e-01   1.00
   1_occ:   1.713  0.014  0.101 21.552  0.008  4.104   2.1782e-01   1.00
   2_bss:   1.713  0.014  0.101 21.552  0.008  4.104   2.1782e-01   1.00
   2_gor:   1.713  0.014  0.101 21.552  0.008  4.104   2.1782e-01   1.00
   2_xyz:   1.319  0.009  0.081 20.886  0.006  4.112   1.4406e-01   1.00
   2_adp:   1.319  0.009  0.081 20.886  0.006  4.112   1.4406e-01   1.00
   2_occ:   1.319  0.009  0.081 20.886  0.006  4.112   1.4406e-01   1.00
   3_bss:   1.319  0.009  0.081 20.886  0.006  4.112   1.4406e-01   1.00
   3_gor:   1.319  0.009  0.081 20.886  0.006  4.115   1.4411e-01   1.00
   3_xyz:   1.434  0.010  0.086 21.236  0.007  4.120   1.6081e-01   1.00
   3_adp:   1.434  0.010  0.086 21.236  0.007  4.120   1.6081e-01   1.00
   3_occ:   1.434  0.010  0.086 21.236  0.007  4.120   1.6081e-01   1.00
   3_bss:   1.434  0.010  0.086 21.236  0.007  4.120   1.6081e-01   1.00
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  53.720  0.760  3.229 88.901  0.249  0.737   4.6785e+00
   1_bss:  53.720  0.760  3.229 88.901  0.249  0.737   4.6785e+00
   1_rbr:  53.720  1.219  3.229 88.901  0.249  1.628   4.8115e+00
   1_bss:  53.720  1.219  3.229 88.901  0.249  1.628   4.8115e+00
   1_gor:  53.720  1.219  3.229 88.901  0.249  1.628   4.8115e+00
   1_xyz:  14.072  0.097  0.449 88.767  0.057  2.225   1.3231e-01
   1_adp:  14.072  0.097  0.449 88.767  0.057  2.225   1.3231e-01
   1_occ:  14.072  0.097  0.449 88.767  0.057  2.225   1.3231e-01
   2_bss:  14.072  0.097  0.449 88.767  0.057  2.225   1.3231e-01
   2_gor:  14.072  0.097  0.449 88.767  0.057  2.225   1.3231e-01
   2_xyz:  12.096  0.073  0.345 83.287  0.058  2.288   7.5169e-02
   2_adp:  12.096  0.073  0.345 83.287  0.058  2.288   7.5169e-02
   2_occ:  12.096  0.073  0.345 83.287  0.058  2.288   7.5169e-02
   3_bss:  12.096  0.073  0.345 83.287  0.058  2.288   7.5169e-02
   3_gor:  12.096  0.073  0.345 83.287  0.058  2.288   7.5197e-02
   3_xyz:  13.135  0.073  0.385 88.986  0.063  2.315   7.5524e-02
   3_adp:  13.135  0.073  0.385 88.986  0.063  2.315   7.5524e-02
   3_occ:  13.135  0.073  0.385 88.986  0.063  2.315   7.5524e-02
   3_bss:  13.135  0.073  0.385 88.986  0.063  2.315   7.5524e-02
------------------------------------------------------------------------
 stage      b_max   b_min   b_ave
   0    :   40.00   10.00   20.18
   1_bss:   40.00   10.00   20.18
   1_rbr:   40.00   10.00   20.18
   1_bss:   40.00   10.00   20.18
   1_gor:   40.00   10.00   20.18
   1_xyz:   40.00   10.00   20.18
   1_adp:  192.78    2.43   69.23
   1_occ:  192.78    2.43   69.23
   2_bss:  192.78    2.43   69.23
   2_gor:  192.78    2.43   69.23
   2_xyz:  192.78    2.43   69.23
   2_adp:  202.30    2.68   75.20
   2_occ:  202.30    2.68   75.20
   3_bss:  202.30    2.68   75.20
   3_gor:  202.30    2.68   75.20
   3_xyz:  202.30    2.68   75.20
   3_adp:  208.36    1.09   74.59
   3_occ:  208.36    1.09   74.59
   3_bss:  280.48   73.20  146.70
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_rbr:    2.342    0.000    1.103
   1_bss:    2.342    0.000    1.103
   1_gor:    2.342    0.000    1.103
   1_xyz:    2.594    0.122    1.127
   1_adp:    2.594    0.122    1.127
   1_occ:    2.594    0.122    1.127
   2_bss:    2.594    0.122    1.127
   2_gor:    2.594    0.122    1.127
   2_xyz:    2.903    0.136    1.144
   2_adp:    2.903    0.136    1.144
   2_occ:    2.903    0.136    1.144
   3_bss:    2.903    0.136    1.144
   3_gor:    2.903    0.136    1.144
   3_xyz:    3.117    0.059    1.169
   3_adp:    3.117    0.059    1.169
   3_occ:    3.117    0.059    1.169
   3_bss:    3.117    0.059    1.169
------------------------------------------------------------------------
 stage         k1_w     k1_t     k3_w     k3_t scale_ml
   0    :    0.0285   0.0298   0.0354   0.0359   1.0000
   1_bss:    0.0778   0.0779   0.0903   0.0896   1.0000
   1_rbr:    0.0824   0.0845   0.0897   0.0918   1.0000
   1_bss:    0.0822   0.0842   0.0895   0.0915   1.0000
   1_gor:    0.0824   0.0848   0.0896   0.0920   1.0000
   1_xyz:    0.0835   0.0839   0.0897   0.0909   1.0000
   1_adp:    0.1090   0.1105   0.1140   0.1163   1.0000
   1_occ:    0.1090   0.1105   0.1140   0.1163   1.0000
   2_bss:    0.1089   0.1112   0.1138   0.1168   1.0000
   2_gor:    0.1089   0.1112   0.1138   0.1168   1.0000
   2_xyz:    0.1110   0.1130   0.1155   0.1185   1.0000
   2_adp:    0.1148   0.1170   0.1194   0.1225   1.0000
   2_occ:    0.1148   0.1170   0.1194   0.1225   1.0000
   3_bss:    0.1140   0.1153   0.1187   0.1205   1.0000
   3_gor:    0.1140   0.1152   0.1187   0.1205   1.0000
   3_xyz:    0.1150   0.1160   0.1192   0.1213   1.0000
   3_adp:    0.1138   0.1150   0.1179   0.1200   1.0000
   3_occ:    0.1138   0.1150   0.1179   0.1200   1.0000
   3_bss:    0.1134   0.1144   0.1177   0.1195   1.0000
------------------------------------------------------------------------

CPU time actual refinement: 569.36


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/home/afonine/public_html/multiple_strategies_example/example_refine_001.pdb
n_use            =  2195
n_use_u_iso      =  2195
n_use_u_aniso    =  2186
n_grad_site      =  0
n_grad_u_iso     =  5
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2195

Writing 2m*Fobs-D*Fmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/afonine/public_html/multiple_strategies_example/example_refine_001_2mFobs-DFmodel.map
Writing m*Fobs-D*Fmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/afonine/public_html/multiple_strategies_example/example_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/home/afonine/public_html/multiple_strategies_example/example_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/home/afonine/public_html/multiple_strategies_example/example_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 569.25 
  Macro-tasks:
    bulk solvent and scale       = 53.39  
    individual site refinement   = 165.67 
    weights calculation          = 19.55  
    collect and process          = 4.19   
    adp group                    = 147.25 
    tls refinement               = 86.65  
    rigid-body refinement        = 108.95 
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 585.79 
  Micro-tasks:
    mask                            = 6.21   
    f_calc                          = 155.30 
    alpha_beta                      = 7.13   
    target                          = 1.49   
    gradients_wrt_atomic_parameters = 290.62 
    fmodel                         = 11.48  
    r_factors                      = 0.40   
    phase_errors                   = 12.46  
    foms                           = 0.40   
    TOTAL for micro-tasks          = 485.49 
NUMBER OF MASK CALCS=  13
Time per interpreted Python bytecode instruction: 7.721 micro seconds
Total CPU time: 9.62 minutes
from_scatterers_fft:    993 calls, 153.97 s
gradients_fft:          867 calls, 276.18 s

=========================== phenix.refine: finished ===========================

# Date 2007-10-25 Time 11:46:26 PDT -0700
Start R-work = 0.5302, R-free = 0.5312 (no bulk solvent and anisotropic scale)
Final R-work = 0.5328, R-free = 0.5210 (no bulk solvent and anisotropic scale)

Start R-work = 0.4755, R-free = 0.4677
Final R-work = 0.2378, R-free = 0.2679