# Date 2008-10-14 Time 08:46:09 PDT -0700 (1223999169.43 s)
#phil __OFF__

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

HOST = chevy.lbl.gov
HOSTTYPE = x86_64-linux
USER = afonine
PID = 2016

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: 1.4
  Release tag: 1
  cctbx tag: 2008_10_09_1338
  Platform: intel-linux-2.6-x86_64 linux
  User: afonine
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Nathaniel Echols,
  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: (125.96, 125.96, 118.44, 90, 90, 120)
  Space group: P 62 2 2 (No. 180)

  Monomer Library directory:
    "/net/chevy/raid1/afonine/PROJ/phenix/phenix-1.4-1/ext_ref_files/mon_lib"
  Total number of atoms: 2195
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        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
    Chain: " "
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Ad-hoc single atom residues: {'MG2': 4}
          Unusual residues: {'SO4': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 4
  Time building chain proxies: 1.11, per 1000 atoms: 0.51

  Number of scatterers: 2195
  At special positions: 0
  Unit cell: (125.96, 125.96, 118.44, 90, 90, 120)
  Space group: P 62 2 2 (No. 180)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       7     16.00
     Mg      4     11.99
     O     404      8.00
     N     381      7.00
     C    1399      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

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

Miller array info: synaptotagmin.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: (125.96, 125.96, 118.44, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
Systematic absences: 0
Centric reflections: 1651
Resolution range: 49.5416 3.20048
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 =  49.5416
                             d_min =   3.2005

Miller array info: synaptotagmin.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: (125.96, 125.96, 118.44, 90, 90, 120)
Space group: P 62 2 2 (No. 180)
Systematic absences: 0
Centric reflections: 1776
Resolution range: 49.5416 3.20048
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: 49.5475 -  6.8896 [1715/1751]  1534   181  10.6%
  bin  2:  6.8896 -  5.4708 [1699/1730]  1532   167   9.8%
  bin  3:  5.4708 -  4.7799 [1698/1730]  1532   166   9.8%
  bin  4:  4.7799 -  4.3431 [1689/1731]  1519   170  10.1%
  bin  5:  4.3431 -  4.0320 [1668/1741]  1504   164   9.8%
  bin  6:  4.0320 -  3.7944 [1669/1747]  1502   167  10.0%
  bin  7:  3.7944 -  3.6044 [1602/1710]  1441   161  10.0%
  bin  8:  3.6044 -  3.4475 [1571/1752]  1411   160  10.2%
  bin  9:  3.4475 -  3.3148 [1537/1710]  1383   154  10.0%
  bin 10:  3.3148 -  3.2005 [1523/1751]  1369   154  10.1%
                                overall 14727  1644  10.0%

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=1
    Symmetry disulfide: pdb=" SG  CYS A 523 " segid="A   " - pdb=" SG  CYS A 523 " segid="A   " distance=2.93 -x+2,-x+y+1,-z+1/3
  Time building geometry restraints manager: 0.09 seconds
  Histogram of bond lengths:
        1.22 -     1.56: 2227
        1.56 -     1.90: 14
        1.90 -     2.24: 0
        2.24 -     2.59: 0
        2.59 -     2.93: 1
  Bond restraints sorted by residual:
                              atom i - atom j                             ideal  model  delta   weight residual sym.op. j
  pdb=" SG  CYS A 523 " segid="A   " - pdb=" SG  CYS A 523 " segid="A   " 2.031  2.927 -0.896 2.50e+03 2.01e+03 -x+2,-x+y+1,-z+1/3
  pdb=" N   GLY A 295 " segid="A   " - pdb=" CA  GLY A 295 " segid="A   " 1.451  1.498 -0.047 3.91e+03 8.56e+00
  pdb=" CB  PRO A 335 " segid="A   " - pdb=" CG  PRO A 335 " segid="A   " 1.492  1.578 -0.086 4.00e+02 2.93e+00
  pdb=" CA  ASN A 554 " segid="A   " - pdb=" C   ASN A 554 " segid="A   " 1.525  1.559 -0.034 2.27e+03 2.66e+00
  pdb=" CA  VAL A 353 " segid="A   " - pdb=" CB  VAL A 353 " segid="A   " 1.540  1.583 -0.043 1.37e+03 2.59e+00
  ... (remaining 2237 not shown)
  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 10
        2.44 -     3.06: 1666
        3.06 -     3.67: 3137
        3.67 -     4.29: 4948
        4.29 -     4.90: 7934
  Nonbonded interactions sorted by model distance:
                              atom i - atom j                              model   vdw sym.op. j
  pdb=" CD1 ILE A 487 " segid="A   " - pdb=" CD1 ILE A 487 " segid="A   "  1.827 3.880 -x+2,-x+y+1,-z+1/3
  pdb=" O   CYS A 298 " segid="A   " - pdb=" O   GLY A 299 " segid="A   "  2.154 3.040
  pdb=" N   VAL A 559 " segid="A   " - pdb=" N   GLU A 560 " segid="A   "  2.162 2.560
  pdb=" O   LEU A 552 " segid="A   " - pdb=" N   ASN A 554 " segid="A   "  2.172 3.120
  pdb=" NE2 HIS A 547 " segid="A   " - pdb=" O   VAL A 559 " segid="A   "  2.203 3.120
  ... (remaining 17690 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    18.00: 654
       18.00 -    35.98: 92
       35.98 -    53.97: 47
       53.97 -    71.96: 30
       71.96 -    89.94: 8
  Dihedral angle restraints sorted by residual:
  pdb=" CA  PHE A 332 " segid="A   "
  pdb=" CB  PHE A 332 " segid="A   "
  pdb=" CG  PHE A 332 " segid="A   "
  pdb=" CD1 PHE A 332 " segid="A   "
      ideal   model   delta periodicty    weight residual
      90.00 -179.40   89.40     2       2.50e-03 2.00e+01
  pdb=" CA  TYR A 307 " segid="A   "
  pdb=" CB  TYR A 307 " segid="A   "
  pdb=" CG  TYR A 307 " segid="A   "
  pdb=" CD1 TYR A 307 " segid="A   "
      ideal   model   delta periodicty    weight residual
      90.00 -175.70   85.70     2       2.50e-03 1.84e+01
  pdb=" CA  PHE A 502 " segid="A   "
  pdb=" CB  PHE A 502 " segid="A   "
  pdb=" CG  PHE A 502 " segid="A   "
  pdb=" CD1 PHE A 502 " segid="A   "
      ideal   model   delta periodicty    weight residual
      90.00  174.73  -84.73     2       2.50e-03 1.79e+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 =====================


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


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

Refinement flags and selection counts:
  individual_sites       =  True (2195 atoms)
  rigid_body             = False (0 atoms in 0 groups)
  individual_adp         =  True (iso = 2195 aniso = 0)
  group_adp              = False (2195 atoms in 280 groups)
  tls                    =  True (2186 atoms in 2 groups)
  occupancies            =  True (0 atoms)
  group_anomalous        = False

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/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/tls/synaptotagmin_refine_001.eff


*** Converting to isotropic. ***

Writing geometry restraints to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/tls/synaptotagmin_refine_001.geo

CPU time processing inputs: 3.92


============================ 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 = 125.9599991 125.9599991 118.4400024 90 90 120
    space_group = "P 62 2 2"
  }
  input {
    pdb {
      file_name = "/net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/tls/synaptotagmin.pdb"
    }
    xray_data {
      file_name = "synaptotagmin.mtz"
      labels = "F-obs(+),SIGF-obs(+),F-obs(-),SIGF-obs(-)"
      r_free_flags {
        file_name = "synaptotagmin.mtz"
        label = "R-free-flags(+),R-free-flags(-)"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "synaptotagmin_refine"
    serial = 1
  }
  refine {
    strategy = *individual_sites rigid_body *individual_adp group_adp *tls \
               *occupancies group_anomalous
    adp {
      tls = "chain A and resseq :424"
      tls = "chain A and resseq 425:"
    }
  }
  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__


=============================== refinement start ==============================


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


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

|--(resolution: 3.20 - 49.54 A; n_refl. = 16371)------------------------------|
|                                                                             |
| r_work= 0.3954   r_free= 0.3818   ksol= 0.00   Bsol= 0.00   scale= 0.047    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 3.429340                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 49.5475 -  7.3200 0.98   1267  152 0.5340 0.4539      4.8057      4.7888|
|  2:  7.3200 -  5.8130 0.99   1298  138 0.3389 0.3755      4.0824      4.1052|
|  3:  5.8130 -  5.0791 0.98   1264  140 0.2924 0.2961      3.7753      3.7055|
|  4:  5.0791 -  4.6151 0.98   1282  146 0.2419 0.2473      3.6044      3.5751|
|  5:  4.6151 -  4.2845 0.98   1278  138 0.2594 0.2981      3.5808      3.5814|
|  6:  4.2845 -  4.0320 0.95   1232  134 0.3389 0.2853      3.5421      3.3447|
|  7:  4.0320 -  3.8301 0.96   1234  139 0.3165 0.3106      3.3152      3.3255|
|  8:  3.8301 -  3.6635 0.94   1244  133 0.2758 0.2751      3.0335      2.9841|
|  9:  3.6635 -  3.5225 0.90   1162  132 0.3200 0.3299      2.9318      2.9889|
| 10:  3.5225 -  3.4010 0.91   1158  134 0.3243 0.3068      2.8157      2.8655|
| 11:  3.4010 -  3.2946 0.90   1197  136 0.3308 0.3372      2.7435      2.6519|
| 12:  3.2946 -  3.2005 0.86   1111  122 0.3707 0.3011      2.6707      2.5179|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 49.5475 -  7.3200  1267   152  0.47  53.53   0.04     0.04       2768.05|
|  2:  7.3200 -  5.8130  1298   138  0.46  54.76   0.05     0.04       1155.98|
|  3:  5.8130 -  5.0791  1264   140  0.77  29.18   0.05     0.05        304.66|
|  4:  5.0791 -  4.6151  1282   146  0.82  24.97   0.06     0.06        192.73|
|  5:  4.6151 -  4.2845  1278   138  0.83  23.84   0.07     0.06        168.86|
|  6:  4.2845 -  4.0320  1232   134  0.78  28.19   0.07     0.06        127.40|
|  7:  4.0320 -  3.8301  1234   139  0.77  29.47   0.06     0.06        104.48|
|  8:  3.8301 -  3.6635  1244   133  0.76  30.92   0.06     0.06         73.70|
|  9:  3.6635 -  3.5225  1162   132  0.72  34.17   0.06     0.06         59.39|
| 10:  3.5225 -  3.4010  1158   134  0.74  32.32   0.07     0.06         45.95|
| 11:  3.4010 -  3.2946  1197   136  0.75  31.42   0.06     0.06         36.46|
| 12:  3.2946 -  3.2005  1111   122  0.75  32.22   0.06     0.05         28.06|
|alpha:            min =        0.04 max =            0.06 mean =         0.06|
|beta:             min =       28.06 max =         2768.05 mean =       436.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           89.99 mean =        33.84|
|phase err.(test): min =        0.00 max =           89.99 mean =        33.74|
|-----------------------------------------------------------------------------|

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

Distribution of F-obs values before outliers rejection:
     0.320 - 18.778     : 8770
    18.778 - 37.236     : 4706
    37.236 - 55.694     : 1808
    55.694 - 74.152     : 633
    74.152 - 92.610     : 244
    92.610 - 111.068    : 94
   111.068 - 129.526    : 49
   129.526 - 147.984    : 41
   147.984 - 166.442    : 21
   166.442 - 184.900    : 5

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

Distribution of F-obs values after outliers rejection:
     0.320 - 18.778     : 8761
    18.778 - 37.236     : 4706
    37.236 - 55.694     : 1808
    55.694 - 74.152     : 633
    74.152 - 92.610     : 244
    92.610 - 111.068    : 94
   111.068 - 129.526    : 49
   129.526 - 147.984    : 41
   147.984 - 166.442    : 21
   166.442 - 184.900    : 5

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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.090:  2241 |   0.000 -   1.544:  2455 |  1.827 -  2.135:        1 |
| 0.090 - 0.179:     0 |   1.544 -   3.088:   389 |  2.135 -  2.442:        9 |
| 0.179 - 0.269:     0 |   3.088 -   4.633:   120 |  2.442 -  2.749:      341 |
| 0.269 - 0.359:     0 |   4.633 -   6.177:    43 |  2.749 -  3.056:     1325 |
| 0.359 - 0.448:     0 |   6.177 -   7.721:    18 |  3.056 -  3.364:     1336 |
| 0.448 - 0.538:     0 |   7.721 -   9.265:     6 |  3.364 -  3.671:     1801 |
| 0.538 - 0.627:     0 |   9.265 -  10.809:     6 |  3.671 -  3.978:     2476 |
| 0.627 - 0.717:     0 |  10.809 -  12.354:     1 |  3.978 -  4.285:     2472 |
| 0.717 - 0.807:     0 |  12.354 -  13.898:     1 |  4.285 -  4.593:     3513 |
| 0.807 - 0.896:     1 |  13.898 -  15.442:     1 |  4.593 -  4.900:     4421 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2242 |   0.021    0.896  0.000 |       0.577 |              |
|     angle |     3040 |   1.630   15.442  0.000 |       0.463 |              |
| chirality |      337 |   0.108    0.410  0.000 |       0.292 |        0.214 |
| planarity |      394 |   0.009    0.098  0.000 |       0.645 |              |
|  dihedral |      831 |  21.090   89.942  0.012 |       1.254 |              |
| nonbonded |     2242 |   4.101    4.900  1.827 |       0.514 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   26.21   300.00  94.26    1.00  1.00   1.00       |
|    all(noH): 2195   2186   26.21   300.00  94.26    1.00  1.00   1.00       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   26.21   300.00  94.26    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:    26.210 -  53.589:  425   |   5:   163.105 - 190.484:  100        |
|      1:    53.589 -  80.968:  585   |   6:   190.484 - 217.863:   43        |
|      2:    80.968 - 108.347:  567   |   7:   217.863 - 245.242:   39        |
|      3:   108.347 - 135.726:  249   |   8:   245.242 - 272.621:   16        |
|      4:   135.726 - 163.105:  162   |   9:   272.621 - 300.000:    9        |
|                               =>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 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.3950   r_free= 0.3642   ksol= 0.00   Bsol= 0.00   scale= 0.047    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 3.429453                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 3.20 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.2908   r_free= 0.2841   ksol= 0.31   Bsol= 50.00   scale= 0.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (15.39,15.39,33.32,-0.00,0.00,0.00); trace/3= 21.37                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 3.336126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.774114              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.041   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.413410              wxu_scale = 0.500            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 88.840   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2908      final r-factor (work) = 0.2694          |
| start r-factor (free) = 0.2841      final r-factor (free) = 0.2864          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3999 = 4.77 * 0.50 * 3.4293 + 1.00 * 0.2138                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9344 = 4.77 * 0.50 * 3.2551 + 1.00 * 0.1643                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2694 r_free = 0.2864 target = 3.256902 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 19)----------------|
| r_work = 0.2688 r_free = 0.2876 target = 3.251085 convergence test = off    |
|-----------------------------------------------------------------------------|

|-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:   73.479 106.85   C   GLY  295  <>   80.161  98.73   O   GLY  424    |
|     2:   81.179 175.21   N   SER  425  <>   86.436 107.22   O   LYS  569    |
|-----------------------------------------------------------------------------|

|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0941304  r_work = 0.2688  r_free = 0.2876      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 21.68    max = 303.88   mean = 94.05   |
| Isotropic B only:              min = 5.00     max = 278.58   mean = 73.03   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      5.000 -   32.358:     424      |       21.682 -   49.902:     379      |
|     32.358 -   59.716:     582      |       49.902 -   78.121:     591      |
|     59.716 -   87.074:     574      |       78.121 -  106.341:     580      |
|     87.074 -  114.432:     256      |      106.341 -  134.560:     254      |
|    114.432 -  141.790:     147      |      134.560 -  162.780:     163      |
|    141.790 -  169.148:     105      |      162.780 -  190.999:     117      |
|    169.148 -  196.506:      43      |      190.999 -  219.219:      43      |
|    196.506 -  223.864:      39      |      219.219 -  247.438:      43      |
|    223.864 -  251.222:      16      |      247.438 -  275.658:      16      |
|    251.222 -  278.580:       9      |      275.658 -  303.877:       9      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7867   56.7904   -3.8978                |
|T11=  0.2113 T22=  0.2113 T33=  0.2113 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) =  101.2982   27.7166    7.3075                |
|T11=  0.3204 T22=  0.3204 T33=  0.3204 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 = 33.69    max = 339.32   mean = 115.37  |
| Isotropic B only:              min = 5.00     max = 278.58   mean = 73.03   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      5.000 -   32.358:     424      |       33.690 -   64.253:     413      |
|     32.358 -   59.716:     582      |       64.253 -   94.815:     533      |
|     59.716 -   87.074:     574      |       94.815 -  125.378:     448      |
|     87.074 -  114.432:     256      |      125.378 -  155.941:     380      |
|    114.432 -  141.790:     147      |      155.941 -  186.503:     147      |
|    141.790 -  169.148:     105      |      186.503 -  217.066:     147      |
|    169.148 -  196.506:      43      |      217.066 -  247.629:      48      |
|    196.506 -  223.864:      39      |      247.629 -  278.191:      53      |
|    223.864 -  251.222:      16      |      278.191 -  308.754:      17      |
|    251.222 -  278.580:       9      |      308.754 -  339.317:       9      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7867   56.7904   -3.8978                |
|T11=  0.1108 T22=  0.5889 T33=  0.3031 T12=  0.0474 T13=  0.0109 T23=  0.0422|
|L11=  1.8960 L22=  2.9898 L33=  2.0038 L12=  1.6787 L13=  0.6770 L23=  0.8129|
|S11= -0.1132 S22=  0.0697 S33= -0.0000 S12=  0.3773 S13= -0.0846 S21= -0.2569|
|S23= -0.0360 S31=  0.0338 S32=  0.1664                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2982   27.7166    7.3075                |
|T11=  0.4846 T22=  0.4967 T33=  0.8422 T12= -0.0491 T13=  0.3321 T23= -0.1388|
|L11= -0.0560 L22=  0.7660 L33=  0.3765 L12=  0.3857 L13= -0.2257 L23= -0.6530|
|S11= -0.6830 S22=  0.2514 S33= -0.0000 S12=  0.2391 S13= -0.7509 S21=  0.2674|
|S23=  0.3038 S31=  0.2660 S32= -0.2002                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 0.0848823  r_work = 0.2539  r_free = 0.2737      |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 2------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 34.18    max = 336.62   mean = 114.62  |
| Isotropic B only:              min = 5.00     max = 278.58   mean = 73.03   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      5.000 -   32.358:     424      |       34.184 -   64.428:     415      |
|     32.358 -   59.716:     582      |       64.428 -   94.671:     527      |
|     59.716 -   87.074:     574      |       94.671 -  124.915:     464      |
|     87.074 -  114.432:     256      |      124.915 -  155.158:     365      |
|    114.432 -  141.790:     147      |      155.158 -  185.402:     158      |
|    141.790 -  169.148:     105      |      185.402 -  215.646:     134      |
|    169.148 -  196.506:      43      |      215.646 -  245.889:      58      |
|    196.506 -  223.864:      39      |      245.889 -  276.133:      49      |
|    223.864 -  251.222:      16      |      276.133 -  306.377:      16      |
|    251.222 -  278.580:       9      |      306.377 -  336.620:       9      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7867   56.7904   -3.8978                |
|T11=  0.1253 T22=  0.5778 T33=  0.3019 T12=  0.0433 T13=  0.0034 T23=  0.0261|
|L11=  2.1230 L22=  2.8963 L33=  2.4475 L12=  1.5974 L13=  0.6825 L23= -0.6534|
|S11= -0.1748 S22=  0.0357 S33= -0.0000 S12=  0.3805 S13= -0.0732 S21= -0.2383|
|S23= -0.0600 S31=  0.0684 S32=  0.1473                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2982   27.7166    7.3075                |
|T11=  0.4679 T22=  0.4849 T33=  0.8162 T12= -0.0603 T13=  0.3229 T23= -0.1443|
|L11= -0.1208 L22=  1.1133 L33=  0.4668 L12=  0.4644 L13= -0.2150 L23= -0.8017|
|S11= -0.6758 S22=  0.2925 S33= -0.0000 S12=  0.2399 S13= -0.6673 S21=  0.1382|
|S23=  0.0799 S31=  0.2496 S32= -0.2146                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
| target_work(ls_wunit_k1) = 0.0845841  r_work = 0.2534  r_free = 0.2733      |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7867   56.7904   -3.8978                |
|T11=  0.1253 T22=  0.5778 T33=  0.3019 T12=  0.0433 T13=  0.0034 T23=  0.0261|
|L11=  2.1230 L22=  2.8963 L33=  2.4475 L12=  1.5974 L13=  0.6825 L23= -0.6534|
|S11= -0.1748 S22=  0.0357 S33= -0.0000 S12=  0.3805 S13= -0.0732 S21= -0.2383|
|S23= -0.0600 S31=  0.0684 S32=  0.1473                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2982   27.7166    7.3075                |
|T11=  0.4679 T22=  0.4849 T33=  0.8162 T12= -0.0603 T13=  0.3229 T23= -0.1443|
|L11= -0.1208 L22=  1.1133 L33=  0.4668 L12=  0.4644 L13= -0.2150 L23= -0.8017|
|S11= -0.6758 S22=  0.2925 S33= -0.0000 S12=  0.2399 S13= -0.6673 S21=  0.1382|
|S23=  0.0799 S31=  0.2496 S32= -0.2146                                       |
|-----------------------------------------------------------------------------|

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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2534      final r-factor (work) = 0.2387          |
| start r-factor (free) = 0.2733      final r-factor (free) = 0.2715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7318 = 0.41 * 0.50 * 3.2671 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6590 = 0.41 * 0.50 * 3.1505 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   29.78   306.62  118.27   0.09  0.72   0.26       |
|    all(noH): 2195   2186   29.78   306.62  118.27   0.09  0.72   0.26       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   29.78   306.62  118.27   0.09  0.72   0.26       |
|    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:    29.782 -  57.466:  353   |   5:   168.201 - 195.885:  187        |
|      1:    57.466 -  85.150:  481   |   6:   195.885 - 223.569:  175        |
|      2:    85.150 - 112.834:  359   |   7:   223.569 - 251.253:   73        |
|      3:   112.834 - 140.518:  326   |   8:   251.253 - 278.936:   47        |
|      4:   140.518 - 168.201:  174   |   9:   278.936 - 306.620:   20        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.091 -   0.154:  286   |   5:     0.407 -   0.470:  122        |
|      1:     0.154 -   0.217:  659   |   6:     0.470 -   0.533:   51        |
|      2:     0.217 -   0.280:  506   |   7:     0.533 -   0.596:   45        |
|      3:     0.280 -   0.344:  247   |   8:     0.596 -   0.660:   32        |
|      4:     0.344 -   0.407:  224   |   9:     0.660 -   0.723:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 3.20 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.2387   r_free= 0.2715   ksol= 0.31   Bsol= 50.00   scale= 0.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (15.39,15.39,33.32,-0.00,0.00,0.00); trace/3= 21.37                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 3.150796                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 3.20 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.2385   r_free= 0.2637   ksol= 0.29   Bsol= 50.00   scale= 0.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (15.39,15.39,33.32,-0.00,0.00,0.00); trace/3= 21.37                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 3.149380                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.592600              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.118  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.352525              wxu_scale = 0.500            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 128.129  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2385      final r-factor (work) = 0.2263          |
| start r-factor (free) = 0.2637      final r-factor (free) = 0.2630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4085 = 4.59 * 0.50 * 3.1547 + 1.00 * 0.1643                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3008 = 4.59 * 0.50 * 3.1205 + 1.00 * 0.1352                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2263 r_free = 0.2630 target = 3.117382 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2225 r_free = 0.2647 target = 3.102430 convergence test = off    |
|-----------------------------------------------------------------------------|

|-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:   73.443 135.74   C   GLY  295  <>   80.122 212.30   O   GLY  424    |
|     2:   81.159 186.37   N   SER  425  <>   86.497 131.96   O   LYS  569    |
|-----------------------------------------------------------------------------|

|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0727574  r_work = 0.2225  r_free = 0.2647      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 29.78    max = 333.98   mean = 114.71  |
| Isotropic B only:              min = 0.00     max = 275.94   mean = 73.13   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   27.594:     418      |       29.782 -   60.203:     432      |
|     27.594 -   55.188:     597      |       60.203 -   90.623:     530      |
|     55.188 -   82.783:     389      |       90.623 -  121.043:     344      |
|     82.783 -  110.377:     288      |      121.043 -  151.463:     301      |
|    110.377 -  137.971:     243      |      151.463 -  181.883:     250      |
|    137.971 -  165.565:     140      |      181.883 -  212.303:     186      |
|    165.565 -  193.160:      81      |      212.303 -  242.723:     108      |
|    193.160 -  220.754:      22      |      242.723 -  273.143:      26      |
|    220.754 -  248.348:      13      |      273.143 -  303.563:      14      |
|    248.348 -  275.942:       4      |      303.563 -  333.983:       4      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7882   56.8070   -3.8910                |
|T11=  0.1255 T22=  0.5778 T33=  0.3020 T12=  0.0433 T13=  0.0035 T23=  0.0261|
|L11=  2.1261 L22=  2.8948 L33=  2.4494 L12=  1.5943 L13=  0.6878 L23= -0.6530|
|S11= -0.1751 S22=  0.0357 S33=  0.0003 S12=  0.3808 S13= -0.0726 S21= -0.2385|
|S23= -0.0602 S31=  0.0686 S32=  0.1474                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2956   27.7062    7.3123                |
|T11=  0.4678 T22=  0.4849 T33=  0.8162 T12= -0.0603 T13=  0.3230 T23= -0.1443|
|L11= -0.1219 L22=  1.1144 L33=  0.4663 L12=  0.4628 L13= -0.2141 L23= -0.8005|
|S11= -0.6752 S22=  0.2922 S33= -0.0003 S12=  0.2398 S13= -0.6668 S21=  0.1382|
|S23=  0.0802 S31=  0.2494 S32= -0.2145                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 32.65    max = 344.61   mean = 119.21  |
| Isotropic B only:              min = 0.00     max = 275.94   mean = 73.13   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   27.594:     418      |       32.647 -   63.844:     445      |
|     27.594 -   55.189:     597      |       63.844 -   95.040:     529      |
|     55.189 -   82.783:     389      |       95.040 -  126.236:     352      |
|     82.783 -  110.377:     288      |      126.236 -  157.432:     291      |
|    110.377 -  137.971:     243      |      157.432 -  188.628:     233      |
|    137.971 -  165.565:     140      |      188.628 -  219.824:     193      |
|    165.565 -  193.160:      81      |      219.824 -  251.020:     106      |
|    193.160 -  220.754:      22      |      251.020 -  282.216:      28      |
|    220.754 -  248.348:      13      |      282.216 -  313.412:      14      |
|    248.348 -  275.942:       4      |      313.412 -  344.608:       4      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7882   56.8070   -3.8910                |
|T11=  0.1016 T22=  0.6809 T33=  0.3095 T12=  0.0587 T13= -0.0127 T23=  0.0247|
|L11=  2.2604 L22=  3.4294 L33=  2.5855 L12=  1.8960 L13=  0.9838 L23= -0.5607|
|S11= -0.1379 S22=  0.0567 S33=  0.0003 S12=  0.3901 S13= -0.0012 S21= -0.2447|
|S23=  0.0636 S31=  0.0879 S32=  0.2074                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2956   27.7062    7.3123                |
|T11=  0.5035 T22=  0.4829 T33=  0.9379 T12= -0.0705 T13=  0.4697 T23= -0.1855|
|L11=  0.3164 L22=  1.3942 L33=  0.9458 L12=  0.4481 L13=  0.4251 L23= -1.2186|
|S11= -0.7963 S22=  0.3032 S33= -0.0003 S12=  0.3460 S13= -0.9037 S21=  0.0650|
|S23=  0.4659 S31=  0.3044 S32= -0.1794                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 0.0720495  r_work = 0.2213  r_free = 0.2613      |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 2------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 32.76    max = 344.64   mean = 119.39  |
| Isotropic B only:              min = 0.00     max = 275.94   mean = 73.13   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   27.594:     418      |       32.763 -   63.951:     445      |
|     27.594 -   55.189:     597      |       63.951 -   95.139:     537      |
|     55.189 -   82.783:     389      |       95.139 -  126.327:     344      |
|     82.783 -  110.377:     288      |      126.327 -  157.516:     291      |
|    110.377 -  137.971:     243      |      157.516 -  188.704:     229      |
|    137.971 -  165.565:     140      |      188.704 -  219.892:     194      |
|    165.565 -  193.160:      81      |      219.892 -  251.080:     109      |
|    193.160 -  220.754:      22      |      251.080 -  282.268:      28      |
|    220.754 -  248.348:      13      |      282.268 -  313.456:      14      |
|    248.348 -  275.942:       4      |      313.456 -  344.644:       4      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7882   56.8070   -3.8910                |
|T11=  0.1030 T22=  0.6844 T33=  0.3084 T12=  0.0580 T13= -0.0162 T23=  0.0238|
|L11=  2.2693 L22=  3.4610 L33=  2.5999 L12=  1.9099 L13=  1.0015 L23= -0.5895|
|S11= -0.1210 S22=  0.0490 S33=  0.0003 S12=  0.3904 S13=  0.0159 S21= -0.2529|
|S23=  0.0970 S31=  0.1108 S32=  0.2573                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2956   27.7062    7.3123                |
|T11=  0.5210 T22=  0.4772 T33=  0.9290 T12= -0.0867 T13=  0.4784 T23= -0.1942|
|L11=  0.3629 L22=  1.4332 L33=  0.9750 L12=  0.4135 L13=  0.4623 L23= -1.2471|
|S11= -0.7700 S22=  0.2472 S33= -0.0003 S12=  0.3517 S13= -0.8741 S21= -0.0195|
|S23=  0.2668 S31=  0.3393 S32= -0.2522                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
| target_work(ls_wunit_k1) = 0.0719996  r_work = 0.2211  r_free = 0.2613      |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7882   56.8070   -3.8910                |
|T11=  0.1030 T22=  0.6844 T33=  0.3084 T12=  0.0580 T13= -0.0162 T23=  0.0238|
|L11=  2.2693 L22=  3.4610 L33=  2.5999 L12=  1.9099 L13=  1.0015 L23= -0.5895|
|S11= -0.1210 S22=  0.0490 S33=  0.0003 S12=  0.3904 S13=  0.0159 S21= -0.2529|
|S23=  0.0970 S31=  0.1108 S32=  0.2573                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2956   27.7062    7.3123                |
|T11=  0.5210 T22=  0.4772 T33=  0.9290 T12= -0.0867 T13=  0.4784 T23= -0.1942|
|L11=  0.3629 L22=  1.4332 L33=  0.9750 L12=  0.4135 L13=  0.4623 L23= -1.2471|
|S11= -0.7700 S22=  0.2472 S33= -0.0003 S12=  0.3517 S13= -0.8741 S21= -0.0195|
|S23=  0.2668 S31=  0.3393 S32= -0.2522                                       |
|-----------------------------------------------------------------------------|

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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2211      final r-factor (work) = 0.2211          |
| start r-factor (free) = 0.2613      final r-factor (free) = 0.2641          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5657 = 0.35 * 0.50 * 3.1051 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5513 = 0.35 * 0.50 * 3.0923 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   28.70   315.66  117.67   0.05  0.78   0.21       |
|    all(noH): 2195   2186   28.70   315.66  117.67   0.05  0.78   0.21       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   28.70   315.66  117.67   0.05  0.78   0.21       |
|    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:    28.702 -  57.398:  355   |   5:   172.179 - 200.875:  217        |
|      1:    57.398 -  86.093:  499   |   6:   200.875 - 229.570:  195        |
|      2:    86.093 - 114.789:  348   |   7:   229.570 - 258.266:   27        |
|      3:   114.789 - 143.484:  322   |   8:   258.266 - 286.961:   23        |
|      4:   143.484 - 172.179:  194   |   9:   286.961 - 315.656:   15        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.051 -   0.124:  436   |   5:     0.414 -   0.486:   58        |
|      1:     0.124 -   0.196:  865   |   6:     0.486 -   0.559:   24        |
|      2:     0.196 -   0.269:  421   |   7:     0.559 -   0.631:   19        |
|      3:     0.269 -   0.341:  218   |   8:     0.631 -   0.704:   11        |
|      4:     0.341 -   0.414:  127   |   9:     0.704 -   0.776:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 3.20 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.2211   r_free= 0.2641   ksol= 0.29   Bsol= 50.00   scale= 0.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (15.39,15.39,33.32,-0.00,0.00,0.00); trace/3= 21.37                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 3.096514                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 3.20 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.2227   r_free= 0.2603   ksol= 0.29   Bsol= 50.00   scale= 0.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (15.39,15.39,33.32,-0.00,0.00,0.00); trace/3= 21.37                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 3.096749                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.627352              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.680  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.337610              wxu_scale = 0.500            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 134.518  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2227      final r-factor (work) = 0.2154          |
| start r-factor (free) = 0.2603      final r-factor (free) = 0.2614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3007 = 4.63 * 0.50 * 3.0971 + 1.00 * 0.1351                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2525 = 4.63 * 0.50 * 3.0766 + 1.00 * 0.1343                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2154 r_free = 0.2614 target = 3.079782 convergence test = off    |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2126 r_free = 0.2616 target = 3.072791 convergence test = off    |
|-----------------------------------------------------------------------------|

|-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:   73.435 136.84   C   GLY  295  <>   80.080 203.97   O   GLY  424    |
|     2:   81.165 193.15   N   SER  425  <>   86.559 134.79   O   LYS  569    |
|-----------------------------------------------------------------------------|

|-TLS refinement: start model-------------------------------------------------|
| target_work(ls_wunit_k1) = 0.0686487  r_work = 0.2126  r_free = 0.2616      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start model-------------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 28.70    max = 327.03   mean = 114.77  |
| Isotropic B only:              min = 0.00     max = 258.33   mean = 68.50   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   25.833:     441      |       28.702 -   58.535:     404      |
|     25.833 -   51.666:     539      |       58.535 -   88.368:     495      |
|     51.666 -   77.499:     430      |       88.368 -  118.201:     372      |
|     77.499 -  103.332:     277      |      118.201 -  148.034:     323      |
|    103.332 -  129.165:     249      |      148.034 -  177.866:     226      |
|    129.165 -  154.997:     149      |      177.866 -  207.699:     192      |
|    154.997 -  180.830:      67      |      207.699 -  237.532:     130      |
|    180.830 -  206.663:      24      |      237.532 -  267.365:      29      |
|    206.663 -  232.496:      15      |      267.365 -  297.198:      20      |
|    232.496 -  258.329:       4      |      297.198 -  327.031:       4      |
|-----------------------------------------------------------------------------|
|-TLS refinement: start parameters--------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7902   56.8222   -3.8819                |
|T11=  0.1030 T22=  0.6843 T33=  0.3085 T12=  0.0581 T13= -0.0161 T23=  0.0237|
|L11=  2.2736 L22=  3.4597 L33=  2.6023 L12=  1.9084 L13=  1.0068 L23= -0.5892|
|S11= -0.1213 S22=  0.0489 S33=  0.0007 S12=  0.3905 S13=  0.0166 S21= -0.2531|
|S23=  0.0967 S31=  0.1109 S32=  0.2575                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2984   27.6948    7.3171                |
|T11=  0.5211 T22=  0.4772 T33=  0.9291 T12= -0.0866 T13=  0.4785 T23= -0.1942|
|L11=  0.3588 L22=  1.4307 L33=  0.9719 L12=  0.4140 L13=  0.4635 L23= -1.2446|
|S11= -0.7694 S22=  0.2467 S33= -0.0004 S12=  0.3515 S13= -0.8733 S21= -0.0195|
|S23=  0.2668 S31=  0.3390 S32= -0.2521                                       |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 1------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 31.95    max = 333.09   mean = 118.48  |
| Isotropic B only:              min = 0.00     max = 258.33   mean = 68.50   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   25.833:     441      |       31.946 -   62.060:     413      |
|     25.833 -   51.666:     539      |       62.060 -   92.174:     497      |
|     51.666 -   77.499:     430      |       92.174 -  122.288:     375      |
|     77.499 -  103.332:     277      |      122.288 -  152.402:     312      |
|    103.332 -  129.165:     249      |      152.402 -  182.516:     210      |
|    129.165 -  154.997:     149      |      182.516 -  212.631:     201      |
|    154.997 -  180.830:      67      |      212.631 -  242.745:     134      |
|    180.830 -  206.663:      24      |      242.745 -  272.859:      29      |
|    206.663 -  232.496:      15      |      272.859 -  302.973:      20      |
|    232.496 -  258.329:       4      |      302.973 -  333.087:       4      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7902   56.8222   -3.8819                |
|T11=  0.1086 T22=  0.7415 T33=  0.3563 T12=  0.0795 T13= -0.0183 T23=  0.0198|
|L11=  2.2910 L22=  3.5080 L33=  2.6226 L12=  1.9153 L13=  1.0169 L23= -0.5799|
|S11= -0.0571 S22=  0.0213 S33=  0.0007 S12=  0.3851 S13=  0.0455 S21= -0.2499|
|S23=  0.0685 S31=  0.1823 S32=  0.2624                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2984   27.6948    7.3171                |
|T11=  0.5771 T22=  0.5055 T33=  1.0051 T12= -0.0984 T13=  0.5259 T23= -0.2132|
|L11=  0.4173 L22=  1.4492 L33=  1.0228 L12=  0.4193 L13=  0.5259 L23= -1.2456|
|S11= -0.8230 S22=  0.3060 S33= -0.0004 S12=  0.3426 S13= -0.9761 S21= -0.0675|
|S23=  0.2392 S31=  0.3959 S32= -0.3160                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 1------------------------------------------|
| target_work(ls_wunit_k1) = 0.0683631  r_work = 0.2125  r_free = 0.2612      |
|-----------------------------------------------------------------------------|

|-TLS refinement: after macrocycle 2------------------------------------------|
| iso = 2195    aniso = 2186    pos. def. = 2195    non-pos. def. = 0         |
| Total B(isotropic equivalent): min = 31.95    max = 333.09   mean = 118.48  |
| Isotropic B only:              min = 0.00     max = 258.33   mean = 68.50   |
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|                     Distribution of isotropic B-factors:                    |
|            Isotropic                |             Total                     |
|      0.000 -   25.833:     441      |       31.946 -   62.061:     413      |
|     25.833 -   51.666:     539      |       62.061 -   92.175:     497      |
|     51.666 -   77.499:     430      |       92.175 -  122.289:     375      |
|     77.499 -  103.332:     277      |      122.289 -  152.403:     312      |
|    103.332 -  129.165:     249      |      152.403 -  182.517:     210      |
|    129.165 -  154.997:     149      |      182.517 -  212.631:     201      |
|    154.997 -  180.830:      67      |      212.631 -  242.745:     134      |
|    180.830 -  206.663:      24      |      242.745 -  272.859:      29      |
|    206.663 -  232.496:      15      |      272.859 -  302.973:      20      |
|    232.496 -  258.329:       4      |      302.973 -  333.087:       4      |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7902   56.8222   -3.8819                |
|T11=  0.1086 T22=  0.7415 T33=  0.3563 T12=  0.0795 T13= -0.0183 T23=  0.0198|
|L11=  2.2910 L22=  3.5080 L33=  2.6226 L12=  1.9153 L13=  1.0169 L23= -0.5799|
|S11= -0.0571 S22=  0.0213 S33=  0.0007 S12=  0.3851 S13=  0.0455 S21= -0.2499|
|S23=  0.0685 S31=  0.1823 S32=  0.2624                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2984   27.6948    7.3171                |
|T11=  0.5771 T22=  0.5055 T33=  1.0051 T12= -0.0984 T13=  0.5259 T23= -0.2132|
|L11=  0.4173 L22=  1.4492 L33=  1.0228 L12=  0.4193 L13=  0.5260 L23= -1.2456|
|S11= -0.8230 S22=  0.3060 S33= -0.0004 S12=  0.3426 S13= -0.9761 S21= -0.0675|
|S23=  0.2392 S31=  0.3959 S32= -0.3160                                       |
|-----------------------------------------------------------------------------|
|-TLS refinement: after macrocycle 2------------------------------------------|
| target_work(ls_wunit_k1) = 0.068363  r_work = 0.2125  r_free = 0.2612       |
|-----------------------------------------------------------------------------|
|-TLS refinement: final values------------------------------------------------|
|TLS group number 1:                                                          |
|               Origin (x,y,z) =   76.7902   56.8222   -3.8819                |
|T11=  0.1086 T22=  0.7415 T33=  0.3563 T12=  0.0795 T13= -0.0183 T23=  0.0198|
|L11=  2.2910 L22=  3.5080 L33=  2.6226 L12=  1.9153 L13=  1.0169 L23= -0.5799|
|S11= -0.0571 S22=  0.0213 S33=  0.0007 S12=  0.3851 S13=  0.0455 S21= -0.2499|
|S23=  0.0685 S31=  0.1823 S32=  0.2624                                       |
|TLS group number 2:                                                          |
|               Origin (x,y,z) =  101.2984   27.6948    7.3171                |
|T11=  0.5771 T22=  0.5055 T33=  1.0051 T12= -0.0984 T13=  0.5259 T23= -0.2132|
|L11=  0.4173 L22=  1.4492 L33=  1.0228 L12=  0.4193 L13=  0.5260 L23= -1.2456|
|S11= -0.8230 S22=  0.3060 S33= -0.0004 S12=  0.3426 S13= -0.9761 S21= -0.0675|
|S23=  0.2392 S31=  0.3959 S32= -0.3160                                       |
|-----------------------------------------------------------------------------|

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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2125      final r-factor (work) = 0.2139          |
| start r-factor (free) = 0.2612      final r-factor (free) = 0.2585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5323 = 0.34 * 0.50 * 3.0741 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5262 = 0.34 * 0.50 * 3.0772 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   31.95   303.19  116.18   0.06  0.69   0.20       |
|    all(noH): 2195   2186   31.95   303.19  116.18   0.06  0.69   0.20       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   31.95   303.19  116.18   0.06  0.69   0.20       |
|    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:    31.946 -  59.071:  382   |   5:   167.568 - 194.692:  197        |
|      1:    59.071 -  86.195:  481   |   6:   194.692 - 221.817:  222        |
|      2:    86.195 - 113.319:  321   |   7:   221.817 - 248.941:   25        |
|      3:   113.319 - 140.444:  334   |   8:   248.941 - 276.065:   24        |
|      4:   140.444 - 167.568:  197   |   9:   276.065 - 303.190:   12        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.061 -   0.125:  446   |   5:     0.377 -   0.441:   69        |
|      1:     0.125 -   0.188:  774   |   6:     0.441 -   0.504:   34        |
|      2:     0.188 -   0.251:  433   |   7:     0.504 -   0.567:   19        |
|      3:     0.251 -   0.314:  238   |   8:     0.567 -   0.630:   13        |
|      4:     0.314 -   0.377:  156   |   9:     0.630 -   0.693:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 3.20 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.2139   r_free= 0.2585   ksol= 0.29   Bsol= 50.00   scale= 0.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (15.39,15.39,33.32,-0.00,0.00,0.00); trace/3= 21.37                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 3.074338                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 41.2335 -  7.3147 0.97   1266  151 0.2664 0.2725      4.3055      4.3342|
|  2:  7.3147 -  5.8111 0.99   1297  136 0.2350 0.2710      3.6032      3.7671|
|  3:  5.8111 -  5.0781 0.98   1260  140 0.1847 0.2495      3.3958      3.5386|
|  4:  5.0781 -  4.6144 0.98   1282  146 0.1540 0.2074      3.2488      3.4261|
|  5:  4.6144 -  4.2841 0.98   1280  138 0.1469 0.2345      3.1124      3.3172|
|  6:  4.2841 -  4.0317 0.95   1233  134 0.1835 0.2007      3.0408      3.0167|
|  7:  4.0317 -  3.8300 0.96   1231  139 0.1918 0.2487      2.8825      3.0844|
|  8:  3.8300 -  3.6633 0.94   1247  133 0.2002 0.2422      2.7641      2.8593|
|  9:  3.6633 -  3.5224 0.90   1159  132 0.2275 0.2552      2.6842      2.7834|
| 10:  3.5224 -  3.4009 0.91   1158  134 0.2491 0.2872      2.6522      2.7796|
| 11:  3.4009 -  3.2946 0.90   1197  136 0.2609 0.3694      2.5757      2.8106|
| 12:  3.2946 -  3.2005 0.86   1111  122 0.2729 0.2886      2.4267      2.4553|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 41.2335 -  7.3147  1266   151  0.80  24.92   0.10     0.11        715.11|
|  2:  7.3147 -  5.8111  1297   136  0.78  28.08   0.10     0.09        284.31|
|  3:  5.8111 -  5.0781  1260   140  0.85  21.31   0.09     0.09        162.81|
|  4:  5.0781 -  4.6144  1282   146  0.87  19.08   0.10     0.09        128.81|
|  5:  4.6144 -  4.2841  1280   138  0.89  16.80   0.10     0.09         85.96|
|  6:  4.2841 -  4.0317  1233   134  0.86  20.51   0.10     0.10         79.31|
|  7:  4.0317 -  3.8300  1231   139  0.86  21.18   0.10     0.09         56.99|
|  8:  3.8300 -  3.6633  1247   133  0.83  24.02   0.10     0.09         47.85|
|  9:  3.6633 -  3.5224  1159   132  0.78  28.50   0.10     0.09         41.42|
| 10:  3.5224 -  3.4009  1158   134  0.77  29.43   0.10     0.09         40.63|
| 11:  3.4009 -  3.2946  1197   136  0.78  29.11   0.10     0.10         34.81|
| 12:  3.2946 -  3.2005  1111   122  0.80  27.51   0.10     0.09         22.77|
|alpha:            min =        0.09 max =            0.11 mean =         0.09|
|beta:             min =       22.77 max =          715.11 mean =       145.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.81 mean =        24.09|
|phase err.(test): min =        0.00 max =           89.22 mean =        23.94|
|-----------------------------------------------------------------------------|

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

|--(resolution: 3.20 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.2136   r_free= 0.2607   ksol= 0.32   Bsol= 103.85   scale= 0.101  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-5.98,-5.98,11.96,-0.00,0.00,0.00); trace/3= 0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 3.051987                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 3.20 - 41.23 A; n_refl. = 16362)------------------------------|
|                                                                             |
| r_work= 0.2136   r_free= 0.2607   ksol= 0.32   Bsol= 103.85   scale= 0.101  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-5.98,-5.98,11.96,-0.00,0.00,0.00); trace/3= 0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 3.051987                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 41.2335 -  7.3147 0.97   1266  151 0.2589 0.2791      4.2538       4.351|
|  2:  7.3147 -  5.8111 0.99   1297  136 0.2340 0.2704      3.5877      3.7493|
|  3:  5.8111 -  5.0781 0.98   1260  140 0.1810 0.2398       3.374      3.5072|
|  4:  5.0781 -  4.6144 0.98   1282  146 0.1521 0.2077      3.2344       3.402|
|  5:  4.6144 -  4.2841 0.98   1280  138 0.1446 0.2301      3.1052      3.3087|
|  6:  4.2841 -  4.0317 0.95   1233  134 0.1835 0.2109      3.0292      3.0284|
|  7:  4.0317 -  3.8300 0.96   1231  139 0.1861 0.2443      2.8669      3.0692|
|  8:  3.8300 -  3.6633 0.94   1247  133 0.1973 0.2322      2.7419      2.8419|
|  9:  3.6633 -  3.5224 0.90   1159  132 0.2231 0.2446      2.6536      2.7551|
| 10:  3.5224 -  3.4009 0.91   1158  134 0.2392 0.2756      2.6211       2.752|
| 11:  3.4009 -  3.2946 0.90   1197  136 0.2518 0.3618      2.5432       2.804|
| 12:  3.2946 -  3.2005 0.86   1111  122 0.2685 0.2778      2.4113      2.4155|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 41.2335 -  7.3147  1266   151  0.80  25.12   0.11     0.11        727.42|
|  2:  7.3147 -  5.8111  1297   136  0.79  27.49   0.09     0.09        269.26|
|  3:  5.8111 -  5.0781  1260   140  0.86  20.65   0.09     0.09        152.80|
|  4:  5.0781 -  4.6144  1282   146  0.88  18.71   0.10     0.09        123.88|
|  5:  4.6144 -  4.2841  1280   138  0.89  16.80   0.10     0.09         86.00|
|  6:  4.2841 -  4.0317  1233   134  0.86  20.81   0.11     0.10         79.43|
|  7:  4.0317 -  3.8300  1231   139  0.86  21.19   0.10     0.09         56.38|
|  8:  3.8300 -  3.6633  1247   133  0.84  23.26   0.10     0.09         45.04|
|  9:  3.6633 -  3.5224  1159   132  0.79  27.68   0.10     0.09         38.60|
| 10:  3.5224 -  3.4009  1158   134  0.79  28.31   0.10     0.09         37.77|
| 11:  3.4009 -  3.2946  1197   136  0.79  28.20   0.11     0.10         32.66|
| 12:  3.2946 -  3.2005  1111   122  0.81  26.36   0.11     0.09         20.78|
|alpha:            min =        0.09 max =            0.11 mean =         0.09|
|beta:             min =       20.78 max =          727.42 mean =       143.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.97 mean =        23.61|
|phase err.(test): min =        0.00 max =           88.72 mean =        23.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 95.548)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2195   2186   53.31   324.56  137.54   0.06  0.69   0.20       |
|    all(noH): 2195   2186   53.31   324.56  137.54   0.06  0.69   0.20       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 2195   2186   53.31   324.56  137.54   0.06  0.69   0.20       |
|    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:    53.314 -  80.438:  382   |   5:   188.936 - 216.060:  197        |
|      1:    80.438 - 107.562:  481   |   6:   216.060 - 243.184:  222        |
|      2:   107.562 - 134.687:  321   |   7:   243.184 - 270.309:   25        |
|      3:   134.687 - 161.811:  334   |   8:   270.309 - 297.433:   24        |
|      4:   161.811 - 188.936:  197   |   9:   297.433 - 324.557:   12        |
|                               =>continue=>                                  |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|                        Distribution of anisotropy:                          |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.061 -   0.125:  446   |   5:     0.377 -   0.441:   69        |
|      1:     0.125 -   0.188:  774   |   6:     0.441 -   0.504:   34        |
|      2:     0.188 -   0.251:  433   |   7:     0.504 -   0.567:   19        |
|      3:     0.251 -   0.314:  238   |   8:     0.567 -   0.630:   13        |
|      4:     0.314 -   0.377:  156   |   9:     0.630 -   0.693:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.50 sigma)= 47          
Filter by distance & map next to the model:
   mapped sites are within: 0.411 - 3.956
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 43 from: 47
   mapped sites are within: 0.773 - 3.956

peak=    3.790 closest distance to pdb=" CA  SER A 302 " segid="A   " =    0.812
peak=    3.810 closest distance to pdb=" O   TYR A 309 " segid="A   " =    3.813
peak=    3.621 closest distance to pdb=" O   TYR A 309 " segid="A   " =    3.393
peak=    3.876 closest distance to pdb=" CD  LYS A 348 " segid="A   " =    3.013
peak=    5.740 closest distance to pdb=" ND1 HIS A 354 " segid="A   " =    3.724
peak=    4.255 closest distance to pdb=" NE2 HIS A 354 " segid="A   " =    2.331
peak=    5.642 closest distance to pdb=" N   LEU A 358 " segid="A   " =    3.956
peak=    5.792 closest distance to pdb=" N   ILE A 361 " segid="A   " =    3.132
peak=    6.600 closest distance to pdb=" N   ILE A 361 " segid="A   " =    3.449
peak=    5.374 closest distance to pdb=" CD2 LEU A 372 " segid="A   " =    2.671
peak=    3.897 closest distance to pdb=" CD1 LEU A 380 " segid="A   " =    1.706
peak=    3.878 closest distance to pdb=" CA  SER A 383 " segid="A   " =    2.122
peak=    3.629 closest distance to pdb=" OH  TYR A 385 " segid="A   " =    2.481
peak=    3.802 closest distance to pdb=" OD2 ASP A 386 " segid="A   " =    2.043
peak=    4.440 closest distance to pdb=" OD2 ASP A 386 " segid="A   " =    2.001
peak=    3.676 closest distance to pdb=" O   GLY A 397 " segid="A   " =    2.247
peak=    3.910 closest distance to pdb=" O   LEU A 405 " segid="A   " =    2.037
peak=    3.793 closest distance to pdb=" O   PRO A 441 " segid="A   " =    2.333
peak=    6.170 closest distance to pdb=" OD2 ASP A 460 " segid="A   " =    2.140
peak=    4.238 closest distance to pdb=" CB  GLU A 476 " segid="A   " =    1.324
peak=    3.690 closest distance to pdb=" CA  GLY A 477 " segid="A   " =    1.748
peak=    4.083 closest distance to pdb=" CD1 LEU A 480 " segid="A   " =    1.524
peak=    4.161 closest distance to pdb=" CD1 LEU A 480 " segid="A   " =    1.200
peak=    3.903 closest distance to pdb=" CD2 LEU A 480 " segid="A   " =    0.878
peak=    3.662 closest distance to pdb=" CD2 LEU A 480 " segid="A   " =    0.838
peak=    3.535 closest distance to pdb=" CE  LYS A 481 " segid="A   " =    2.844
peak=    3.903 closest distance to pdb=" CE  LYS A 481 " segid="A   " =    2.438
peak=    3.580 closest distance to pdb=" NZ  LYS A 482 " segid="A   " =    1.658
peak=    5.638 closest distance to pdb=" NZ  LYS A 484 " segid="A   " =    1.507
peak=    3.587 closest distance to pdb=" CB  THR A 485 " segid="A   " =    1.638
peak=    3.803 closest distance to pdb=" ND2 ASN A 493 " segid="A   " =    2.318
peak=    3.710 closest distance to pdb=" CD2 TYR A 496 " segid="A   " =    1.845
peak=    3.835 closest distance to pdb=" CE1 HIS A 526 " segid="A   " =    0.992
peak=    4.494 closest distance to pdb=" CE1 HIS A 526 " segid="A   " =    1.136
peak=    3.705 closest distance to pdb=" CA  VAL A 535 " segid="A   " =    0.773
peak=    3.538 closest distance to pdb=" CD  PRO A 537 " segid="A   " =    1.395
peak=    3.866 closest distance to pdb=" C   GLU A 538 " segid="A   " =    1.288
peak=    3.590 closest distance to pdb=" CD  PRO A 555 " segid="A   " =    2.194
peak=    5.298 closest distance to pdb=" CG  PRO A 555 " segid="A   " =    1.069
peak=    4.566 closest distance to pdb=" CE3 TRP A 562 " segid="A   " =    1.223
peak=    4.758 closest distance to pdb="MG+2 MG2   590 " =    1.294
peak=    3.865 closest distance to pdb="MG+2 MG2   591 " =    2.455
peak=    7.611 closest distance to pdb="MG+2 MG2   593 " =    1.440

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.50 sigma)= 32          
Filter by distance & map next to the model:
   mapped sites are within: 0.568 - 5.069
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 30 from: 32
   mapped sites are within: 0.895 - 5.069

peak=   -4.153 closest distance to pdb=" CB  TYR A 307 " segid="A   " =    3.365
peak=   -4.979 closest distance to pdb=" CB  ALA A 321 " segid="A   " =    3.057
peak=   -4.311 closest distance to pdb=" OG1 THR A 365 " segid="A   " =    3.096
peak=   -3.893 closest distance to pdb=" OE1 GLN A 367 " segid="A   " =    1.493
peak=   -4.011 closest distance to pdb=" O   ASP A 386 " segid="A   " =    1.161
peak=   -3.989 closest distance to pdb=" O   ASP A 386 " segid="A   " =    1.795
peak=   -5.189 closest distance to pdb=" CD2 PHE A 390 " segid="A   " =    2.610
peak=   -4.716 closest distance to pdb=" CD2 PHE A 390 " segid="A   " =    2.572
peak=   -4.788 closest distance to pdb=" CE2 PHE A 390 " segid="A   " =    2.778
peak=   -9.956 closest distance to pdb=" CZ  PHE A 390 " segid="A   " =    3.293
peak=   -9.433 closest distance to pdb=" CZ  PHE A 390 " segid="A   " =    3.238
peak=   -7.929 closest distance to pdb=" CZ  PHE A 390 " segid="A   " =    3.372
peak=   -3.798 closest distance to pdb=" CD1 LEU A 405 " segid="A   " =    3.500
peak=   -3.724 closest distance to pdb=" N   ALA A 408 " segid="A   " =    2.166
peak=   -3.914 closest distance to pdb=" CA  ALA A 408 " segid="A   " =    3.115
peak=   -4.052 closest distance to pdb=" CD1 LEU A 416 " segid="A   " =    2.527
peak=   -4.135 closest distance to pdb=" CD2 LEU A 421 " segid="A   " =    1.246
peak=   -3.702 closest distance to pdb=" CD2 LEU A 421 " segid="A   " =    1.712
peak=   -3.896 closest distance to pdb=" C   LEU A 445 " segid="A   " =    0.999
peak=   -4.196 closest distance to pdb=" O   LEU A 445 " segid="A   " =    1.091
peak=   -3.640 closest distance to pdb=" C   LEU A 473 " segid="A   " =    1.255
peak=   -3.599 closest distance to pdb=" CD1 LEU A 500 " segid="A   " =    2.487
peak=   -3.775 closest distance to pdb=" N   VAL A 512 " segid="A   " =    0.895
peak=   -3.977 closest distance to pdb=" O   LEU A 514 " segid="A   " =    2.270
peak=   -3.743 closest distance to pdb=" O   LEU A 514 " segid="A   " =    1.688
peak=   -3.650 closest distance to pdb=" C   SER A 515 " segid="A   " =    0.963
peak=   -3.710 closest distance to pdb=" CB  GLU A 567 " segid="A   " =    1.215
peak=   -3.748 closest distance to pdb=" CG  GLU A 567 " segid="A   " =    2.987
peak=   -3.804 closest distance to pdb=" CD  GLU A 567 " segid="A   " =    1.144
peak=   -3.685 closest distance to pdb=" O1  SO4   594 " =    5.069

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

****************** 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_occ: refinement of 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    :  0.3950 0.3642   3.429453e+00   3.386237e+00
   1_bss:  0.2908 0.2841   3.336126e+00   3.277374e+00
   1_xyz:  0.2694 0.2864   3.256902e+00   3.296367e+00
   1_adp:  0.2387 0.2715   3.150796e+00   3.241754e+00
   2_bss:  0.2385 0.2637   3.149380e+00   3.225384e+00
   2_xyz:  0.2263 0.2630   3.117382e+00   3.220624e+00
   2_adp:  0.2211 0.2641   3.096514e+00   3.216132e+00
   3_bss:  0.2227 0.2603   3.096749e+00   3.206246e+00
   3_xyz:  0.2154 0.2614   3.079782e+00   3.208455e+00
   3_adp:  0.2139 0.2585   3.074338e+00   3.202374e+00
   3_bss:  0.2136 0.2607   3.051987e+00   3.187127e+00
------------------------------------------------------------------------
 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:  0.305  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   1_xyz:  0.305  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   1_adp:  0.305  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   2_bss:  0.295  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   2_xyz:  0.295  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   2_adp:  0.295  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   3_bss:  0.293  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   3_xyz:  0.293  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   3_adp:  0.293  50.000  15.389  15.389  33.324  -0.000   0.000   0.000
   3_bss:  0.321 103.851  -5.978  -5.978  11.957  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.324 0.7235  0.0556      401.469
   1_bss:  27.558 0.7887  0.0855      159.983
   1_xyz:  27.956 0.7843  0.0837      167.527
   1_adp:  25.866 0.8067  0.0944      162.018
   2_bss:  25.432 0.8112  0.0944      152.991
   2_xyz:  24.985 0.8162  0.0952      150.925
   2_adp:  24.652 0.8196  0.0942      150.752
   3_bss:  24.413 0.8219  0.0943      147.220
   3_xyz:  24.345 0.8231  0.0944      148.295
   3_adp:  24.074 0.8257  0.0942      145.918
   3_bss:  23.587 0.8307  0.0949      143.328
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.630  0.021  0.108 21.090  0.009  4.101   2.1385e-01
   1_bss:   1.630  0.021  0.108 21.090  0.009  4.101   2.1385e-01
   1_xyz:   1.413  0.010  0.089 21.046  0.006  4.105   1.6425e-01
   1_adp:   1.413  0.010  0.089 21.046  0.006  4.105   1.6425e-01
   2_bss:   1.413  0.010  0.089 21.046  0.006  4.105   1.6425e-01
   2_xyz:   1.261  0.008  0.080 20.481  0.006  4.113   1.3523e-01
   2_adp:   1.261  0.008  0.080 20.481  0.006  4.113   1.3523e-01
   3_bss:   1.261  0.008  0.080 20.481  0.006  4.113   1.3523e-01
   3_xyz:   1.244  0.008  0.080 20.464  0.006  4.120   1.3431e-01
   3_adp:   1.244  0.008  0.080 20.464  0.006  4.120   1.3431e-01
   3_bss:   1.244  0.008  0.080 20.464  0.006  4.120   1.3431e-01
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  15.442  0.896  0.410 89.942  0.098  1.827   2.1746e-01
   1_bss:  15.442  0.896  0.410 89.942  0.098  1.827   2.1746e-01
   1_xyz:  13.276  0.115  0.425 89.244  0.056  2.236   1.0043e-01
   1_adp:  13.276  0.115  0.425 89.244  0.056  2.236   1.0043e-01
   2_bss:  13.276  0.115  0.425 89.244  0.056  2.236   1.0043e-01
   2_xyz:  10.690  0.105  0.349 87.229  0.065  2.255   1.0526e-01
   2_adp:  10.690  0.105  0.349 87.229  0.065  2.255   1.0526e-01
   3_bss:  10.690  0.105  0.349 87.229  0.065  2.255   1.0526e-01
   3_xyz:  10.206  0.097  0.406 88.945  0.065  2.271   6.2375e-02
   3_adp:  10.206  0.097  0.406 88.945  0.065  2.271   6.2375e-02
   3_bss:  10.206  0.097  0.406 88.945  0.065  2.271   6.2375e-02
------------------------------------------------------------------------
 stage      b_max   b_min   b_ave
   0    :  300.00   26.21   94.26
   1_bss:  300.00   26.21   94.26
   1_xyz:  300.00   26.21   94.26
   1_adp:  306.62   29.78  118.27
   2_bss:  306.62   29.78  118.27
   2_xyz:  306.62   29.78  118.27
   2_adp:  315.66   28.70  117.67
   3_bss:  315.66   28.70  117.67
   3_xyz:  315.66   28.70  117.67
   3_adp:  303.19   31.95  116.18
   3_bss:  324.56   53.31  137.54
------------------------------------------------------------------------
 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_xyz:    1.116    0.008    0.142
   1_adp:    1.116    0.008    0.142
   2_bss:    1.116    0.008    0.142
   2_xyz:    0.954    0.013    0.188
   2_adp:    0.954    0.013    0.188
   3_bss:    0.954    0.013    0.188
   3_xyz:    1.236    0.008    0.247
   3_adp:    1.236    0.008    0.247
   3_bss:    1.236    0.008    0.247
------------------------------------------------------------------------

CPU time actual refinement: 495.28


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

Writing refined structure to PDB file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/tls/synaptotagmin_refine_001.pdb
n_use            =  2195
n_use_u_iso      =  2195
n_use_u_aniso    =  2186
n_grad_site      =  0
n_grad_u_iso     =  2195
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 2mFo-DFc XPLOR map to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/tls/synaptotagmin_refine_001_2mFo-DFc.map
Writing mFo-DFc XPLOR map to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/tls/synaptotagmin_refine_001_mFo-DFc.map
Writing map coefficients to MTZ file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/tls/synaptotagmin_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/tls/synaptotagmin_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 495.19 
  Macro-tasks:
    bulk solvent and scale       = 21.42  
    weights calculation          = 17.63  
    collect and process          = 3.67   
    adp group                    = 83.99  
    tls refinement               = 172.61 
    model show statistics        = 0.49   
    TOTAL for macro-tasks        = 299.81 
  Micro-tasks:
    mask                            = 2.84   
    f_calc                          = 148.72 
    alpha_beta                      = 6.44   
    target                          = 0.74   
    gradients_wrt_atomic_parameters = 264.21 
    fmodel                         = 4.44   
    r_factors                      = 0.32   
    phase_errors                   = 9.18   
    foms                           = 0.38   
    TOTAL for micro-tasks          = 437.27 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 8.486 micro seconds
Total CPU time: 8.40 minutes
from_scatterers_fft:    550 calls, 148.49 s
gradients_fft:          494 calls, 260.82 s

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

# Date 2008-10-14 Time 08:54:32 PDT -0700 (1223999672.29 s)
wall clock time: 502.86 s

Start R-work = 0.3950, R-free = 0.3642 (no bulk solvent and anisotropic scale)
Final R-work = 0.4681, R-free = 0.4242 (no bulk solvent and anisotropic scale)

Start R-work = 0.2908, R-free = 0.2841
Final R-work = 0.2136, R-free = 0.2607