# Date 2008-01-16 Time 01:38:55 PST -0800 (1200476335.11 s)
#phil __OFF__

Command line arguments: "../500.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1389
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 500

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.9914, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.96265
Completeness in resolution range: 0.955654
Completeness with d_max=infinity: 0.952726

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9627

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.96265
Completeness in resolution range: 0.955654
Completeness with d_max=infinity: 0.952726

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2000 [2155/2179]  1937   218  10.1%
  bin  2:  4.2000 -  3.3460 [2058/2078]  1854   204   9.9%
  bin  3:  3.3460 -  2.9267 [2050/2069]  1844   206  10.0%
  bin  4:  2.9267 -  2.6607 [2026/2056]  1825   201   9.9%
  bin  5:  2.6607 -  2.4709 [2004/2023]  1806   198   9.9%
  bin  6:  2.4709 -  2.3258 [1994/2019]  1792   202  10.1%
  bin  7:  2.3258 -  2.2097 [1997/2025]  1793   204  10.2%
  bin  8:  2.2097 -  2.1138 [1987/2023]  1792   195   9.8%
  bin  9:  2.1138 -  2.0326 [1969/2011]  1775   194   9.9%
  bin 10:  2.0326 -  1.9626 [1349/2015]  1212   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_500/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 33
        2.39 -     3.01: 2045
        3.01 -     3.64: 4696
        3.64 -     4.27: 9271
        4.27 -     4.90: 12577
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.758 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28617 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

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


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


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

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


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

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

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


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

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
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 =  2823

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

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

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

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_500/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_500/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 69.89875 45.9914 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4724   r_free= 0.4662   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.279103                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.6847 0.99   1400  155 0.4019 0.3902      6.5947      6.6214|
|  2:  4.6847 -  3.7375 0.99   1345  151 0.3926 0.3632      6.7891      6.7261|
|  3:  3.7375 -  3.2707 0.99   1317  143 0.4201 0.3823      6.6649      6.6517|
|  4:  3.2707 -  2.9743 0.99   1319  151 0.4621 0.4409      6.5315      6.4863|
|  5:  2.9743 -  2.7625 0.99   1301  145 0.5022 0.4932      6.3625      6.3873|
|  6:  2.7625 -  2.6005 0.99   1298  140 0.5008 0.5442      6.2854      6.1964|
|  7:  2.6005 -  2.4709 0.99   1286  142 0.5049 0.4806      6.2374       6.224|
|  8:  2.4709 -  2.3638 0.98   1277  145 0.5250 0.5064      6.1906      6.1848|
|  9:  2.3638 -  2.2731 0.98   1276  142 0.5124 0.5314        6.11      6.1601|
| 10:  2.2731 -  2.1949 1.00   1299  147 0.5205 0.5312      6.1089      6.0737|
| 11:  2.1949 -  2.1265 0.97   1267  136 0.5039 0.4805      6.0285      6.0609|
| 12:  2.1265 -  2.0659 0.98   1262  145 0.5105 0.5577      5.9769      6.0194|
| 13:  2.0659 -  2.0116 0.99   1287  135 0.5191 0.5168      5.8756      5.8179|
| 14:  2.0116 -  1.9626 0.54    696   82 0.5610 0.5297      5.9001      5.7902|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.6847  1400   155  0.66  37.34   0.79     0.72      82439.12|
|  2:  4.6847 -  3.7375  1345   151  0.72  33.59   0.87     0.80     100335.34|
|  3:  3.7375 -  3.2707  1317   143  0.63  41.32   0.87     0.76     104955.99|
|  4:  3.2707 -  2.9743  1319   151  0.54  48.96   0.81     0.63      94582.78|
|  5:  2.9743 -  2.7625  1301   145  0.41  59.08   0.75     0.50      82624.58|
|  6:  2.7625 -  2.6005  1298   140  0.38  61.39   0.72     0.43      73194.95|
|  7:  2.6005 -  2.4709  1286   142  0.32  65.84   0.75     0.38      70386.76|
|  8:  2.4709 -  2.3638  1277   145  0.30  67.18   0.74     0.37      64000.11|
|  9:  2.3638 -  2.2731  1276   142  0.33  65.27   0.74     0.39      56274.40|
| 10:  2.2731 -  2.1949  1299   147  0.36  62.91   0.76     0.43      47581.68|
| 11:  2.1949 -  2.1265  1267   136  0.36  63.30   0.78     0.44      46220.06|
| 12:  2.1265 -  2.0659  1262   145  0.31  66.98   0.80     0.39      44421.19|
| 13:  2.0659 -  2.0116  1287   135  0.28  69.55   0.72     0.35      39603.16|
| 14:  2.0116 -  1.9626   696    82  0.31  66.66   0.73     0.35      30998.12|
|alpha:            min =        0.35 max =            0.80 mean =         0.50|
|beta:             min =    30998.12 max =       104955.99 mean =     68569.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.24|
|phase err.(test): min =        0.00 max =           89.98 mean =        57.30|
|-----------------------------------------------------------------------------|

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

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

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.996191             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.440   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.367039              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.793   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       34 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      705 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1530 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2685 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3984 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5129 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6612 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7836 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.203 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.110 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    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:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4791   r_free= 0.4700   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.281491                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4641   r_free= 0.4537   ksol= 0.36   Bsol= 5.50   scale= 1.002    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.82,10.47,7.71,0.00,0.00,0.00); trace/3= 8.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.272274                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.103509             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.756   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.216539              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.249   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4641      final r-factor (work) = 0.3861          |
| start r-factor (free) = 0.4537      final r-factor (free) = 0.4083          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.1902 = 12.10 * 0.50 * 6.2770 + 1.00 * 53.2030                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6123 = 12.10 * 0.50 * 6.1926 + 1.00 * 0.1362                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3861      final r-factor (work) = 0.3383          |
| start r-factor (free) = 0.4083      final r-factor (free) = 0.3940          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5479 = 1.22 * 1.00 * 6.1926 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4498 = 1.22 * 1.00 * 6.1099 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.87   13.41    None  None   None       |
|    all(noH): 2823   0      0.00    78.87   13.41    None  None   None       |
|    Sol.    : 438    0      0.00    78.87   24.50    None  None   None       |
|    Mac.    : 2385   0      0.00    78.17   11.38    None  None   None       |
|    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:     0.000 -   7.887: 1131   |   5:    39.434 -  47.321:   46        |
|      1:     7.887 -  15.774:  767   |   6:    47.321 -  55.208:   41        |
|      2:    15.774 -  23.661:  447   |   7:    55.208 -  63.095:   12        |
|      3:    23.661 -  31.547:  248   |   8:    63.095 -  70.981:    2        |
|      4:    31.547 -  39.434:  127   |   9:    70.981 -  78.868:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3383 r_free = 0.3940             target_work(ml) = 6.093         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3379 r_free = 0.3938             target_work(ml) = 6.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3379   r_free= 0.3938   ksol= 0.36   Bsol= 5.50   scale= 1.111    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.82,10.47,7.71,0.00,0.00,0.00); trace/3= 8.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.092011                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3346   r_free= 0.3889   ksol= 0.33   Bsol= 20.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,6.16,4.71,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.091858                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.812614              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.193  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.609409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.225  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3346      final r-factor (work) = 0.2759          |
| start r-factor (free) = 0.3889      final r-factor (free) = 0.3335          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8798 = 5.81 * 0.50 * 6.1052 + 1.00 * 0.1362                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5255 = 5.81 * 0.50 * 6.0038 + 1.00 * 0.0765                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2759      final r-factor (work) = 0.2599          |
| start r-factor (free) = 0.3335      final r-factor (free) = 0.3258          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6760 = 0.61 * 1.00 * 6.0038 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6154 = 0.61 * 1.00 * 5.8995 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.79   13.53    None  None   None       |
|    all(noH): 2823   0      0.00    83.79   13.53    None  None   None       |
|    Sol.    : 438    0      0.00    81.54   27.71    None  None   None       |
|    Mac.    : 2385   0      0.00    83.79   10.92    None  None   None       |
|    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:     0.000 -   8.380: 1209   |   5:    41.897 -  50.277:   52        |
|      1:     8.380 -  16.759:  759   |   6:    50.277 -  58.656:   18        |
|      2:    16.759 -  25.139:  424   |   7:    58.656 -  67.036:    9        |
|      3:    25.139 -  33.518:  240   |   8:    67.036 -  75.415:    0        |
|      4:    33.518 -  41.897:  109   |   9:    75.415 -  83.795:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2599 r_free = 0.3258             target_work(ml) = 5.886         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2597 r_free = 0.3261             target_work(ml) = 5.886         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2597   r_free= 0.3261   ksol= 0.33   Bsol= 20.00   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,6.16,4.71,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.885765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2586   r_free= 0.3236   ksol= 0.34   Bsol= 39.90   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.50,3.64,3.63,0.00,0.00,0.00); trace/3= 3.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.885347                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.176433              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.506  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.438667              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.522  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2586      final r-factor (work) = 0.2093          |
| start r-factor (free) = 0.3236      final r-factor (free) = 0.2699          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4459 = 3.18 * 0.50 * 5.8993 + 1.00 * 0.0765                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2644 = 3.18 * 0.50 * 5.7907 + 1.00 * 0.0674                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2093      final r-factor (work) = 0.1877          |
| start r-factor (free) = 0.2699      final r-factor (free) = 0.2497          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.1371 = 2.44 * 1.00 * 5.7907 + 1.00 * 0.0154                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7786 = 2.44 * 1.00 * 5.6427 + 1.00 * 0.0180                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.81   14.62    None  None   None       |
|    all(noH): 2823   0      0.00    99.81   14.62    None  None   None       |
|    Sol.    : 438    0      1.17    95.89   38.35    None  None   None       |
|    Mac.    : 2385   0      0.00    99.81   10.26    None  None   None       |
|    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:     0.000 -   9.981: 1555   |   5:    49.903 -  59.884:   78        |
|      1:     9.981 -  19.961:  615   |   6:    59.884 -  69.864:   37        |
|      2:    19.961 -  29.942:  226   |   7:    69.864 -  79.845:   12        |
|      3:    29.942 -  39.923:  156   |   8:    79.845 -  89.826:    3        |
|      4:    39.923 -  49.903:  139   |   9:    89.826 -  99.806:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1877 r_free = 0.2497             target_work(ml) = 5.605         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1876 r_free = 0.2495             target_work(ml) = 5.604         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1876   r_free= 0.2495   ksol= 0.34   Bsol= 39.90   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.50,3.64,3.63,0.00,0.00,0.00); trace/3= 3.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.604325                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1873   r_free= 0.2490   ksol= 0.33   Bsol= 42.82   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.81,2.31,3.17,0.00,0.00,0.00); trace/3= 2.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.603804                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.269228              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.427   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.765545              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.859  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1873      final r-factor (work) = 0.1545          |
| start r-factor (free) = 0.2490      final r-factor (free) = 0.2118          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4713 = 2.27 * 0.50 * 5.6441 + 1.00 * 0.0674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3154 = 2.27 * 0.50 * 5.5194 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1545      final r-factor (work) = 0.1441          |
| start r-factor (free) = 0.2118      final r-factor (free) = 0.1989          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2444 = 0.77 * 1.00 * 5.5194 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6030 = 0.77 * 1.00 * 5.4067 + 1.00 * 0.4639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 37     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.95  14.06    None  None   None       |
|    all(noH): 2823   0      0.00    101.95  14.06    None  None   None       |
|    Sol.    : 438    0      2.22    95.96   39.24    None  None   None       |
|    Mac.    : 2385   0      0.00    101.95  9.44     None  None   None       |
|    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:     0.000 -  10.195: 1722   |   5:    50.973 -  61.168:   85        |
|      1:    10.195 -  20.389:  540   |   6:    61.168 -  71.362:   35        |
|      2:    20.389 -  30.584:  164   |   7:    71.362 -  81.557:   11        |
|      3:    30.584 -  40.779:  129   |   8:    81.557 -  91.752:    5        |
|      4:    40.779 -  50.973:  130   |   9:    91.752 - 101.946:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1441 r_free = 0.1989             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1437 r_free = 0.1985             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1437   r_free= 0.1985   ksol= 0.33   Bsol= 42.82   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.81,2.31,3.17,0.00,0.00,0.00); trace/3= 2.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.368508                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1441   r_free= 0.1985   ksol= 0.32   Bsol= 42.82   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,1.75,3.09,0.00,0.00,0.00); trace/3= 2.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.367325                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.982371              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.656  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.695128              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.843   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1441      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1985      final r-factor (free) = 0.1798          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4109 = 1.98 * 0.50 * 5.4055 + 1.00 * 0.0531                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3251 = 1.98 * 0.50 * 5.3184 + 1.00 * 0.0535                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1275      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1798      final r-factor (free) = 0.1753          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.9897 = 4.70 * 1.00 * 5.3184 + 1.00 * 0.0190                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.6566 = 4.70 * 1.00 * 5.2483 + 1.00 * 0.0150                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.65  13.99    None  None   None       |
|    all(noH): 2823   0      0.00    111.65  13.99    None  None   None       |
|    Sol.    : 438    0      1.78    102.79  40.59    None  None   None       |
|    Mac.    : 2385   0      0.00    111.65  9.10     None  None   None       |
|    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:     0.000 -  11.165: 1873   |   5:    55.824 -  66.989:   65        |
|      1:    11.165 -  22.330:  451   |   6:    66.989 -  78.154:   41        |
|      2:    22.330 -  33.495:  156   |   7:    78.154 -  89.319:   10        |
|      3:    33.495 -  44.660:  122   |   8:    89.319 - 100.484:    5        |
|      4:    44.660 -  55.824:   98   |   9:   100.484 - 111.649:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1232 r_free = 0.1753             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1752             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1752   ksol= 0.32   Bsol= 42.82   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,1.75,3.09,0.00,0.00,0.00); trace/3= 2.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234404                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.6847 0.99   1400  155 0.1016 0.1331      5.4187      5.5785|
|  2:  4.6847 -  3.7375 0.99   1345  151 0.0907 0.1259       5.491      5.7207|
|  3:  3.7375 -  3.2707 0.99   1317  143 0.1147 0.1503       5.554      5.8653|
|  4:  3.2707 -  2.9743 0.99   1319  151 0.1357 0.1931       5.544      5.7145|
|  5:  2.9743 -  2.7625 0.99   1301  145 0.1473 0.1990      5.4103      5.6763|
|  6:  2.7625 -  2.6005 0.99   1298  140 0.1303 0.2037      5.2888      5.5222|
|  7:  2.6005 -  2.4709 0.99   1286  142 0.1386 0.1809      5.2536      5.4477|
|  8:  2.4709 -  2.3638 0.98   1277  145 0.1368 0.1921      5.2057      5.4325|
|  9:  2.3638 -  2.2731 0.98   1276  142 0.1353 0.1923      5.1523      5.3935|
| 10:  2.2731 -  2.1949 1.00   1299  147 0.1269 0.1890      5.0609      5.2967|
| 11:  2.1949 -  2.1265 0.97   1267  136 0.1262 0.2036      5.0382      5.3901|
| 12:  2.1265 -  2.0659 0.98   1262  145 0.1256 0.1970      4.9812      5.3043|
| 13:  2.0659 -  2.0116 0.99   1287  135 0.1266 0.1955      4.8719      5.1163|
| 14:  2.0116 -  1.9626 0.54    696   82 0.1058 0.1576      4.7242       4.903|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.6847  1400   155  0.93  10.03   0.98     0.95       8214.06|
|  2:  4.6847 -  3.7375  1345   151  0.95   8.75   1.03     1.01      10289.66|
|  3:  3.7375 -  3.2707  1317   143  0.92  12.82   1.05     1.04      12326.29|
|  4:  3.2707 -  2.9743  1319   151  0.90  15.59   1.03     1.01      12493.01|
|  5:  2.9743 -  2.7625  1301   145  0.89  17.57   1.01     0.98       9837.55|
|  6:  2.7625 -  2.6005  1298   140  0.88  17.88   0.99     0.95       8435.53|
|  7:  2.6005 -  2.4709  1286   142  0.89  17.78   1.00     0.96       7583.30|
|  8:  2.4709 -  2.3638  1277   145  0.88  18.28   1.00     0.97       7102.82|
|  9:  2.3638 -  2.2731  1276   142  0.89  17.62   1.00     0.95       6346.70|
| 10:  2.2731 -  2.1949  1299   147  0.88  18.08   1.00     0.96       5582.15|
| 11:  2.1949 -  2.1265  1267   136  0.88  18.38   1.00     0.95       5337.82|
| 12:  2.1265 -  2.0659  1262   145  0.89  17.67   1.02     1.01       4992.15|
| 13:  2.0659 -  2.0116  1287   135  0.88  18.49   1.01     0.99       4025.88|
| 14:  2.0116 -  1.9626   696    82  0.91  15.07   1.00     0.97       2945.22|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2945.22 max =        12493.01 mean =      7729.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.96|
|phase err.(test): min =        0.00 max =           89.70 mean =        15.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1751   ksol= 0.32   Bsol= 46.04   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,-0.49,0.95,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234142                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1751   ksol= 0.32   Bsol= 46.04   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,-0.49,0.95,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234142                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.6847 0.99   1400  155 0.1015 0.1330       5.417      5.5773|
|  2:  4.6847 -  3.7375 0.99   1345  151 0.0908 0.1262      5.4916      5.7222|
|  3:  3.7375 -  3.2707 0.99   1317  143 0.1148 0.1504      5.5548      5.8662|
|  4:  3.2707 -  2.9743 0.99   1319  151 0.1357 0.1930      5.5439      5.7139|
|  5:  2.9743 -  2.7625 0.99   1301  145 0.1472 0.1989      5.4098      5.6756|
|  6:  2.7625 -  2.6005 0.99   1298  140 0.1302 0.2035      5.2882      5.5213|
|  7:  2.6005 -  2.4709 0.99   1286  142 0.1386 0.1811      5.2532       5.448|
|  8:  2.4709 -  2.3638 0.98   1277  145 0.1368 0.1920      5.2054      5.4318|
|  9:  2.3638 -  2.2731 0.98   1276  142 0.1353 0.1922      5.1521      5.3931|
| 10:  2.2731 -  2.1949 1.00   1299  147 0.1268 0.1890      5.0608      5.2972|
| 11:  2.1949 -  2.1265 0.97   1267  136 0.1261 0.2036      5.0383      5.3903|
| 12:  2.1265 -  2.0659 0.98   1262  145 0.1255 0.1970      4.9811      5.3045|
| 13:  2.0659 -  2.0116 0.99   1287  135 0.1266 0.1952      4.8715      5.1149|
| 14:  2.0116 -  1.9626 0.54    696   82 0.1058 0.1575      4.7233      4.9021|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.6847  1400   155  0.93  10.01   0.98     0.95       8176.86|
|  2:  4.6847 -  3.7375  1345   151  0.95   8.75   1.03     1.01      10288.00|
|  3:  3.7375 -  3.2707  1317   143  0.92  12.84   1.05     1.04      12351.56|
|  4:  3.2707 -  2.9743  1319   151  0.90  15.59   1.03     1.01      12494.47|
|  5:  2.9743 -  2.7625  1301   145  0.89  17.56   1.01     0.98       9823.01|
|  6:  2.7625 -  2.6005  1298   140  0.88  17.87   0.99     0.96       8424.72|
|  7:  2.6005 -  2.4709  1286   142  0.89  17.76   1.00     0.96       7572.38|
|  8:  2.4709 -  2.3638  1277   145  0.88  18.27   1.00     0.97       7095.90|
|  9:  2.3638 -  2.2731  1276   142  0.89  17.62   1.01     0.96       6343.29|
| 10:  2.2731 -  2.1949  1299   147  0.88  18.09   1.01     0.96       5583.88|
| 11:  2.1949 -  2.1265  1267   136  0.88  18.39   1.01     0.95       5341.60|
| 12:  2.1265 -  2.0659  1262   145  0.89  17.66   1.02     1.01       4991.39|
| 13:  2.0659 -  2.0116  1287   135  0.88  18.47   1.01     0.99       4020.35|
| 14:  2.0116 -  1.9626   696    82  0.91  15.04   1.00     0.98       2936.83|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2936.83 max =        12494.47 mean =      7724.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.96|
|phase err.(test): min =        0.00 max =           89.73 mean =        15.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.23    113.88  16.21    None  None   None       |
|    all(noH): 2823   0      2.23    113.88  16.21    None  None   None       |
|    Sol.    : 438    0      4.00    105.02  42.82    None  None   None       |
|    Mac.    : 2385   0      2.23    113.88  11.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.227 -  13.392: 1873   |   5:    58.051 -  69.216:   65        |
|      1:    13.392 -  24.557:  451   |   6:    69.216 -  80.381:   41        |
|      2:    24.557 -  35.722:  156   |   7:    80.381 -  91.546:   10        |
|      3:    35.722 -  46.887:  122   |   8:    91.546 - 102.711:    5        |
|      4:    46.887 -  58.051:   98   |   9:   102.711 - 113.876:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.250 - 3.820
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 328
   mapped sites are within: 0.736 - 3.820

peak=    9.762 closest distance to " CB  VAL A 296 " =    1.500
peak=    9.537 closest distance to " CB  VAL A 230 " =    1.426
peak=    7.821 closest distance to " O   HOH Z 130 " =    1.779
peak=    7.179 closest distance to " CG  ARG A 138 " =    1.176
peak=    6.697 closest distance to " CD2 LEU A   5 " =    1.339
peak=    6.588 closest distance to " CD1AILE A 234 " =    1.165
peak=    5.886 closest distance to " NE2 GLN A  11 " =    1.156
peak=    5.820 closest distance to " O   HOH Z  65 " =    1.637
peak=    5.414 closest distance to " O   HOH Z 424 " =    1.355
peak=    5.343 closest distance to " CB  PRO A  54 " =    1.090
peak=    5.301 closest distance to " O   HOH Z   9 " =    1.659
peak=    5.186 closest distance to " NH1 ARG A 138 " =    0.980
peak=    5.153 closest distance to " CG  LEU A   5 " =    1.205
peak=    5.152 closest distance to " O   HOH Z 124 " =    1.524
peak=    5.058 closest distance to " CB  VAL A 230 " =    1.164
peak=    5.030 closest distance to " O   HOH Z 142 " =    2.024
peak=    5.001 closest distance to " CG  PRO A  54 " =    1.399
peak=    4.982 closest distance to " O   HOH Z 375 " =    1.103
peak=    4.923 closest distance to " CD2 LEU A 228 " =    1.206
peak=    4.922 closest distance to " O   HOH Z 222 " =    1.292
peak=    4.913 closest distance to " O   HOH Z 425 " =    1.618
peak=    4.907 closest distance to " NH2 ARG A  56 " =    2.016
peak=    4.906 closest distance to " CD  ARG A 138 " =    0.838
peak=    4.895 closest distance to " O   HOH Z 112 " =    1.372
peak=    4.859 closest distance to " O   HOH Z 232 " =    2.235
peak=    4.806 closest distance to " O   HOH Z 417 " =    1.504
peak=    4.760 closest distance to " CB  ARG A 275 " =    1.044
peak=    4.756 closest distance to " O   HOH Z 427 " =    2.258
peak=    4.749 closest distance to " O   PRO A 198 " =    1.324
peak=    4.700 closest distance to " O   HOH Z 126 " =    2.015
peak=    4.619 closest distance to " O   HOH Z   7 " =    1.511
peak=    4.586 closest distance to " O   HOH Z 385 " =    1.131
peak=    4.584 closest distance to " O   HOH Z 225 " =    1.575
peak=    4.573 closest distance to " CB  ASN A 148 " =    1.391
peak=    4.569 closest distance to " O   HOH Z 418 " =    1.109
peak=    4.564 closest distance to " O   HOH Z 427 " =    1.138
peak=    4.554 closest distance to " O   HOH Z 139 " =    1.345
peak=    4.507 closest distance to " CB  SER A   3 " =    1.392
peak=    4.494 closest distance to " O   HOH Z  78 " =    1.679
peak=    4.458 closest distance to " O   HOH Z  59 " =    1.609
peak=    4.427 closest distance to " O   HOH Z   2 " =    2.096
peak=    4.412 closest distance to " CG  LEU A 228 " =    1.121
peak=    4.362 closest distance to " CB  GLN A 183 " =    1.209
peak=    4.327 closest distance to " O   HOH Z 380 " =    1.986
peak=    4.293 closest distance to " O   HOH Z 316 " =    2.976
peak=    4.288 closest distance to " O   HOH Z 419 " =    2.187
peak=    4.270 closest distance to " O   HOH Z  63 " =    1.609
peak=    4.241 closest distance to " O   HOH Z 369 " =    2.272
peak=    4.240 closest distance to " CG  LEU A 167 " =    1.231
peak=    4.237 closest distance to " O   HOH Z 425 " =    2.079
peak=    4.226 closest distance to " O   HOH Z 423 " =    1.722
peak=    4.215 closest distance to " O   HOH Z  91 " =    2.434
peak=    4.209 closest distance to " O   HOH Z 361 " =    1.319
peak=    4.208 closest distance to " O   HOH Z 392 " =    1.293
peak=    4.205 closest distance to " O   HOH Z 371 " =    2.829
peak=    4.177 closest distance to " CG  PRO A 213 " =    1.219
peak=    4.176 closest distance to " CB  SER A  63 " =    1.330
peak=    4.171 closest distance to " O   HOH Z 422 " =    2.407
peak=    4.135 closest distance to " CG  PRO A 198 " =    1.198
peak=    4.122 closest distance to " O   HOH Z   1 " =    1.715
peak=    4.120 closest distance to " O   HOH Z 193 " =    1.458
peak=    4.116 closest distance to " O   HOH Z 410 " =    1.457
peak=    4.108 closest distance to " O   HOH Z 287 " =    1.719
peak=    4.106 closest distance to " CB  SER A 216 " =    0.929
peak=    4.080 closest distance to " O   HOH Z 298 " =    1.790
peak=    4.061 closest distance to " CB  VAL A 202 " =    1.693
peak=    4.038 closest distance to " O   HOH Z 214 " =    1.144
peak=    4.022 closest distance to " O   HOH Z  68 " =    2.231
peak=    4.010 closest distance to " O   HOH Z 389 " =    1.416
peak=    4.006 closest distance to " O   HOH Z 236 " =    1.640
peak=    3.983 closest distance to " O   HOH Z 290 " =    0.992
peak=    3.965 closest distance to " O   HOH Z 193 " =    1.730
peak=    3.954 closest distance to " O   HOH Z  30 " =    1.920
peak=    3.944 closest distance to " N   GLN A 278 " =    1.084
peak=    3.938 closest distance to " O   HOH Z  11 " =    1.423
peak=    3.928 closest distance to " CB  GLU A 277 " =    3.521
peak=    3.918 closest distance to " O   HOH Z  39 " =    1.572
peak=    3.914 closest distance to " CB  GLN A 223 " =    1.509
peak=    3.899 closest distance to " O   HOH Z 123 " =    1.095
peak=    3.898 closest distance to " N   GLU A   2 " =    1.363
peak=    3.895 closest distance to " CG  LYS A  76 " =    1.651
peak=    3.893 closest distance to " CA  PHE A 283 " =    1.370
peak=    3.892 closest distance to " O   HOH Z 366 " =    2.948
peak=    3.868 closest distance to " O   HOH Z 402 " =    1.459
peak=    3.865 closest distance to " NE1 TRP A 274 " =    1.001
peak=    3.853 closest distance to " O   HOH Z 130 " =    2.033
peak=    3.853 closest distance to " O   HOH Z 426 " =    1.064
peak=    3.839 closest distance to " O   HOH Z  69 " =    2.344
peak=    3.829 closest distance to " NE2 GLN A  58 " =    3.799
peak=    3.813 closest distance to " O   HOH Z 405 " =    1.579
peak=    3.801 closest distance to " O   HOH Z 422 " =    0.844
peak=    3.798 closest distance to " CB  GLU A 128 " =    1.059
peak=    3.770 closest distance to " CB  TRP A 179 " =    1.438
peak=    3.767 closest distance to " O   HOH Z   2 " =    1.291
peak=    3.755 closest distance to " O   HOH Z 352 " =    1.649
peak=    3.753 closest distance to " O   HOH Z 259 " =    2.244
peak=    3.748 closest distance to " O   HOH Z 346 " =    1.656
peak=    3.747 closest distance to " O   HOH Z 415 " =    1.041
peak=    3.746 closest distance to " O   HOH Z 214 " =    2.097
peak=    3.739 closest distance to " ND2 ASN A 249 " =    0.846
peak=    3.737 closest distance to " OG  SER A  62 " =    3.032
peak=    3.737 closest distance to " O   HOH Z 117 " =    1.930
peak=    3.734 closest distance to " CB  LEU A 237 " =    0.875
peak=    3.726 closest distance to " CB  SER A 276 " =    1.157
peak=    3.724 closest distance to " CA  ASN A 127 " =    1.090
peak=    3.705 closest distance to " CE  MET A  93 " =    1.479
peak=    3.701 closest distance to " O   HOH Z 384 " =    1.291
peak=    3.694 closest distance to " O   HOH Z 145 " =    1.825
peak=    3.682 closest distance to " CE3 TRP A 150 " =    1.093
peak=    3.682 closest distance to " N   PHE A 130 " =    1.272
peak=    3.663 closest distance to " O   HOH Z 119 " =    1.504
peak=    3.663 closest distance to " OD2 ASP A 286 " =    2.410
peak=    3.662 closest distance to " O   HOH Z  51 " =    1.340
peak=    3.659 closest distance to " O   HOH Z 233 " =    1.541
peak=    3.656 closest distance to " N   ASN A 127 " =    1.286
peak=    3.654 closest distance to " NZ  LYS A 117 " =    3.172
peak=    3.650 closest distance to " O   HOH Z 272 " =    1.807
peak=    3.635 closest distance to " O   HOH Z 303 " =    2.237
peak=    3.630 closest distance to " O  BHOH Z  74 " =    1.328
peak=    3.626 closest distance to " CG2 THR A 221 " =    1.251
peak=    3.624 closest distance to " CB  TRP A 266 " =    1.093
peak=    3.612 closest distance to " CB  ASN A 142 " =    1.055
peak=    3.611 closest distance to " CG  GLN A  11 " =    2.189
peak=    3.611 closest distance to " OG  SER A  62 " =    2.556
peak=    3.611 closest distance to " CB  VAL A 265 " =    1.308
peak=    3.608 closest distance to " CB  LYS A 117 " =    1.178
peak=    3.605 closest distance to " O   HOH Z 293 " =    1.447
peak=    3.601 closest distance to " O   HOH Z 358 " =    1.385
peak=    3.599 closest distance to " O   HOH Z 403 " =    1.373
peak=    3.597 closest distance to " O   HOH Z 359 " =    1.245
peak=    3.589 closest distance to " O   HOH Z 234 " =    3.491
peak=    3.586 closest distance to " SG ACYS A 201 " =    0.739
peak=    3.584 closest distance to " CA  GLY A 267 " =    1.135
peak=    3.583 closest distance to " O   HOH Z 368 " =    3.473
peak=    3.578 closest distance to " CG BARG A 102 " =    1.885
peak=    3.571 closest distance to " O   HOH Z 250 " =    1.367
peak=    3.560 closest distance to " NZ BLYS A 290 " =    0.973
peak=    3.560 closest distance to " CH2 TRP A 266 " =    1.070
peak=    3.559 closest distance to " CG2 ILE A 120 " =    1.102
peak=    3.552 closest distance to " CB BVAL A  41 " =    1.123
peak=    3.550 closest distance to " O   HOH Z 189 " =    2.699
peak=    3.547 closest distance to " CD1 ILE A  33 " =    1.775
peak=    3.542 closest distance to " CG1BVAL A 121 " =    2.212
peak=    3.529 closest distance to " O   HOH Z 133 " =    1.248
peak=    3.528 closest distance to " O   HOH Z 158 " =    2.878
peak=    3.527 closest distance to " O   ALA A 165 " =    1.250
peak=    3.520 closest distance to " CE3 TRP A 274 " =    2.344
peak=    3.518 closest distance to " O   HOH Z 172 " =    2.774
peak=    3.517 closest distance to " N   SER A 271 " =    1.039
peak=    3.510 closest distance to " O   HOH Z  78 " =    1.945
peak=    3.505 closest distance to " O   HOH Z 414 " =    1.155
peak=    3.504 closest distance to " O   HOH Z 258 " =    2.243
peak=    3.502 closest distance to " CD1 LEU A 281 " =    0.977
peak=    3.498 closest distance to " NH2BARG A 145 " =    2.146
peak=    3.494 closest distance to " O   HOH Z 305 " =    3.358
peak=    3.491 closest distance to " O   HOH Z   4 " =    1.386
peak=    3.490 closest distance to " CB  LEU A 143 " =    1.021
peak=    3.486 closest distance to " OG BSER A  99 " =    2.133
peak=    3.485 closest distance to " CG2 ILE A 234 " =    0.801
peak=    3.484 closest distance to " CA  ILE A 234 " =    1.024
peak=    3.481 closest distance to " CA  ASN A 215 " =    1.134
peak=    3.477 closest distance to " CA  LYS A 290 " =    1.392
peak=    3.472 closest distance to " OG BSER A 212 " =    2.915
peak=    3.471 closest distance to " O   HOH Z 329 " =    3.757
peak=    3.471 closest distance to " O   HOH Z 195 " =    1.428
peak=    3.469 closest distance to " O   HOH Z  30 " =    1.516
peak=    3.469 closest distance to " O   HOH Z 344 " =    1.151
peak=    3.462 closest distance to " CD  ARG A 159 " =    0.736
peak=    3.462 closest distance to " OD1 ASN A  45 " =    1.272
peak=    3.460 closest distance to " O   HOH Z   9 " =    1.784
peak=    3.459 closest distance to " O   HOH Z  55 " =    1.814
peak=    3.458 closest distance to " CB  MET A  40 " =    0.873
peak=    3.456 closest distance to " CA  ARG A 195 " =    1.367
peak=    3.452 closest distance to " O   HOH Z 423 " =    1.697
peak=    3.450 closest distance to " N   ALA A   1 " =    1.145
peak=    3.446 closest distance to " O   HOH Z 143 " =    1.338
peak=    3.445 closest distance to " O   HOH Z  61 " =    1.586
peak=    3.442 closest distance to " CA  LEU A 282 " =    1.119
peak=    3.439 closest distance to " CB  ASN A  39 " =    0.989
peak=    3.437 closest distance to " O   HOH Z 129 " =    0.798
peak=    3.433 closest distance to " O   HOH Z  65 " =    1.607
peak=    3.430 closest distance to " NE2 GLN A  73 " =    1.443
peak=    3.429 closest distance to " O   HOH Z  88 " =    3.073
peak=    3.428 closest distance to " O   HOH Z 371 " =    1.800
peak=    3.424 closest distance to " O   HOH Z 327 " =    1.545
peak=    3.415 closest distance to " O   HOH Z 128 " =    2.186
peak=    3.415 closest distance to " CB  ASP A 124 " =    0.928
peak=    3.414 closest distance to " OE1 GLU A   2 " =    1.894
peak=    3.407 closest distance to " CB  PHE A 225 " =    1.358
peak=    3.407 closest distance to " O   HOH Z 390 " =    2.313
peak=    3.405 closest distance to " O   HOH Z 167 " =    1.856
peak=    3.403 closest distance to " O   HOH Z  47 " =    1.415
peak=    3.403 closest distance to " O   HOH Z 411 " =    3.528
peak=    3.401 closest distance to " CB  ALA A 248 " =    1.328
peak=    3.394 closest distance to " CB  TYR A  30 " =    1.801
peak=    3.390 closest distance to " O   HOH Z  26 " =    1.498
peak=    3.388 closest distance to " OE1 GLN A  58 " =    3.820
peak=    3.388 closest distance to " O   HOH Z 153 " =    3.602
peak=    3.385 closest distance to " O   HOH Z 145 " =    1.998
peak=    3.384 closest distance to " CA  LEU A 101 " =    1.507
peak=    3.383 closest distance to " O   HOH Z 207 " =    2.494
peak=    3.375 closest distance to " O   HOH Z 133 " =    2.575
peak=    3.371 closest distance to " CE  MET A  40 " =    1.039
peak=    3.363 closest distance to " N   ALA A   1 " =    2.720
peak=    3.363 closest distance to " N   TYR A  15 " =    0.952
peak=    3.361 closest distance to " O   HOH Z 424 " =    2.064
peak=    3.360 closest distance to " NH2AARG A 190 " =    1.766
peak=    3.358 closest distance to " O   HOH Z 209 " =    2.371
peak=    3.354 closest distance to " O   HOH Z 368 " =    1.923
peak=    3.353 closest distance to " CG  PRO A 243 " =    1.169
peak=    3.350 closest distance to " O   HOH Z 125 " =    1.765
peak=    3.350 closest distance to " O   HOH Z 323 " =    1.608
peak=    3.349 closest distance to " CA  ALA A  51 " =    1.112
peak=    3.348 closest distance to " NH1AARG A 145 " =    1.141
peak=    3.346 closest distance to " O   HOH Z  22 " =    2.013
peak=    3.337 closest distance to " O   HOH Z 263 " =    1.574
peak=    3.337 closest distance to " OG1 THR A 221 " =    1.342
peak=    3.336 closest distance to " NE AARG A 275 " =    1.317
peak=    3.336 closest distance to " CB  VAL A 250 " =    1.005
peak=    3.333 closest distance to " CB  ARG A 190 " =    1.760
peak=    3.330 closest distance to " O   HOH Z 390 " =    1.161
peak=    3.327 closest distance to " O   HOH Z 403 " =    1.326
peak=    3.326 closest distance to " N   ARG A 156 " =    1.290
peak=    3.326 closest distance to " O   HOH Z 261 " =    2.470
peak=    3.326 closest distance to " O   HOH Z 108 " =    2.485
peak=    3.325 closest distance to " CB  ILE A 234 " =    1.202
peak=    3.319 closest distance to " O   HOH Z 357 " =    2.121
peak=    3.317 closest distance to " O   CYS A 168 " =    1.438
peak=    3.312 closest distance to " CB  THR A  31 " =    1.655
peak=    3.311 closest distance to " O   HOH Z 128 " =    1.963
peak=    3.311 closest distance to " CG1 ILE A  33 " =    1.360
peak=    3.308 closest distance to " O   HOH Z 385 " =    3.489
peak=    3.308 closest distance to " O   HOH Z 127 " =    0.999
peak=    3.305 closest distance to " O   HOH Z 211 " =    1.032
peak=    3.301 closest distance to " CB  GLN A  89 " =    1.155
peak=    3.300 closest distance to " OH  TYR A 116 " =    1.111
peak=    3.299 closest distance to " O   HOH Z 356 " =    1.261
peak=    3.299 closest distance to " N   TRP A 177 " =    1.667
peak=    3.294 closest distance to " CG2 VAL A 257 " =    0.879
peak=    3.288 closest distance to " CD  ARG A 269 " =    1.032
peak=    3.285 closest distance to " O   ASN A 301 " =    2.155
peak=    3.283 closest distance to " O   HOH Z 222 " =    2.096
peak=    3.283 closest distance to " O   HOH Z 345 " =    3.260
peak=    3.282 closest distance to " CB  ALA A 114 " =    1.112
peak=    3.282 closest distance to " CA  ALA A 158 " =    1.199
peak=    3.282 closest distance to " CA  ALA A 299 " =    1.051
peak=    3.280 closest distance to " O   HOH Z 244 " =    1.692
peak=    3.278 closest distance to " NH1 ARG A  14 " =    1.102
peak=    3.278 closest distance to " O   HOH Z 132 " =    1.062
peak=    3.277 closest distance to " O   HOH Z  44 " =    2.606
peak=    3.277 closest distance to " CB  ARG A 138 " =    0.957
peak=    3.276 closest distance to " O   HOH Z  58 " =    1.804
peak=    3.276 closest distance to " OG1 THR A 157 " =    1.082
peak=    3.272 closest distance to " OE2 GLU A   2 " =    2.025
peak=    3.269 closest distance to " O   HOH Z  50 " =    1.468
peak=    3.262 closest distance to " CG  ARG A 156 " =    1.080
peak=    3.255 closest distance to " O   HOH Z 193 " =    2.002
peak=    3.255 closest distance to " NH2AARG A 145 " =    0.958
peak=    3.253 closest distance to " O   HOH Z 389 " =    2.841
peak=    3.252 closest distance to " CB  LEU A 300 " =    0.884
peak=    3.252 closest distance to " CB  ASN A 187 " =    1.112
peak=    3.236 closest distance to " CG  GLN A  88 " =    1.168
peak=    3.235 closest distance to " ND2 ASN A 187 " =    1.752
peak=    3.235 closest distance to " O   HOH Z 353 " =    2.287
peak=    3.233 closest distance to " O   HOH Z  55 " =    1.565
peak=    3.232 closest distance to " O   HOH Z 175 " =    2.003
peak=    3.230 closest distance to " O   HOH Z 222 " =    1.810
peak=    3.228 closest distance to " O   HOH Z 410 " =    2.051
peak=    3.226 closest distance to " O   HOH Z 388 " =    2.090
peak=    3.225 closest distance to " CE AMET A  47 " =    1.300
peak=    3.223 closest distance to " CB  SER A  62 " =    1.083
peak=    3.223 closest distance to " O   HOH Z 392 " =    1.865
peak=    3.222 closest distance to " CZ  PHE A  38 " =    1.206
peak=    3.220 closest distance to " N   ALA A 256 " =    0.997
peak=    3.219 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.217 closest distance to " ND2 ASN A 110 " =    1.678
peak=    3.211 closest distance to " CB  ALA A 114 " =    1.508
peak=    3.209 closest distance to " CD BLYS A 290 " =    1.043
peak=    3.204 closest distance to " O   GLY A 302 " =    2.118
peak=    3.200 closest distance to " O   HOH Z  40 " =    2.028
peak=    3.197 closest distance to " CB  PHE A 204 " =    0.920
peak=    3.194 closest distance to " O   HOH Z  44 " =    1.847
peak=    3.192 closest distance to " CG  LYS A 119 " =    1.053
peak=    3.191 closest distance to " O   HOH Z 166 " =    1.544
peak=    3.188 closest distance to " O   HOH Z  32 " =    2.190
peak=    3.185 closest distance to " O   HOH Z 302 " =    1.466
peak=    3.181 closest distance to " O   HOH Z 213 " =    1.584
peak=    3.179 closest distance to " CG2 ILE A  20 " =    1.634
peak=    3.179 closest distance to " CB  ALA A 291 " =    1.365
peak=    3.178 closest distance to " O   HOH Z 122 " =    2.006
peak=    3.174 closest distance to " OD1 ASP A 171 " =    1.098
peak=    3.174 closest distance to " CG1 VAL A 153 " =    0.816
peak=    3.174 closest distance to " O   HOH Z 362 " =    2.038
peak=    3.173 closest distance to " O   THR A 294 " =    1.191
peak=    3.172 closest distance to " CA  GLY A 136 " =    1.084
peak=    3.162 closest distance to " OG1 THR A 246 " =    1.350
peak=    3.161 closest distance to " O   HOH Z 128 " =    2.062
peak=    3.156 closest distance to " CB  ASN A 110 " =    1.094
peak=    3.155 closest distance to " O   HOH Z 109 " =    2.328
peak=    3.149 closest distance to " O   PRO A 213 " =    1.263
peak=    3.146 closest distance to " ND1 HIS A  81 " =    1.565
peak=    3.141 closest distance to " O   HOH Z 406 " =    1.543
peak=    3.133 closest distance to " CB  SER A 210 " =    0.851
peak=    3.130 closest distance to " CB  PRO A  90 " =    1.224
peak=    3.126 closest distance to " CB  ASP A 140 " =    1.025
peak=    3.112 closest distance to " O   HOH Z 272 " =    2.217
peak=    3.111 closest distance to " CZ3 TRP A  92 " =    1.049
peak=    3.109 closest distance to " O   HOH Z 220 " =    1.245
peak=    3.107 closest distance to " CD  LYS A 166 " =    1.407
peak=    3.103 closest distance to " CA  MET A 105 " =    0.862
peak=    3.102 closest distance to " O   HOH Z 334 " =    1.266
peak=    3.092 closest distance to " ND2BASN A 224 " =    0.773
peak=    3.084 closest distance to " O   HOH Z 158 " =    2.977
peak=    3.084 closest distance to " CB  HIS A 108 " =    0.830
peak=    3.083 closest distance to " CG2 VAL A 197 " =    1.119
peak=    3.081 closest distance to " O   HOH Z 438 " =    2.156
peak=    3.078 closest distance to " CZ3 TRP A 274 " =    1.342
peak=    3.078 closest distance to " O   HOH Z 350 " =    1.456
peak=    3.073 closest distance to " CG1BVAL A  72 " =    1.041
peak=    3.071 closest distance to " NZ  LYS A  76 " =    1.515
peak=    3.067 closest distance to " O   HOH Z 214 " =    3.164
peak=    3.058 closest distance to " CB  LEU A 143 " =    0.824
peak=    3.058 closest distance to " O   HOH Z 118 " =    1.533
peak=    3.051 closest distance to " O   HOH Z 234 " =    2.075
peak=    3.034 closest distance to " CG  ARG A 159 " =    0.950

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.724 - 5.931
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.724 - 5.931

peak=   -5.175 closest distance to " CD  ARG A 138 " =    1.179
peak=   -4.548 closest distance to " OG BSER A 134 " =    1.380
peak=   -4.366 closest distance to " CG2 VAL A 230 " =    0.878
peak=   -4.204 closest distance to " O   HOH Z 266 " =    4.793
peak=   -4.169 closest distance to " O   PRO A 198 " =    1.142
peak=   -4.110 closest distance to " O   HOH Z 185 " =    2.025
peak=   -4.090 closest distance to " CA  GLY A  98 " =    1.883
peak=   -4.074 closest distance to " O   HOH Z 359 " =    1.705
peak=   -4.063 closest distance to " CD  ARG A 156 " =    1.861
peak=   -4.058 closest distance to " CE2 PHE A 218 " =    2.489
peak=   -4.016 closest distance to " O   HOH Z 103 " =    1.406
peak=   -4.011 closest distance to " O   HOH Z 131 " =    3.998
peak=   -3.985 closest distance to " CB  TYR A  15 " =    2.114
peak=   -3.962 closest distance to " O   HOH Z 415 " =    1.068
peak=   -3.934 closest distance to " CB  ALA A 248 " =    2.005
peak=   -3.890 closest distance to " O   HOH Z 350 " =    1.760
peak=   -3.889 closest distance to " CG2 VAL A 296 " =    2.268
peak=   -3.888 closest distance to " CE2 TYR A 116 " =    3.040
peak=   -3.886 closest distance to " CD  ARG A  14 " =    3.102
peak=   -3.876 closest distance to " CB  ALA A  43 " =    2.362
peak=   -3.868 closest distance to " OG  SER A  87 " =    1.377
peak=   -3.865 closest distance to " NH2 ARG A  79 " =    2.049
peak=   -3.845 closest distance to " O   HOH Z 412 " =    5.756
peak=   -3.835 closest distance to " CD1 LEU A 255 " =    2.861
peak=   -3.817 closest distance to " CG  ARG A 138 " =    0.941
peak=   -3.801 closest distance to " CB  ASN A  39 " =    2.237
peak=   -3.797 closest distance to " O   HOH Z  24 " =    1.134
peak=   -3.784 closest distance to " O   HOH Z 385 " =    1.131
peak=   -3.782 closest distance to " ND2 ASN A 187 " =    1.499
peak=   -3.774 closest distance to " CA  ASP A  27 " =    2.358
peak=   -3.774 closest distance to " OG ASER A 134 " =    1.077
peak=   -3.767 closest distance to " OG  SER A  26 " =    1.072
peak=   -3.759 closest distance to " N   THR A 157 " =    1.505
peak=   -3.759 closest distance to " O   HOH Z 427 " =    1.788
peak=   -3.755 closest distance to " O   HOH Z 359 " =    3.445
peak=   -3.746 closest distance to " N   ALA A   1 " =    1.122
peak=   -3.744 closest distance to " CD1 LEU A 101 " =    2.209
peak=   -3.741 closest distance to " CA  GLY A 133 " =    2.032
peak=   -3.735 closest distance to " N   VAL A  72 " =    1.905
peak=   -3.728 closest distance to " O   HOH Z  43 " =    1.845
peak=   -3.708 closest distance to " CG  GLN A 223 " =    2.337
peak=   -3.705 closest distance to " O   HOH Z 407 " =    2.980
peak=   -3.694 closest distance to " CZ2 TRP A 274 " =    0.915
peak=   -3.693 closest distance to " C   HIS A 108 " =    1.228
peak=   -3.692 closest distance to " O   HOH Z 286 " =    1.755
peak=   -3.672 closest distance to " CD2 LEU A   5 " =    1.043
peak=   -3.667 closest distance to " O   HOH Z 231 " =    1.969
peak=   -3.653 closest distance to " CB  GLN A  55 " =    1.157
peak=   -3.648 closest distance to " O   HOH Z  69 " =    2.120
peak=   -3.646 closest distance to " O   GLY A  80 " =    2.479
peak=   -3.645 closest distance to " O   SER A  22 " =    2.437
peak=   -3.642 closest distance to " O   HOH Z  11 " =    1.886
peak=   -3.640 closest distance to " OG  SER A 245 " =    1.342
peak=   -3.600 closest distance to " O   ILE A  49 " =    1.702
peak=   -3.594 closest distance to " OE1 GLU A 277 " =    2.246
peak=   -3.587 closest distance to " O   PRO A 243 " =    2.439
peak=   -3.580 closest distance to " N   PRO A 163 " =    1.563
peak=   -3.572 closest distance to " N   GLN A  58 " =    1.290
peak=   -3.571 closest distance to " O   HOH Z 298 " =    0.999
peak=   -3.570 closest distance to " CB  VAL A 230 " =    0.992
peak=   -3.567 closest distance to " O   ALA A  84 " =    1.642
peak=   -3.561 closest distance to " O   HOH Z  52 " =    0.985
peak=   -3.560 closest distance to " CB  PHE A 130 " =    1.135
peak=   -3.537 closest distance to " CG  MET A 105 " =    0.917
peak=   -3.532 closest distance to " O   HOH Z 351 " =    1.587
peak=   -3.530 closest distance to " O   SER A 135 " =    1.577
peak=   -3.529 closest distance to " CD2 TYR A 293 " =    1.840
peak=   -3.522 closest distance to " O   HOH Z  47 " =    1.583
peak=   -3.521 closest distance to " OG  SER A 206 " =    1.752
peak=   -3.504 closest distance to " O   HOH Z 352 " =    2.142
peak=   -3.501 closest distance to " OE2 GLU A 152 " =    1.099
peak=   -3.488 closest distance to " O   PRO A 163 " =    1.800
peak=   -3.486 closest distance to " O   ALA A   1 " =    1.281
peak=   -3.483 closest distance to " CB  PRO A 243 " =    2.574
peak=   -3.476 closest distance to " O   HOH Z 107 " =    2.183
peak=   -3.467 closest distance to " O   HOH Z 298 " =    2.807
peak=   -3.466 closest distance to " O   HOH Z 423 " =    2.635
peak=   -3.464 closest distance to " O   HOH Z 339 " =    1.841
peak=   -3.456 closest distance to " CE2 TRP A  70 " =    2.356
peak=   -3.450 closest distance to " N   ALA A 248 " =    1.529
peak=   -3.445 closest distance to " O   HOH Z 414 " =    2.171
peak=   -3.437 closest distance to " CA  ASN A 127 " =    1.106
peak=   -3.434 closest distance to " CD  LYS A 289 " =    2.391
peak=   -3.431 closest distance to " O   HOH Z 414 " =    2.102
peak=   -3.419 closest distance to " O   HOH Z  65 " =    1.171
peak=   -3.415 closest distance to " N   SER A 276 " =    1.162
peak=   -3.412 closest distance to " O   HOH Z 377 " =    1.256
peak=   -3.410 closest distance to " CD  LYS A 166 " =    2.511
peak=   -3.407 closest distance to " O   HOH Z 292 " =    1.570
peak=   -3.404 closest distance to " CE2 TYR A  30 " =    2.658
peak=   -3.402 closest distance to " OG  SER A  97 " =    2.168
peak=   -3.400 closest distance to " CG1 VAL A 197 " =    2.407
peak=   -3.399 closest distance to " CG  GLN A  58 " =    1.051
peak=   -3.397 closest distance to " OD2 ASP A  27 " =    1.511
peak=   -3.392 closest distance to " O   HOH Z 435 " =    2.248
peak=   -3.391 closest distance to " O   HOH Z  67 " =    3.106
peak=   -3.390 closest distance to " O   HOH Z 368 " =    2.511
peak=   -3.389 closest distance to " O   HOH Z  60 " =    1.825
peak=   -3.389 closest distance to " O   HOH Z 211 " =    1.268
peak=   -3.381 closest distance to " O   ASN A 301 " =    1.426
peak=   -3.379 closest distance to " ND2 ASN A 252 " =    1.995
peak=   -3.379 closest distance to " CG  PRO A 163 " =    2.568
peak=   -3.378 closest distance to " NE2 GLN A  94 " =    1.637
peak=   -3.377 closest distance to " ND2 ASN A 285 " =    2.060
peak=   -3.373 closest distance to " N   ALA A  43 " =    2.503
peak=   -3.366 closest distance to " CA  TYR A  30 " =    2.848
peak=   -3.351 closest distance to " O   SER A 271 " =    2.066
peak=   -3.345 closest distance to " OG  SER A  63 " =    1.355
peak=   -3.330 closest distance to " CA  GLY A  35 " =    1.965
peak=   -3.326 closest distance to " O   VAL A 197 " =    1.545
peak=   -3.309 closest distance to " O   HOH Z 137 " =    1.362
peak=   -3.308 closest distance to " CA  GLY A 203 " =    2.347
peak=   -3.307 closest distance to " NH2 ARG A 219 " =    1.794
peak=   -3.307 closest distance to " O   MET A  40 " =    2.770
peak=   -3.307 closest distance to " O   GLN A  11 " =    1.536
peak=   -3.303 closest distance to " O   HOH Z 126 " =    1.976
peak=   -3.291 closest distance to " CG2 ILE A  20 " =    2.843
peak=   -3.289 closest distance to " CB  PHE A 192 " =    1.739
peak=   -3.287 closest distance to " O   HOH Z   9 " =    1.717
peak=   -3.287 closest distance to " CG  PHE A 283 " =    2.472
peak=   -3.286 closest distance to " O   HOH Z 389 " =    1.417
peak=   -3.285 closest distance to " CZ  TYR A 169 " =    1.889
peak=   -3.281 closest distance to " O   ALA A 292 " =    1.989
peak=   -3.278 closest distance to " O   HOH Z  52 " =    1.394
peak=   -3.273 closest distance to " O   HOH Z 313 " =    1.387
peak=   -3.269 closest distance to " OD2 ASP A 191 " =    1.424
peak=   -3.266 closest distance to " C   ILE A 239 " =    2.091
peak=   -3.266 closest distance to " O   VAL A  67 " =    2.710
peak=   -3.264 closest distance to " CZ  PHE A  59 " =    1.506
peak=   -3.261 closest distance to " OD2 ASP A  50 " =    1.547
peak=   -3.260 closest distance to " O   HOH Z 125 " =    3.404
peak=   -3.258 closest distance to " O   HOH Z 198 " =    2.215
peak=   -3.253 closest distance to " O   HOH Z 134 " =    3.769
peak=   -3.253 closest distance to " O   HOH Z 347 " =    1.049
peak=   -3.250 closest distance to " CD1 TRP A 179 " =    1.105
peak=   -3.247 closest distance to " OE1 GLN A  88 " =    1.157
peak=   -3.246 closest distance to " O   HOH Z 189 " =    1.578
peak=   -3.246 closest distance to " CD1 ILE A 199 " =    2.474
peak=   -3.244 closest distance to " O   HOH Z 166 " =    1.521
peak=   -3.243 closest distance to " O   ASP A 270 " =    1.574
peak=   -3.240 closest distance to " C   ALA A 158 " =    1.384
peak=   -3.238 closest distance to " O   HOH Z  90 " =    2.789
peak=   -3.234 closest distance to " O   HOH Z  39 " =    1.181
peak=   -3.233 closest distance to " O   HOH Z 207 " =    1.973
peak=   -3.232 closest distance to " CD2 HIS A 207 " =    2.431
peak=   -3.223 closest distance to " O   ALA A 180 " =    1.213
peak=   -3.219 closest distance to " O   HOH Z 336 " =    5.931
peak=   -3.219 closest distance to " O   HOH Z 238 " =    1.077
peak=   -3.214 closest distance to " CE  MET A 105 " =    2.406
peak=   -3.211 closest distance to " O   HOH Z 111 " =    4.367
peak=   -3.207 closest distance to " O   HOH Z  63 " =    2.341
peak=   -3.203 closest distance to " CB  ALA A 114 " =    2.376
peak=   -3.199 closest distance to " OG  SER A  62 " =    4.236
peak=   -3.197 closest distance to " N   ASP A 171 " =    2.669
peak=   -3.196 closest distance to " C   ARG A 269 " =    1.330
peak=   -3.192 closest distance to " N   LEU A 282 " =    2.087
peak=   -3.186 closest distance to " O   HOH Z 389 " =    2.085
peak=   -3.184 closest distance to " CD2 LEU A 237 " =    2.500
peak=   -3.183 closest distance to " CB  TYR A  68 " =    1.080
peak=   -3.182 closest distance to " NH1 ARG A  56 " =    2.387
peak=   -3.181 closest distance to " O   HOH Z 388 " =    2.183
peak=   -3.179 closest distance to " N   VAL A 125 " =    1.064
peak=   -3.171 closest distance to " O   HOH Z 426 " =    1.617
peak=   -3.171 closest distance to " O   GLN A 194 " =    1.453
peak=   -3.170 closest distance to " O   HOH Z 345 " =    1.871
peak=   -3.170 closest distance to " CG  TRP A 266 " =    1.811
peak=   -3.170 closest distance to " CB  ASP A 171 " =    2.100
peak=   -3.169 closest distance to " O   ASP A 191 " =    1.888
peak=   -3.168 closest distance to " CB  CYS A 201 " =    1.989
peak=   -3.167 closest distance to " C   MET A 188 " =    1.543
peak=   -3.167 closest distance to " N   ALA A 226 " =    2.065
peak=   -3.165 closest distance to " CD1 TRP A 274 " =    1.249
peak=   -3.162 closest distance to " CD  GLN A  77 " =    1.251
peak=   -3.159 closest distance to " O   HOH Z 166 " =    1.612
peak=   -3.156 closest distance to " CE BMET A  47 " =    0.891
peak=   -3.156 closest distance to " O   HOH Z 404 " =    1.486
peak=   -3.144 closest distance to " CG2 THR A 178 " =    2.065
peak=   -3.143 closest distance to " O   HOH Z  52 " =    0.881
peak=   -3.140 closest distance to " O   HOH Z 364 " =    1.881
peak=   -3.136 closest distance to " O   HOH Z 149 " =    1.203
peak=   -3.134 closest distance to " O   HOH Z 393 " =    2.897
peak=   -3.133 closest distance to " N   HIS A 115 " =    2.132
peak=   -3.133 closest distance to " N   VAL A 232 " =    2.114
peak=   -3.133 closest distance to " O   HOH Z 426 " =    2.152
peak=   -3.130 closest distance to " O   HOH Z  68 " =    1.192
peak=   -3.128 closest distance to " CA  GLY A 241 " =    2.143
peak=   -3.124 closest distance to " O   GLN A 240 " =    1.922
peak=   -3.122 closest distance to " O   HOH Z 421 " =    3.134
peak=   -3.110 closest distance to " N   THR A 235 " =    1.213
peak=   -3.106 closest distance to " O   HOH Z 250 " =    1.251
peak=   -3.105 closest distance to " O   HOH Z 111 " =    1.128
peak=   -3.099 closest distance to " CE  LYS A 166 " =    1.120
peak=   -3.095 closest distance to " O   HOH Z 151 " =    1.434
peak=   -3.094 closest distance to " C   PHE A 155 " =    0.724
peak=   -3.090 closest distance to " O   HOH Z 234 " =    3.789
peak=   -3.083 closest distance to " OG  SER A   3 " =    1.581
peak=   -3.080 closest distance to " C   ASN A 285 " =    2.034
peak=   -3.067 closest distance to " CB  ASN A 301 " =    1.924
peak=   -3.065 closest distance to " N   GLN A  58 " =    1.944
peak=   -3.030 closest distance to " CB  ASP A 132 " =    2.356
peak=   -3.027 closest distance to " CG1 ILE A 263 " =    1.993
peak=   -3.015 closest distance to " O   HOH Z 193 " =    1.936

================= 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 individual 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    :  0.4724 0.4662   6.279103e+00   6.264273e+00
   1_bss:  0.4641 0.4537   6.272274e+00   6.252256e+00
   1_xyz:  0.3861 0.4083   6.166516e+00   6.197471e+00
   1_adp:  0.3383 0.3940   6.092539e+00   6.181688e+00
   1_occ:  0.3379 0.3938   6.092011e+00   6.182168e+00
   2_bss:  0.3346 0.3889   6.091858e+00   6.179396e+00
   2_xyz:  0.2759 0.3335   5.925368e+00   6.056265e+00
   2_adp:  0.2599 0.3258   5.885863e+00   6.031768e+00
   2_occ:  0.2597 0.3261   5.885765e+00   6.032027e+00
   3_bss:  0.2586 0.3236   5.885347e+00   6.029317e+00
   3_xyz:  0.2093 0.2699   5.696357e+00   5.877175e+00
   3_adp:  0.1877 0.2497   5.604833e+00   5.817677e+00
   3_occ:  0.1876 0.2495   5.604325e+00   5.817278e+00
   4_bss:  0.1873 0.2490   5.603804e+00   5.815587e+00
   4_xyz:  0.1545 0.2118   5.433783e+00   5.660765e+00
   4_adp:  0.1441 0.1989   5.370151e+00   5.598763e+00
   4_occ:  0.1437 0.1985   5.368508e+00   5.597291e+00
   5_bss:  0.1441 0.1985   5.367325e+00   5.596453e+00
   5_xyz:  0.1275 0.1798   5.262515e+00   5.502416e+00
   5_adp:  0.1232 0.1753   5.234706e+00   5.476323e+00
   5_occ:  0.1232 0.1752   5.234404e+00   5.475747e+00
   5_bss:  0.1231 0.1751   5.234142e+00   5.475556e+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:  0.365   5.500   6.821  10.469   7.711   0.000   0.000   0.000
   1_xyz:  0.365   5.500   6.821  10.469   7.711   0.000   0.000   0.000
   1_adp:  0.365   5.500   6.821  10.469   7.711   0.000   0.000   0.000
   1_occ:  0.365   5.500   6.821  10.469   7.711   0.000   0.000   0.000
   2_bss:  0.333  20.000   3.652   6.157   4.709   0.000   0.000   0.000
   2_xyz:  0.333  20.000   3.652   6.157   4.709   0.000   0.000   0.000
   2_adp:  0.333  20.000   3.652   6.157   4.709   0.000   0.000   0.000
   2_occ:  0.333  20.000   3.652   6.157   4.709   0.000   0.000   0.000
   3_bss:  0.339  39.900   2.496   3.635   3.628   0.000   0.000   0.000
   3_xyz:  0.339  39.900   2.496   3.635   3.628   0.000   0.000   0.000
   3_adp:  0.339  39.900   2.496   3.635   3.628   0.000   0.000   0.000
   3_occ:  0.339  39.900   2.496   3.635   3.628   0.000   0.000   0.000
   4_bss:  0.327  42.815   1.809   2.312   3.173   0.000   0.000   0.000
   4_xyz:  0.327  42.815   1.809   2.312   3.173   0.000   0.000   0.000
   4_adp:  0.327  42.815   1.809   2.312   3.173   0.000   0.000   0.000
   4_occ:  0.327  42.815   1.809   2.312   3.173   0.000   0.000   0.000
   5_bss:  0.320  42.815   1.683   1.751   3.088   0.000   0.000   0.000
   5_xyz:  0.320  42.815   1.683   1.751   3.088   0.000   0.000   0.000
   5_adp:  0.320  42.815   1.683   1.751   3.088   0.000   0.000   0.000
   5_occ:  0.320  42.815   1.683   1.751   3.088   0.000   0.000   0.000
   5_bss:  0.317  46.037  -0.460  -0.486   0.945   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.245 0.4291  0.5033    68568.924
   1_bss:  56.507 0.4371  0.6492    65306.700
   1_xyz:  48.135 0.5422  0.7932    50719.077
   1_adp:  45.171 0.5795  0.8930    47135.518
   1_occ:  45.284 0.5781  0.8896    47207.216
   2_bss:  44.798 0.5839  0.7968    46478.195
   2_xyz:  35.726 0.6925  0.9285    31489.048
   2_adp:  34.047 0.7122  0.9602    29315.976
   2_occ:  34.066 0.7120  0.9599    29362.814
   3_bss:  33.778 0.7153  0.9112    29054.135
   3_xyz:  27.096 0.7887  0.9785    19117.153
   3_adp:  24.515 0.8164  0.9894    16067.664
   3_occ:  24.490 0.8167  0.9892    16030.954
   4_bss:  24.441 0.8172  0.9606    15981.935
   4_xyz:  20.616 0.8549  0.9827    11371.947
   4_adp:  18.812 0.8729  0.9843    10009.627
   4_occ:  18.780 0.8731  0.9838     9968.359
   5_bss:  18.741 0.8734  0.9746     9923.674
   5_xyz:  16.593 0.8929  0.9857     8130.885
   5_adp:  15.918 0.8992  0.9795     7744.676
   5_occ:  15.911 0.8993  0.9793     7729.458
   5_bss:  15.904 0.8993  0.9813     7724.570
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3203e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3203e+01
   1_xyz:   1.654  0.013  0.104 18.200  0.006  4.106   1.3622e-01
   1_adp:   1.654  0.013  0.104 18.200  0.006  4.106   1.3622e-01
   1_occ:   1.654  0.013  0.104 18.200  0.006  4.106   1.3622e-01
   2_bss:   1.654  0.013  0.104 18.200  0.006  4.106   1.3622e-01
   2_xyz:   1.105  0.008  0.078 15.786  0.005  4.120   7.6489e-02
   2_adp:   1.105  0.008  0.078 15.786  0.005  4.120   7.6489e-02
   2_occ:   1.105  0.008  0.078 15.786  0.005  4.120   7.6489e-02
   3_bss:   1.105  0.008  0.078 15.786  0.005  4.120   7.6489e-02
   3_xyz:   1.063  0.007  0.075 15.714  0.004  4.106   6.7442e-02
   3_adp:   1.063  0.007  0.075 15.714  0.004  4.106   6.7442e-02
   3_occ:   1.063  0.007  0.075 15.714  0.004  4.106   6.7442e-02
   4_bss:   1.063  0.007  0.075 15.714  0.004  4.106   6.7442e-02
   4_xyz:   0.883  0.006  0.065 15.308  0.003  4.109   5.3082e-02
   4_adp:   0.883  0.006  0.065 15.308  0.003  4.109   5.3082e-02
   4_occ:   0.883  0.006  0.065 15.308  0.003  4.109   5.3082e-02
   5_bss:   0.883  0.006  0.065 15.308  0.003  4.109   5.3082e-02
   5_xyz:   0.908  0.005  0.068 15.310  0.003  4.113   5.3537e-02
   5_adp:   0.908  0.005  0.068 15.310  0.003  4.113   5.3537e-02
   5_occ:   0.908  0.005  0.068 15.310  0.003  4.113   5.3537e-02
   5_bss:   0.908  0.005  0.068 15.310  0.003  4.113   5.3537e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8951e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8951e+00
   1_xyz:  13.039  0.180  0.404 88.144  0.035  2.135   9.5241e-02
   1_adp:  13.039  0.180  0.404 88.144  0.035  2.135   9.5241e-02
   1_occ:  13.039  0.180  0.404 88.144  0.035  2.135   9.5241e-02
   2_bss:  13.039  0.180  0.404 88.144  0.035  2.135   9.5241e-02
   2_xyz:   7.174  0.087  0.305 84.794  0.039  2.181   5.6433e-02
   2_adp:   7.174  0.087  0.305 84.794  0.039  2.181   5.6433e-02
   2_occ:   7.174  0.087  0.305 84.794  0.039  2.181   5.6433e-02
   3_bss:   7.174  0.087  0.305 84.794  0.039  2.181   5.6433e-02
   3_xyz:   7.435  0.046  0.354 85.512  0.025  2.305   6.4047e-02
   3_adp:   7.435  0.046  0.354 85.512  0.025  2.305   6.4047e-02
   3_occ:   7.435  0.046  0.354 85.512  0.025  2.305   6.4047e-02
   4_bss:   7.435  0.046  0.354 85.512  0.025  2.305   6.4047e-02
   4_xyz:   6.467  0.086  0.209 83.052  0.031  2.353   5.5967e-02
   4_adp:   6.467  0.086  0.209 83.052  0.031  2.353   5.5967e-02
   4_occ:   6.467  0.086  0.209 83.052  0.031  2.353   5.5967e-02
   5_bss:   6.467  0.086  0.209 83.052  0.031  2.353   5.5967e-02
   5_xyz:   6.624  0.049  0.247 82.284  0.031  2.357   4.1727e-02
   5_adp:   6.624  0.049  0.247 82.284  0.031  2.357   4.1727e-02
   5_occ:   6.624  0.049  0.247 82.284  0.031  2.357   4.1727e-02
   5_bss:   6.624  0.049  0.247 82.284  0.031  2.357   4.1727e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  78.87   0.00  13.41  78.17   0.00  11.38  78.87   0.00  24.50
   1_occ:  78.87   0.00  13.41  78.17   0.00  11.38  78.87   0.00  24.50
   2_bss:  78.87   0.00  13.41  78.17   0.00  11.38  78.87   0.00  24.50
   2_xyz:  78.87   0.00  13.41  78.17   0.00  11.38  78.87   0.00  24.50
   2_adp:  83.79   0.00  13.53  83.79   0.00  10.92  81.54   0.00  27.71
   2_occ:  83.79   0.00  13.53  83.79   0.00  10.92  81.54   0.00  27.71
   3_bss:  83.79   0.00  13.53  83.79   0.00  10.92  81.54   0.00  27.71
   3_xyz:  83.79   0.00  13.53  83.79   0.00  10.92  81.54   0.00  27.71
   3_adp:  99.81   0.00  14.62  99.81   0.00  10.26  95.89   1.17  38.35
   3_occ:  99.81   0.00  14.62  99.81   0.00  10.26  95.89   1.17  38.35
   4_bss:  99.81   0.00  14.62  99.81   0.00  10.26  95.89   1.17  38.35
   4_xyz:  99.81   0.00  14.62  99.81   0.00  10.26  95.89   1.17  38.35
   4_adp: 101.95   0.00  14.06 101.95   0.00   9.44  95.96   2.22  39.24
   4_occ: 101.95   0.00  14.06 101.95   0.00   9.44  95.96   2.22  39.24
   5_bss: 101.95   0.00  14.06 101.95   0.00   9.44  95.96   2.22  39.24
   5_xyz: 101.95   0.00  14.06 101.95   0.00   9.44  95.96   2.22  39.24
   5_adp: 111.65   0.00  13.99 111.65   0.00   9.10 102.79   1.78  40.59
   5_occ: 111.65   0.00  13.99 111.65   0.00   9.10 102.79   1.78  40.59
   5_bss: 113.88   2.23  16.21 113.88   2.23  11.33 105.02   4.00  42.82
------------------------------------------------------------------------
 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:    1.248    0.018    0.408
   1_adp:    1.248    0.018    0.408
   1_occ:    1.248    0.018    0.408
   2_bss:    1.248    0.018    0.408
   2_xyz:    1.509    0.037    0.546
   2_adp:    1.509    0.037    0.546
   2_occ:    1.509    0.037    0.546
   3_bss:    1.509    0.037    0.546
   3_xyz:    1.539    0.045    0.630
   3_adp:    1.539    0.045    0.630
   3_occ:    1.539    0.045    0.630
   4_bss:    1.539    0.045    0.630
   4_xyz:    1.797    0.043    0.705
   4_adp:    1.797    0.043    0.705
   4_occ:    1.797    0.043    0.705
   5_bss:    1.797    0.043    0.705
   5_xyz:    1.851    0.037    0.736
   5_adp:    1.851    0.037    0.736
   5_occ:    1.851    0.037    0.736
   5_bss:    1.851    0.037    0.736
------------------------------------------------------------------------

CPU time actual refinement: 340.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_500/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_500/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_500/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_500/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_500/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.95 
  Macro-tasks:
    bulk solvent and scale       = 46.66  
    individual site refinement   = 140.28 
    weights calculation          = 31.60  
    collect and process          = 6.47   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 225.14 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 103.24 
    alpha_beta                      = 8.27   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 114.03 
    fmodel                         = 8.25   
    r_factors                      = 0.25   
    phase_errors                   = 10.46  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 248.26 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.794 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    635 calls, 102.94 s
gradients_fft:          580 calls, 100.95 s

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

# Date 2008-01-16 Time 01:44:48 PST -0800 (1200476688.43 s)
Start R-work = 0.4724, R-free = 0.4662 (no bulk solvent and anisotropic scale)
Final R-work = 0.1391, R-free = 0.1884 (no bulk solvent and anisotropic scale)

Start R-work = 0.4641, R-free = 0.4537
Final R-work = 0.1231, R-free = 0.1751