# Date 2008-01-16 Time 02:13:24 PST -0800 (1200478404.26 s)
#phil __OFF__

Command line arguments: "../737.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 = 18233
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 737

-------------------------------------------------------------------------------
  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: (70.6012, 45.9914, 84.2302, 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: (70.6012, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95103
Completeness in resolution range: 0.953422
Completeness with d_max=infinity: 0.950553

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9510

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: (70.6012, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95103
Completeness in resolution range: 0.953422
Completeness with d_max=infinity: 0.950553

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1757 [2155/2181]  1943   212   9.8%
  bin  2:  4.1757 -  3.3264 [2081/2100]  1872   209  10.0%
  bin  3:  3.3264 -  2.9094 [2034/2053]  1828   206  10.1%
  bin  4:  2.9094 -  2.6450 [2026/2056]  1828   198   9.8%
  bin  5:  2.6450 -  2.4563 [2037/2056]  1830   207  10.2%
  bin  6:  2.4563 -  2.3121 [1990/2015]  1787   203  10.2%
  bin  7:  2.3121 -  2.1966 [1998/2026]  1801   197   9.9%
  bin  8:  2.1966 -  2.1013 [1984/2020]  1790   194   9.8%
  bin  9:  2.1013 -  2.0206 [1976/2018]  1777   199  10.1%
  bin 10:  2.0206 -  1.9510 [1308/2021]  1174   134  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_737/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: 0.14 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:
        1.51 -     2.19: 27
        2.19 -     2.87: 1261
        2.87 -     3.55: 4570
        3.55 -     4.22: 9399
        4.22 -     4.90: 13625
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.514 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.680 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.702 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.736 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.798 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28877 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_737/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_737/model_refine_001.geo

CPU time processing inputs: 9.27


============================ 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 = 70.60125 45.9914 84.23025 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: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5097   r_free= 0.5114   ksol= 0.00   Bsol= 0.00   scale= 0.781    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.305656                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6578 0.99   1400  158 0.4343 0.4586      6.6462      6.7192|
|  2:  4.6578 -  3.7157 0.99   1350  143 0.4583 0.4343      6.8741      6.8241|
|  3:  3.7157 -  3.2515 0.99   1314  147 0.4804 0.4642       6.726      6.8011|
|  4:  3.2515 -  2.9568 0.99   1329  157 0.5069 0.4662       6.581      6.5208|
|  5:  2.9568 -  2.7462 0.99   1299  139 0.5354 0.5485      6.3924      6.3732|
|  6:  2.7462 -  2.5852 0.99   1296  148 0.5333 0.5691      6.2975      6.3058|
|  7:  2.5852 -  2.4563 0.99   1313  140 0.5301 0.4713      6.2702      6.1784|
|  8:  2.4563 -  2.3498 0.98   1263  144 0.5495 0.5339      6.1776      6.1872|
|  9:  2.3498 -  2.2597 0.98   1291  149 0.5371 0.5608      6.1357      6.1641|
| 10:  2.2597 -  2.1819 0.99   1281  137 0.5526 0.5718      6.1091      6.1252|
| 11:  2.1819 -  2.1139 0.98   1283  138 0.5258 0.5358      6.0529      6.0568|
| 12:  2.1139 -  2.0536 0.97   1255  143 0.5305 0.5976      5.9771      6.0288|
| 13:  2.0536 -  1.9997 0.99   1274  142 0.5549 0.5287      5.8846      5.8225|
| 14:  1.9997 -  1.9510 0.52    682   74 0.5709 0.5574      5.8481         5.8|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6578  1400   158  0.58  44.18   0.78     0.65     107597.23|
|  2:  4.6578 -  3.7157  1350   143  0.61  42.55   0.84     0.71     147889.63|
|  3:  3.7157 -  3.2515  1314   147  0.50  51.88   0.82     0.66     151516.95|
|  4:  3.2515 -  2.9568  1329   157  0.41  58.77   0.79     0.53     129202.08|
|  5:  2.9568 -  2.7462  1299   139  0.30  67.28   0.73     0.38      98745.65|
|  6:  2.7462 -  2.5852  1296   148  0.29  68.13   0.71     0.35      84172.99|
|  7:  2.5852 -  2.4563  1313   140  0.27  69.73   0.75     0.31      71832.89|
|  8:  2.4563 -  2.3498  1263   144  0.26  70.72   0.71     0.33      66944.50|
|  9:  2.3498 -  2.2597  1291   149  0.22  73.21   0.73     0.26      61448.85|
| 10:  2.2597 -  2.1819  1281   137  0.20  75.26   0.74     0.25      58874.31|
| 11:  2.1819 -  2.1139  1283   138  0.16  78.38   0.78     0.20      55751.84|
| 12:  2.1139 -  2.0536  1255   143  0.17  77.43   0.78     0.22      50041.86|
| 13:  2.0536 -  1.9997  1274   142  0.17  77.42   0.72     0.23      42403.85|
| 14:  1.9997 -  1.9510   682    74  0.21  74.80   0.72     0.25      34004.59|
|alpha:            min =        0.20 max =            0.71 mean =         0.39|
|beta:             min =    34004.59 max =       151516.95 mean =     85287.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.82|
|phase err.(test): min =        0.00 max =           89.82 mean =        66.08|
|-----------------------------------------------------------------------------|

============================== 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 = 24.289201             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.876   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.548831              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.299   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      187 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      729 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1549 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2700 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3995 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5191 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6646 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7868 |
|-----------------------------------------------------------------------------|
|-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 |       52.901 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.196 |       2.335 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    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 = 11.426)------------------------------------------|
|    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: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5140   r_free= 0.5132   ksol= 0.00   Bsol= 0.00   scale= 0.751    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.306363                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5020   r_free= 0.4991   ksol= 0.36   Bsol= 0.00   scale= 0.963    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.39,8.80,8.61,0.00,0.00,0.00); trace/3= 7.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.300942                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.925222             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.753   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.175414              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.478   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5020      final r-factor (work) = 0.4517          |
| start r-factor (free) = 0.4991      final r-factor (free) = 0.4728          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 109.3790 = 17.93 * 0.50 * 6.3015 + 1.00 * 52.9015                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.2551 = 17.93 * 0.50 * 6.2606 + 1.00 * 0.1435                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4517      final r-factor (work) = 0.4162          |
| start r-factor (free) = 0.4728      final r-factor (free) = 0.4729          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.6339 = 2.18 * 1.00 * 6.2606 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.5549 = 2.18 * 1.00 * 6.2198 + 1.00 * 0.0243                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.10  17.47    None  None   None       |
|    all(noH): 2823   0      0.00    116.10  17.47    None  None   None       |
|    Sol.    : 438    0      0.00    116.10  23.71    None  None   None       |
|    Mac.    : 2385   0      0.00    92.84   16.33    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:     0.000 -  11.610: 1147   |   5:    58.051 -  69.661:   29        |
|      1:    11.610 -  23.221:  884   |   6:    69.661 -  81.272:    3        |
|      2:    23.221 -  34.831:  456   |   7:    81.272 -  92.882:    6        |
|      3:    34.831 -  46.441:  213   |   8:    92.882 - 104.492:    1        |
|      4:    46.441 -  58.051:   83   |   9:   104.492 - 116.102:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4162 r_free = 0.4729             target_work(ml) = 6.215         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4162 r_free = 0.4737             target_work(ml) = 6.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4162   r_free= 0.4737   ksol= 0.36   Bsol= 0.00   scale= 1.124    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.39,8.80,8.61,0.00,0.00,0.00); trace/3= 7.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.214832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4140   r_free= 0.4697   ksol= 0.36   Bsol= 33.67   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,4.34,5.11,0.00,0.00,0.00); trace/3= 4.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.215785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.063557             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.300  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.808259              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.865  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4140      final r-factor (work) = 0.3638          |
| start r-factor (free) = 0.4697      final r-factor (free) = 0.4349          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.8539 = 14.06 * 0.50 * 6.2161 + 1.00 * 0.1435                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.4526 = 14.06 * 0.50 * 6.1650 + 1.00 * 0.1014                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3638      final r-factor (work) = 0.3473          |
| start r-factor (free) = 0.4349      final r-factor (free) = 0.4211          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0073 = 0.81 * 1.00 * 6.1650 + 1.00 * 0.0243                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9517 = 0.81 * 1.00 * 6.1113 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.41  16.42    None  None   None       |
|    all(noH): 2823   0      0.00    112.41  16.42    None  None   None       |
|    Sol.    : 438    0      0.00    112.41  26.15    None  None   None       |
|    Mac.    : 2385   0      0.00    95.39   14.63    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 -  11.241: 1135   |   5:    56.205 -  67.446:   14        |
|      1:    11.241 -  22.482: 1006   |   6:    67.446 -  78.687:    5        |
|      2:    22.482 -  33.723:  427   |   7:    78.687 -  89.928:    2        |
|      3:    33.723 -  44.964:  176   |   8:    89.928 - 101.169:    3        |
|      4:    44.964 -  56.205:   54   |   9:   101.169 - 112.410:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3473 r_free = 0.4211             target_work(ml) = 6.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3471 r_free = 0.4211             target_work(ml) = 6.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3471   r_free= 0.4211   ksol= 0.36   Bsol= 33.67   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,4.34,5.11,0.00,0.00,0.00); trace/3= 4.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.095514                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3458   r_free= 0.4207   ksol= 0.33   Bsol= 37.29   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.63,2.17,2.85,0.00,0.00,0.00); trace/3= 2.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.096854                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.828773              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.720  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.390168              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.557  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3458      final r-factor (work) = 0.2875          |
| start r-factor (free) = 0.4207      final r-factor (free) = 0.3590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.9630 = 6.83 * 0.50 * 6.1099 + 1.00 * 0.1014                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6874 = 6.83 * 0.50 * 6.0359 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2875      final r-factor (work) = 0.2616          |
| start r-factor (free) = 0.3590      final r-factor (free) = 0.3452          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4031 = 1.39 * 1.00 * 6.0359 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2353 = 1.39 * 1.00 * 5.9110 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.61  17.42    None  None   None       |
|    all(noH): 2823   0      0.00    116.61  17.42    None  None   None       |
|    Sol.    : 438    0      0.00    116.61  36.18    None  None   None       |
|    Mac.    : 2385   0      0.00    107.95  13.97    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 -  11.661: 1297   |   5:    58.304 -  69.965:   41        |
|      1:    11.661 -  23.322:  814   |   6:    69.965 -  81.626:   15        |
|      2:    23.322 -  34.983:  353   |   7:    81.626 -  93.287:    2        |
|      3:    34.983 -  46.643:  194   |   8:    93.287 - 104.948:    2        |
|      4:    46.643 -  58.304:  103   |   9:   104.948 - 116.608:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2616 r_free = 0.3452             target_work(ml) = 5.891         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2613 r_free = 0.3452             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2613   r_free= 0.3452   ksol= 0.33   Bsol= 37.29   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.63,2.17,2.85,0.00,0.00,0.00); trace/3= 2.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.890396                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2606   r_free= 0.3442   ksol= 0.34   Bsol= 46.99   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.66,0.68,1.49,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.889519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.691555              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.017   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.516840              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.257  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2606      final r-factor (work) = 0.2048          |
| start r-factor (free) = 0.3442      final r-factor (free) = 0.2748          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8979 = 5.69 * 0.50 * 5.9103 + 1.00 * 0.0784                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5862 = 5.69 * 0.50 * 5.8007 + 1.00 * 0.0786                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2048      final r-factor (work) = 0.1811          |
| start r-factor (free) = 0.2748      final r-factor (free) = 0.2523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8170 = 1.52 * 1.00 * 5.8007 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5676 = 1.52 * 1.00 * 5.6381 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.67  17.05    None  None   None       |
|    all(noH): 2823   0      0.00    122.67  17.05    None  None   None       |
|    Sol.    : 438    0      3.20    122.67  44.39    None  None   None       |
|    Mac.    : 2385   0      0.00    108.08  12.03    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 -  12.267: 1615   |   5:    61.335 -  73.602:   65        |
|      1:    12.267 -  24.534:  628   |   6:    73.602 -  85.869:   29        |
|      2:    24.534 -  36.801:  214   |   7:    85.869 -  98.136:    6        |
|      3:    36.801 -  49.068:  154   |   8:    98.136 - 110.403:    3        |
|      4:    49.068 -  61.335:  108   |   9:   110.403 - 122.670:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1811 r_free = 0.2523             target_work(ml) = 5.586         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1808 r_free = 0.2519             target_work(ml) = 5.585         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1808   r_free= 0.2519   ksol= 0.34   Bsol= 46.99   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.66,0.68,1.49,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.585051                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1806   r_free= 0.2507   ksol= 0.32   Bsol= 45.05   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.22,0.77,-0.00,0.00,0.00); trace/3= 0.23                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.580774                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.573289              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.866   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.558788              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.724  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1806      final r-factor (work) = 0.1512          |
| start r-factor (free) = 0.2507      final r-factor (free) = 0.2091          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1533 = 3.57 * 0.50 * 5.6389 + 1.00 * 0.0786                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9141 = 3.57 * 0.50 * 5.5146 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1512      final r-factor (work) = 0.1412          |
| start r-factor (free) = 0.2091      final r-factor (free) = 0.1960          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0968 = 0.56 * 1.00 * 5.5146 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0232 = 0.56 * 1.00 * 5.3891 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.51  16.42    None  None   None       |
|    all(noH): 2823   0      0.00    121.51  16.42    None  None   None       |
|    Sol.    : 438    0      4.41    121.51  44.22    None  None   None       |
|    Mac.    : 2385   0      0.00    109.08  11.32    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 -  12.151: 1735   |   5:    60.753 -  72.904:   63        |
|      1:    12.151 -  24.301:  582   |   6:    72.904 -  85.055:   33        |
|      2:    24.301 -  36.452:  165   |   7:    85.055 -  97.205:    9        |
|      3:    36.452 -  48.603:  132   |   8:    97.205 - 109.356:    3        |
|      4:    48.603 -  60.753:  100   |   9:   109.356 - 121.507:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1412 r_free = 0.1960             target_work(ml) = 5.350         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1410 r_free = 0.1955             target_work(ml) = 5.349         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1410   r_free= 0.1955   ksol= 0.32   Bsol= 45.05   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.22,0.77,-0.00,0.00,0.00); trace/3= 0.23                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.348582                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6578 0.99   1400  158 0.1094 0.1491      5.5227      5.7127|
|  2:  4.6578 -  3.7157 0.99   1350  143 0.1033 0.1457      5.6268      5.8987|
|  3:  3.7157 -  3.2515 0.99   1314  147 0.1366 0.1756      5.6988      5.9506|
|  4:  3.2515 -  2.9568 0.99   1329  157 0.1526 0.2138      5.6657       5.868|
|  5:  2.9568 -  2.7462 0.99   1299  139 0.1639 0.2120      5.5202      5.7142|
|  6:  2.7462 -  2.5852 0.99   1296  148 0.1568 0.2221      5.4316      5.6415|
|  7:  2.5852 -  2.4563 0.99   1313  140 0.1571 0.2263      5.3792      5.6062|
|  8:  2.4563 -  2.3498 0.98   1263  144 0.1578 0.2212      5.2945      5.5575|
|  9:  2.3498 -  2.2597 0.98   1291  149 0.1506 0.2080      5.2296      5.4401|
| 10:  2.2597 -  2.1819 0.99   1281  137 0.1487 0.2115      5.1662      5.3784|
| 11:  2.1819 -  2.1139 0.98   1283  138 0.1467 0.2223      5.1228      5.4665|
| 12:  2.1139 -  2.0536 0.97   1255  143 0.1345 0.1844      5.0516      5.2545|
| 13:  2.0536 -  1.9997 0.99   1274  142 0.1475 0.2265      4.9932      5.2717|
| 14:  1.9997 -  1.9510 0.52    682   74 0.1466 0.2097      4.9071      5.1479|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6578  1400   158  0.92  11.70   0.98     0.96      10295.31|
|  2:  4.6578 -  3.7157  1350   143  0.93  10.99   1.04     1.02      13754.82|
|  3:  3.7157 -  3.2515  1314   147  0.90  15.71   1.06     1.06      16752.79|
|  4:  3.2515 -  2.9568  1329   157  0.88  18.07   1.04     0.99      16107.22|
|  5:  2.9568 -  2.7462  1299   139  0.86  20.53   1.02     0.97      12681.63|
|  6:  2.7462 -  2.5852  1296   148  0.86  20.87   1.00     0.97      11501.08|
|  7:  2.5852 -  2.4563  1313   140  0.85  21.19   1.02     0.99      10376.32|
|  8:  2.4563 -  2.3498  1263   144  0.85  21.12   1.01     0.96       8447.07|
|  9:  2.3498 -  2.2597  1291   149  0.87  19.25   1.02     1.01       7480.62|
| 10:  2.2597 -  2.1819  1281   137  0.87  19.61   1.03     0.99       6514.51|
| 11:  2.1819 -  2.1139  1283   138  0.86  20.09   1.03     0.98       6218.68|
| 12:  2.1139 -  2.0536  1255   143  0.88  19.28   1.04     1.02       5868.45|
| 13:  2.0536 -  1.9997  1274   142  0.86  21.17   1.02     1.01       5100.90|
| 14:  1.9997 -  1.9510   682    74  0.86  20.52   1.02     0.98       4257.19|
|alpha:            min =        0.96 max =            1.06 mean =         0.99|
|beta:             min =     4257.19 max =        16752.79 mean =      9916.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.90 mean =        18.43|
|phase err.(test): min =        0.00 max =           88.84 mean =        17.64|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.1953   ksol= 0.31   Bsol= 39.16   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,-0.55,0.38,-0.00,0.00,0.00); trace/3= -0.13                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.348945                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.1953   ksol= 0.31   Bsol= 39.16   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,-0.55,0.38,-0.00,0.00,0.00); trace/3= -0.13                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.348945                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6578 0.99   1400  158 0.1104 0.1455      5.5149      5.6889|
|  2:  4.6578 -  3.7157 0.99   1350  143 0.1047 0.1462       5.627      5.9003|
|  3:  3.7157 -  3.2515 0.99   1314  147 0.1373 0.1758       5.701      5.9496|
|  4:  3.2515 -  2.9568 0.99   1329  157 0.1535 0.2141      5.6682      5.8741|
|  5:  2.9568 -  2.7462 0.99   1299  139 0.1637 0.2127      5.5218      5.7152|
|  6:  2.7462 -  2.5852 0.99   1296  148 0.1570 0.2231      5.4337      5.6465|
|  7:  2.5852 -  2.4563 0.99   1313  140 0.1571 0.2259      5.3811       5.607|
|  8:  2.4563 -  2.3498 0.98   1263  144 0.1576 0.2221      5.2961      5.5603|
|  9:  2.3498 -  2.2597 0.98   1291  149 0.1503 0.2081      5.2307      5.4415|
| 10:  2.2597 -  2.1819 0.99   1281  137 0.1487 0.2117      5.1662      5.3784|
| 11:  2.1819 -  2.1139 0.98   1283  138 0.1466 0.2219      5.1223      5.4654|
| 12:  2.1139 -  2.0536 0.97   1255  143 0.1345 0.1842       5.052      5.2555|
| 13:  2.0536 -  1.9997 0.99   1274  142 0.1474 0.2265      4.9935      5.2723|
| 14:  1.9997 -  1.9510 0.52    682   74 0.1465 0.2097       4.907      5.1485|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6578  1400   158  0.92  11.32   0.97     0.95       9817.18|
|  2:  4.6578 -  3.7157  1350   143  0.93  10.88   1.04     1.02      13479.80|
|  3:  3.7157 -  3.2515  1314   147  0.90  15.75   1.06     1.05      16790.27|
|  4:  3.2515 -  2.9568  1329   157  0.88  18.15   1.03     0.98      16195.71|
|  5:  2.9568 -  2.7462  1299   139  0.86  20.62   1.01     0.96      12787.54|
|  6:  2.7462 -  2.5852  1296   148  0.86  20.94   0.99     0.95      11583.15|
|  7:  2.5852 -  2.4563  1313   140  0.85  21.25   1.01     0.97      10446.77|
|  8:  2.4563 -  2.3498  1263   144  0.85  21.21   0.99     0.94       8517.38|
|  9:  2.3498 -  2.2597  1291   149  0.87  19.29   1.00     0.99       7517.22|
| 10:  2.2597 -  2.1819  1281   137  0.87  19.63   1.01     0.97       6529.76|
| 11:  2.1819 -  2.1139  1283   138  0.87  20.08   1.01     0.96       6215.86|
| 12:  2.1139 -  2.0536  1255   143  0.88  19.28   1.02     1.00       5874.01|
| 13:  2.0536 -  1.9997  1274   142  0.86  21.18   1.00     0.98       5106.05|
| 14:  1.9997 -  1.9510   682    74  0.86  20.54   1.00     0.95       4258.50|
|alpha:            min =        0.94 max =            1.05 mean =         0.98|
|beta:             min =     4258.50 max =        16790.27 mean =      9895.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.43|
|phase err.(test): min =        0.00 max =           89.17 mean =        17.65|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.426)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.51  16.42    None  None   None       |
|    all(noH): 2823   0      0.00    121.51  16.42    None  None   None       |
|    Sol.    : 438    0      4.42    121.51  44.23    None  None   None       |
|    Mac.    : 2385   0      0.00    109.08  11.32    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:     0.003 -  12.154: 1735   |   5:    60.756 -  72.907:   63        |
|      1:    12.154 -  24.304:  582   |   6:    72.907 -  85.058:   33        |
|      2:    24.304 -  36.455:  165   |   7:    85.058 -  97.208:    9        |
|      3:    36.455 -  48.606:  132   |   8:    97.208 - 109.359:    3        |
|      4:    48.606 -  60.756:  100   |   9:   109.359 - 121.510:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.724 - 5.352
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 338
   mapped sites are within: 0.724 - 5.352

peak=    9.143 closest distance to " CB  VAL A 230 " =    1.407
peak=    8.028 closest distance to " O   HOH Z 390 " =    1.505
peak=    7.575 closest distance to " O   HOH Z 130 " =    1.557
peak=    7.562 closest distance to " O   HOH Z 138 " =    1.190
peak=    6.913 closest distance to " CG2 VAL A 296 " =    1.193
peak=    6.783 closest distance to " O   HOH Z 205 " =    1.680
peak=    6.585 closest distance to " O   HOH Z 385 " =    1.457
peak=    6.435 closest distance to " O   HOH Z  61 " =    1.668
peak=    5.942 closest distance to " O   HOH Z 278 " =    2.335
peak=    5.857 closest distance to " O   HOH Z 350 " =    1.378
peak=    5.783 closest distance to " O   HOH Z  65 " =    1.734
peak=    5.644 closest distance to " O   HOH Z  37 " =    1.729
peak=    5.605 closest distance to " O   HOH Z 120 " =    1.087
peak=    5.512 closest distance to " O   HOH Z 289 " =    1.428
peak=    5.492 closest distance to " O   HOH Z  97 " =    1.756
peak=    5.447 closest distance to " CG  ARG A 138 " =    1.316
peak=    5.388 closest distance to " CD1AILE A 234 " =    1.032
peak=    5.337 closest distance to " O   HOH Z 222 " =    1.436
peak=    5.275 closest distance to " CD2 LEU A   5 " =    1.401
peak=    5.253 closest distance to " O   HOH Z 199 " =    1.365
peak=    5.240 closest distance to " CD  ARG A 138 " =    0.938
peak=    5.225 closest distance to " O   HOH Z 403 " =    1.713
peak=    5.189 closest distance to " O   HOH Z 374 " =    1.167
peak=    5.134 closest distance to " O   HOH Z 427 " =    2.584
peak=    5.111 closest distance to " O   HOH Z 214 " =    1.765
peak=    5.079 closest distance to " O   PRO A 198 " =    1.434
peak=    5.076 closest distance to " O   HOH Z 269 " =    1.506
peak=    5.006 closest distance to " NE2 GLN A  11 " =    1.332
peak=    4.987 closest distance to " O   HOH Z  15 " =    0.942
peak=    4.971 closest distance to " O   HOH Z 193 " =    1.779
peak=    4.935 closest distance to " NH2 ARG A  56 " =    2.208
peak=    4.885 closest distance to " CB  PRO A  54 " =    1.093
peak=    4.882 closest distance to " O   HOH Z   7 " =    2.058
peak=    4.872 closest distance to " O   HOH Z 247 " =    1.298
peak=    4.804 closest distance to " O   HOH Z 179 " =    1.017
peak=    4.797 closest distance to " O   HOH Z 424 " =    1.551
peak=    4.795 closest distance to " O   HOH Z 375 " =    1.187
peak=    4.787 closest distance to " O   HOH Z 344 " =    1.453
peak=    4.737 closest distance to " O   HOH Z 134 " =    1.552
peak=    4.632 closest distance to " O   HOH Z 347 " =    1.097
peak=    4.608 closest distance to " CG1AVAL A 121 " =    1.164
peak=    4.593 closest distance to " CG  LEU A   5 " =    1.253
peak=    4.539 closest distance to " O   HOH Z 381 " =    1.108
peak=    4.534 closest distance to " O   HOH Z 124 " =    1.817
peak=    4.485 closest distance to " O   HOH Z 291 " =    1.300
peak=    4.480 closest distance to " O   HOH Z 123 " =    1.296
peak=    4.465 closest distance to " O   HOH Z 279 " =    1.170
peak=    4.401 closest distance to " O   HOH Z 112 " =    1.254
peak=    4.399 closest distance to " O   HOH Z 429 " =    1.031
peak=    4.385 closest distance to " O   HOH Z 427 " =    1.366
peak=    4.370 closest distance to " O   HOH Z 186 " =    1.385
peak=    4.360 closest distance to " O   HOH Z 392 " =    1.419
peak=    4.360 closest distance to " O   HOH Z 326 " =    1.637
peak=    4.352 closest distance to " O   HOH Z 316 " =    2.657
peak=    4.340 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.339 closest distance to " CG2 THR A 279 " =    1.171
peak=    4.328 closest distance to " O   HOH Z 363 " =    1.258
peak=    4.326 closest distance to " O   HOH Z 358 " =    1.532
peak=    4.304 closest distance to " CG2 THR A 246 " =    0.967
peak=    4.290 closest distance to " O   HOH Z 143 " =    1.693
peak=    4.282 closest distance to " CB  ARG A 275 " =    1.102
peak=    4.278 closest distance to " O   HOH Z 117 " =    1.378
peak=    4.274 closest distance to " O   HOH Z 126 " =    1.514
peak=    4.255 closest distance to " CD2 LEU A 228 " =    1.200
peak=    4.231 closest distance to " NH1 ARG A 138 " =    1.020
peak=    4.222 closest distance to " O   HOH Z 202 " =    1.811
peak=    4.192 closest distance to " O   HOH Z 132 " =    1.688
peak=    4.181 closest distance to " O   HOH Z 259 " =    2.090
peak=    4.181 closest distance to " O   HOH Z 220 " =    1.579
peak=    4.171 closest distance to " CB  ASN A 148 " =    1.361
peak=    4.169 closest distance to " O   HOH Z   2 " =    1.959
peak=    4.125 closest distance to " O   HOH Z 178 " =    1.220
peak=    4.124 closest distance to " O   HOH Z 144 " =    1.966
peak=    4.107 closest distance to " CA  ALA A 295 " =    0.987
peak=    4.104 closest distance to " O   HOH Z 425 " =    1.530
peak=    4.101 closest distance to " O   HOH Z 414 " =    1.559
peak=    4.101 closest distance to " O   HOH Z 272 " =    1.934
peak=    4.086 closest distance to " O   HOH Z  63 " =    1.779
peak=    4.078 closest distance to " CG  GLN A  11 " =    2.175
peak=    4.078 closest distance to " CB  VAL A 230 " =    1.125
peak=    4.072 closest distance to " O   HOH Z 361 " =    1.560
peak=    4.068 closest distance to " O   HOH Z 217 " =    1.515
peak=    4.068 closest distance to " CG  ASN A  60 " =    1.168
peak=    4.061 closest distance to " CB  ASN A  60 " =    0.927
peak=    4.057 closest distance to " O   SER A  62 " =    0.880
peak=    4.053 closest distance to " O   HOH Z  89 " =    1.560
peak=    4.032 closest distance to " CD2 TRP A 179 " =    2.043
peak=    4.027 closest distance to " O   HOH Z 250 " =    2.130
peak=    4.022 closest distance to " O   HOH Z  78 " =    1.831
peak=    4.013 closest distance to " CB  SER A   3 " =    1.323
peak=    4.011 closest distance to " O   HOH Z 406 " =    1.195
peak=    4.006 closest distance to " O   HOH Z 364 " =    1.549
peak=    4.004 closest distance to " O   HOH Z 192 " =    1.525
peak=    3.987 closest distance to " O   HOH Z 426 " =    1.206
peak=    3.982 closest distance to " CB  VAL A 296 " =    1.123
peak=    3.976 closest distance to " NH2BARG A 145 " =    1.439
peak=    3.968 closest distance to " O   HOH Z  39 " =    1.522
peak=    3.966 closest distance to " O   HOH Z 289 " =    1.285
peak=    3.960 closest distance to " CG  PRO A 198 " =    1.426
peak=    3.946 closest distance to " CB  SER A 216 " =    0.992
peak=    3.941 closest distance to " O   HOH Z 116 " =    1.324
peak=    3.934 closest distance to " OG ASER A 134 " =    1.342
peak=    3.928 closest distance to " O   HOH Z 171 " =    2.502
peak=    3.924 closest distance to " CG  LEU A 228 " =    1.309
peak=    3.919 closest distance to " O   HOH Z 400 " =    0.853
peak=    3.916 closest distance to " O   HOH Z 411 " =    3.460
peak=    3.902 closest distance to " OD2 ASP A 286 " =    2.427
peak=    3.885 closest distance to " O   HOH Z  28 " =    1.719
peak=    3.884 closest distance to " NE2 GLN A  55 " =    1.378
peak=    3.875 closest distance to " CB  TRP A 179 " =    1.416
peak=    3.875 closest distance to " O   HOH Z  53 " =    2.259
peak=    3.867 closest distance to " CE AMET A  47 " =    1.232
peak=    3.860 closest distance to " O   HOH Z 261 " =    1.881
peak=    3.858 closest distance to " O   HOH Z 388 " =    1.203
peak=    3.849 closest distance to " O   HOH Z 410 " =    1.297
peak=    3.849 closest distance to " O   HOH Z 193 " =    1.610
peak=    3.849 closest distance to " N   GLN A 278 " =    1.054
peak=    3.836 closest distance to " NH2BARG A 190 " =    1.677
peak=    3.835 closest distance to " CE AMET A  47 " =    1.567
peak=    3.832 closest distance to " O   HOH Z  97 " =    2.029
peak=    3.828 closest distance to " O   HOH Z 371 " =    1.705
peak=    3.826 closest distance to " O   HOH Z 126 " =    1.863
peak=    3.825 closest distance to " CG2 THR A 221 " =    1.431
peak=    3.820 closest distance to " O   HOH Z 357 " =    1.821
peak=    3.818 closest distance to " O   HOH Z 280 " =    1.510
peak=    3.811 closest distance to " CA  LEU A 282 " =    1.234
peak=    3.810 closest distance to " CB  GLN A 183 " =    1.144
peak=    3.801 closest distance to " O   HOH Z 375 " =    2.025
peak=    3.801 closest distance to " O   HOH Z 417 " =    1.379
peak=    3.791 closest distance to " O   HOH Z 425 " =    1.977
peak=    3.791 closest distance to " O   HOH Z 133 " =    1.689
peak=    3.790 closest distance to " OD1 ASN A  45 " =    1.161
peak=    3.787 closest distance to " O   HOH Z 282 " =    1.513
peak=    3.786 closest distance to " O   HOH Z 102 " =    1.164
peak=    3.786 closest distance to " O   HOH Z  58 " =    1.728
peak=    3.783 closest distance to " O   HOH Z 236 " =    1.690
peak=    3.735 closest distance to " CG  LEU A 167 " =    1.211
peak=    3.732 closest distance to " O   HOH Z 127 " =    1.154
peak=    3.727 closest distance to " NZ BLYS A 290 " =    1.149
peak=    3.718 closest distance to " O   HOH Z 438 " =    2.698
peak=    3.716 closest distance to " O   SER A 164 " =    0.819
peak=    3.709 closest distance to " O   HOH Z 147 " =    1.460
peak=    3.706 closest distance to " NE2 GLN A  73 " =    1.688
peak=    3.695 closest distance to " NE AARG A 275 " =    1.333
peak=    3.692 closest distance to " CG  LYS A  76 " =    1.588
peak=    3.691 closest distance to " O   HOH Z  88 " =    2.878
peak=    3.686 closest distance to " CB  GLU A 277 " =    3.571
peak=    3.677 closest distance to " O   HOH Z  30 " =    1.547
peak=    3.675 closest distance to " O   HOH Z 359 " =    1.452
peak=    3.662 closest distance to " O   HOH Z 369 " =    2.263
peak=    3.661 closest distance to " O   HOH Z  69 " =    1.198
peak=    3.659 closest distance to " C   ASP A 298 " =    1.361
peak=    3.655 closest distance to " O   HOH Z 327 " =    1.615
peak=    3.653 closest distance to " O   ALA A 165 " =    1.089
peak=    3.652 closest distance to " O   HOH Z 117 " =    2.161
peak=    3.638 closest distance to " O   HOH Z 293 " =    1.389
peak=    3.632 closest distance to " O   HOH Z 183 " =    1.232
peak=    3.632 closest distance to " O   HOH Z 180 " =    2.122
peak=    3.629 closest distance to " O   HOH Z  59 " =    1.361
peak=    3.627 closest distance to " O   HOH Z 214 " =    1.420
peak=    3.620 closest distance to " O   HOH Z 295 " =    1.248
peak=    3.609 closest distance to " O   HOH Z 389 " =    1.344
peak=    3.604 closest distance to " N   TYR A  15 " =    1.142
peak=    3.590 closest distance to " O   HOH Z   9 " =    1.071
peak=    3.586 closest distance to " CG  LYS A 119 " =    1.145
peak=    3.584 closest distance to " O   HOH Z 287 " =    1.455
peak=    3.583 closest distance to " CA  THR A 264 " =    0.725
peak=    3.580 closest distance to " O   HOH Z 172 " =    2.901
peak=    3.569 closest distance to " O   ALA A 100 " =    1.708
peak=    3.565 closest distance to " NZ  LYS A 117 " =    1.214
peak=    3.565 closest distance to " CB  ASN A 187 " =    1.069
peak=    3.564 closest distance to " O   HOH Z  51 " =    1.229
peak=    3.539 closest distance to " CA  ALA A  21 " =    1.294
peak=    3.536 closest distance to " O   HOH Z 260 " =    1.495
peak=    3.534 closest distance to " O   HOH Z 143 " =    2.409
peak=    3.532 closest distance to " CB  PRO A 198 " =    1.075
peak=    3.531 closest distance to " NH2BARG A 102 " =    0.969
peak=    3.531 closest distance to " O   HOH Z  11 " =    1.716
peak=    3.528 closest distance to " CZ2 TRP A 179 " =    2.442
peak=    3.524 closest distance to " CB  ARG A 102 " =    0.838
peak=    3.522 closest distance to " O   HOH Z 360 " =    1.079
peak=    3.517 closest distance to " O   HOH Z 389 " =    1.549
peak=    3.505 closest distance to " CB  LEU A 300 " =    0.950
peak=    3.503 closest distance to " O   HOH Z  89 " =    2.093
peak=    3.500 closest distance to " O   HOH Z 371 " =    3.114
peak=    3.495 closest distance to " O   HOH Z 151 " =    1.827
peak=    3.488 closest distance to " CB  VAL A 202 " =    1.685
peak=    3.484 closest distance to " OD1 ASP A  50 " =    1.008
peak=    3.482 closest distance to " CE  MET A  93 " =    1.423
peak=    3.482 closest distance to " CB  TYR A 169 " =    0.787
peak=    3.480 closest distance to " N   GLU A   2 " =    1.582
peak=    3.472 closest distance to " O   HOH Z 227 " =    1.799
peak=    3.470 closest distance to " O   HOH Z 302 " =    1.559
peak=    3.461 closest distance to " CA  VAL A 126 " =    1.249
peak=    3.460 closest distance to " N   PHE A 130 " =    1.326
peak=    3.441 closest distance to " CA  ILE A 234 " =    1.025
peak=    3.440 closest distance to " O   HOH Z  54 " =    1.010
peak=    3.432 closest distance to " NE2 GLN A  58 " =    5.192
peak=    3.431 closest distance to " O   HOH Z  22 " =    2.066
peak=    3.422 closest distance to " OG  SER A  62 " =    3.404
peak=    3.418 closest distance to " O   HOH Z 422 " =    2.764
peak=    3.418 closest distance to " NH1 ARG A  14 " =    0.982
peak=    3.416 closest distance to " CD2 LEU A 255 " =    1.285
peak=    3.414 closest distance to " O   HOH Z  46 " =    1.100
peak=    3.412 closest distance to " CB  MET A  47 " =    1.388
peak=    3.411 closest distance to " O   HOH Z 182 " =    2.093
peak=    3.397 closest distance to " CD2 TRP A  70 " =    1.708
peak=    3.396 closest distance to " CA  GLY A 267 " =    1.310
peak=    3.396 closest distance to " CG  ASP A 238 " =    0.850
peak=    3.392 closest distance to " CB  ASP A 200 " =    0.964
peak=    3.390 closest distance to " CD  LYS A 119 " =    1.225
peak=    3.386 closest distance to " CB  VAL A 265 " =    1.335
peak=    3.385 closest distance to " O   HOH Z 108 " =    1.758
peak=    3.383 closest distance to " CD1 LEU A   5 " =    1.773
peak=    3.380 closest distance to " O   GLY A 302 " =    2.114
peak=    3.376 closest distance to " O   HOH Z  54 " =    1.298
peak=    3.375 closest distance to " CA  ASP A  50 " =    0.969
peak=    3.372 closest distance to " O   HOH Z 290 " =    1.132
peak=    3.370 closest distance to " O   HOH Z 166 " =    1.195
peak=    3.368 closest distance to " N   SER A  63 " =    0.803
peak=    3.368 closest distance to " O   HOH Z 134 " =    2.133
peak=    3.367 closest distance to " O   HOH Z 273 " =    1.121
peak=    3.366 closest distance to " CB  ILE A 234 " =    0.841
peak=    3.361 closest distance to " CA  MET A  93 " =    1.387
peak=    3.360 closest distance to " CG  ARG A  66 " =    2.235
peak=    3.359 closest distance to " O   HOH Z 204 " =    1.700
peak=    3.359 closest distance to " N   TRP A 177 " =    1.629
peak=    3.357 closest distance to " OG1 THR A 221 " =    1.486
peak=    3.355 closest distance to " CB  ALA A   1 " =    4.467
peak=    3.349 closest distance to " O   HOH Z 211 " =    1.334
peak=    3.348 closest distance to " CB  PHE A 225 " =    1.282
peak=    3.341 closest distance to " O   HOH Z 276 " =    1.715
peak=    3.337 closest distance to " O   HOH Z 234 " =    3.556
peak=    3.330 closest distance to " O   HOH Z 269 " =    2.930
peak=    3.329 closest distance to " O   HOH Z 428 " =    1.179
peak=    3.324 closest distance to " O   HOH Z  95 " =    1.466
peak=    3.322 closest distance to " O   HOH Z 153 " =    4.029
peak=    3.319 closest distance to " CD BLYS A 290 " =    1.054
peak=    3.315 closest distance to " CG1BVAL A 121 " =    2.164
peak=    3.314 closest distance to " O   HOH Z 331 " =    1.220
peak=    3.314 closest distance to " CG  GLN A  88 " =    1.031
peak=    3.313 closest distance to " CA  ILE A 199 " =    1.575
peak=    3.311 closest distance to " O   HOH Z  33 " =    1.653
peak=    3.304 closest distance to " O   HOH Z  91 " =    2.296
peak=    3.303 closest distance to " CZ3 TRP A  70 " =    0.863
peak=    3.290 closest distance to " CG2 VAL A 257 " =    0.972
peak=    3.288 closest distance to " O   HOH Z 143 " =    2.017
peak=    3.288 closest distance to " O   HOH Z 423 " =    1.633
peak=    3.286 closest distance to " O   HOH Z 217 " =    3.566
peak=    3.286 closest distance to " CE  LYS A  48 " =    1.018
peak=    3.284 closest distance to " O   HOH Z 158 " =    3.039
peak=    3.282 closest distance to " O   HOH Z 134 " =    2.459
peak=    3.278 closest distance to " CA  ARG A 195 " =    1.371
peak=    3.276 closest distance to " O   HOH Z 124 " =    1.677
peak=    3.276 closest distance to " OE2 GLU A   2 " =    1.901
peak=    3.274 closest distance to " O   HOH Z 262 " =    1.318
peak=    3.274 closest distance to " O   HOH Z 334 " =    1.773
peak=    3.273 closest distance to " O   HOH Z  48 " =    1.705
peak=    3.272 closest distance to " O   HOH Z   4 " =    1.332
peak=    3.270 closest distance to " O   HOH Z 353 " =    1.901
peak=    3.264 closest distance to " CG2 THR A 251 " =    1.670
peak=    3.263 closest distance to " CZ3 TRP A 123 " =    1.317
peak=    3.261 closest distance to " O   HOH Z 248 " =    2.362
peak=    3.260 closest distance to " CG2 ILE A 234 " =    0.933
peak=    3.258 closest distance to " O   GLN A 278 " =    1.303
peak=    3.252 closest distance to " O   HOH Z 368 " =    3.822
peak=    3.241 closest distance to " O   HOH Z 216 " =    1.949
peak=    3.237 closest distance to " O   HOH Z 197 " =    1.307
peak=    3.234 closest distance to " O   HOH Z  66 " =    2.179
peak=    3.227 closest distance to " OD1 ASP A 286 " =    1.213
peak=    3.226 closest distance to " O   HOH Z 116 " =    3.071
peak=    3.225 closest distance to " O   HOH Z 416 " =    1.386
peak=    3.224 closest distance to " CB  ALA A  51 " =    1.205
peak=    3.222 closest distance to " O   HOH Z 139 " =    5.352
peak=    3.221 closest distance to " O   HOH Z 116 " =    2.681
peak=    3.217 closest distance to " CB  PHE A 130 " =    1.508
peak=    3.217 closest distance to " CB  PHE A 204 " =    1.087
peak=    3.216 closest distance to " CB  ALA A   1 " =    0.931
peak=    3.215 closest distance to " O   HOH Z 129 " =    1.007
peak=    3.214 closest distance to " NE2 GLN A  89 " =    1.318
peak=    3.214 closest distance to " O   HOH Z 419 " =    1.882
peak=    3.211 closest distance to " CB  ASP A 107 " =    1.022
peak=    3.211 closest distance to " CG1 VAL A 153 " =    0.833
peak=    3.208 closest distance to " CG  PRO A 280 " =    0.867
peak=    3.204 closest distance to " O   HOH Z 185 " =    1.325
peak=    3.204 closest distance to " O   HOH Z 423 " =    1.781
peak=    3.199 closest distance to " NZ  LYS A  76 " =    1.356
peak=    3.197 closest distance to " N   GLN A  73 " =    1.250
peak=    3.195 closest distance to " OG  SER A 276 " =    1.076
peak=    3.195 closest distance to " NH2 ARG A 219 " =    1.740
peak=    3.195 closest distance to " OH  TYR A  30 " =    1.176
peak=    3.195 closest distance to " OG  SER A  62 " =    3.827
peak=    3.194 closest distance to " O   HOH Z 130 " =    2.215
peak=    3.190 closest distance to " CD  PRO A 243 " =    1.726
peak=    3.187 closest distance to " CD2 LEU A  25 " =    1.127
peak=    3.186 closest distance to " CA  ASP A 124 " =    0.724
peak=    3.184 closest distance to " CB  PHE A  16 " =    0.922
peak=    3.183 closest distance to " CG BARG A 275 " =    1.196
peak=    3.181 closest distance to " O   HOH Z 342 " =    0.969
peak=    3.176 closest distance to " CA  ASN A  74 " =    1.247
peak=    3.171 closest distance to " O   HOH Z 219 " =    4.467
peak=    3.166 closest distance to " O   HOH Z 355 " =    1.755
peak=    3.160 closest distance to " O   HOH Z 209 " =    1.108
peak=    3.160 closest distance to " CA  ASN A 217 " =    1.126
peak=    3.159 closest distance to " O   HOH Z 158 " =    2.348
peak=    3.158 closest distance to " O   HOH Z  28 " =    2.099
peak=    3.158 closest distance to " NZ  LYS A 117 " =    1.478
peak=    3.155 closest distance to " OD1 ASP A 200 " =    1.494
peak=    3.155 closest distance to " C   ALA A 299 " =    0.923
peak=    3.149 closest distance to " CB  SER A  63 " =    1.397
peak=    3.148 closest distance to " O   HOH Z  88 " =    3.606
peak=    3.147 closest distance to " OE1 GLN A 240 " =    1.474
peak=    3.146 closest distance to " O   HOH Z 373 " =    1.166
peak=    3.146 closest distance to " O   HOH Z 265 " =    1.948
peak=    3.141 closest distance to " O   HOH Z 234 " =    2.337
peak=    3.138 closest distance to " N   ASN A 209 " =    1.664
peak=    3.137 closest distance to " CG1 ILE A  49 " =    0.996
peak=    3.136 closest distance to " NH2 ARG A  79 " =    1.382
peak=    3.136 closest distance to " O   HOH Z 353 " =    2.244
peak=    3.133 closest distance to " O   HOH Z  93 " =    2.053
peak=    3.132 closest distance to " O   HOH Z 152 " =    2.003
peak=    3.131 closest distance to " O   HOH Z  80 " =    2.276
peak=    3.131 closest distance to " O   HOH Z 345 " =    3.244
peak=    3.127 closest distance to " O   VAL A  72 " =    0.939
peak=    3.127 closest distance to " O   ARG A  14 " =    1.060
peak=    3.126 closest distance to " CB  ASP A 140 " =    0.924
peak=    3.120 closest distance to " OD1 ASN A  69 " =    2.457
peak=    3.118 closest distance to " O   HOH Z 184 " =    1.555
peak=    3.114 closest distance to " O   HOH Z 287 " =    2.197
peak=    3.112 closest distance to " O   HOH Z 211 " =    2.510
peak=    3.108 closest distance to " O   HOH Z 162 " =    1.315
peak=    3.102 closest distance to " NE BARG A 275 " =    1.110
peak=    3.091 closest distance to " O   HOH Z 395 " =    0.998
peak=    3.076 closest distance to " CG  PRO A  54 " =    1.302
peak=    3.032 closest distance to " O   HOH Z 258 " =    1.503
peak=    3.024 closest distance to " O   HOH Z 378 " =    1.284

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.704 - 5.886
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 206
   mapped sites are within: 0.704 - 5.886

peak=   -5.354 closest distance to " CD  ARG A 138 " =    1.066
peak=   -5.139 closest distance to " OG ASER A 134 " =    1.003
peak=   -4.710 closest distance to " O   PRO A 198 " =    1.131
peak=   -4.386 closest distance to " CG2 VAL A 230 " =    0.820
peak=   -4.267 closest distance to " O   SER A  62 " =    1.231
peak=   -4.259 closest distance to " O   HOH Z 388 " =    1.389
peak=   -4.244 closest distance to " CG2BVAL A 121 " =    0.968
peak=   -4.116 closest distance to " O   SER A 135 " =    1.546
peak=   -4.098 closest distance to " NH2 ARG A  79 " =    1.693
peak=   -4.097 closest distance to " CG2 THR A   4 " =    2.036
peak=   -4.074 closest distance to " O   PRO A 163 " =    1.903
peak=   -4.022 closest distance to " O   HOH Z  98 " =    1.587
peak=   -3.930 closest distance to " O   HOH Z 117 " =    0.872
peak=   -3.914 closest distance to " CB  SER A 146 " =    2.109
peak=   -3.911 closest distance to " C   SER A  63 " =    1.080
peak=   -3.853 closest distance to " O   HOH Z 407 " =    3.129
peak=   -3.850 closest distance to " O   HOH Z 231 " =    1.684
peak=   -3.850 closest distance to " OG1 THR A 178 " =    1.031
peak=   -3.830 closest distance to " OG BSER A 134 " =    1.545
peak=   -3.778 closest distance to " O   HOH Z 266 " =    4.535
peak=   -3.756 closest distance to " O   HOH Z 179 " =    1.123
peak=   -3.753 closest distance to " CA  GLN A  55 " =    1.241
peak=   -3.752 closest distance to " CA  ASP A  27 " =    2.530
peak=   -3.733 closest distance to " O   HOH Z  95 " =    1.236
peak=   -3.730 closest distance to " OG  SER A  97 " =    2.270
peak=   -3.703 closest distance to " CE BMET A  47 " =    1.394
peak=   -3.692 closest distance to " ND2BASN A 224 " =    1.548
peak=   -3.689 closest distance to " O   ILE A  49 " =    1.627
peak=   -3.686 closest distance to " O   HOH Z 198 " =    2.331
peak=   -3.685 closest distance to " O   LYS A 119 " =    0.798
peak=   -3.669 closest distance to " CD1 LEU A  96 " =    2.165
peak=   -3.661 closest distance to " O   HOH Z  56 " =    0.855
peak=   -3.659 closest distance to " CD2 LEU A 237 " =    2.549
peak=   -3.649 closest distance to " CA  GLY A  35 " =    1.897
peak=   -3.645 closest distance to " OE1 GLU A 277 " =    2.324
peak=   -3.642 closest distance to " O   GLY A 287 " =    2.048
peak=   -3.639 closest distance to " O   HOH Z 317 " =    2.941
peak=   -3.639 closest distance to " O   HOH Z 415 " =    1.063
peak=   -3.635 closest distance to " O   HOH Z 220 " =    0.784
peak=   -3.628 closest distance to " O   HOH Z 389 " =    2.027
peak=   -3.624 closest distance to " ND2 ASN A  45 " =    1.025
peak=   -3.621 closest distance to " CD2 LEU A 228 " =    0.891
peak=   -3.619 closest distance to " CA  GLY A 133 " =    1.957
peak=   -3.606 closest distance to " O   GLN A  11 " =    1.741
peak=   -3.605 closest distance to " CZ2 TRP A  92 " =    2.544
peak=   -3.602 closest distance to " O   SER A  22 " =    2.574
peak=   -3.602 closest distance to " O   HOH Z 431 " =    1.295
peak=   -3.602 closest distance to " O   TRP A  70 " =    1.309
peak=   -3.599 closest distance to " O   HOH Z  19 " =    2.089
peak=   -3.584 closest distance to " O   HOH Z 290 " =    0.964
peak=   -3.574 closest distance to " O   HOH Z 352 " =    0.872
peak=   -3.573 closest distance to " O   HOH Z 435 " =    1.991
peak=   -3.565 closest distance to " C   ALA A 158 " =    1.342
peak=   -3.561 closest distance to " O   HOH Z 385 " =    0.814
peak=   -3.557 closest distance to " O   ALA A   1 " =    1.080
peak=   -3.553 closest distance to " O   ALA A  51 " =    1.285
peak=   -3.548 closest distance to " CD  PRO A 198 " =    1.304
peak=   -3.544 closest distance to " CD  ARG A  14 " =    3.120
peak=   -3.540 closest distance to " O   HOH Z 359 " =    1.937
peak=   -3.532 closest distance to " O   HOH Z 381 " =    1.019
peak=   -3.531 closest distance to " O   HOH Z 134 " =    2.147
peak=   -3.528 closest distance to " N   VAL A 125 " =    1.227
peak=   -3.521 closest distance to " NH2AARG A 275 " =    5.437
peak=   -3.515 closest distance to " CE2 PHE A 218 " =    2.592
peak=   -3.510 closest distance to " C   ASN A 285 " =    2.105
peak=   -3.507 closest distance to " O   SER A 146 " =    1.350
peak=   -3.492 closest distance to " CD2 LEU A   5 " =    0.874
peak=   -3.476 closest distance to " O   HOH Z 390 " =    2.539
peak=   -3.476 closest distance to " O   HOH Z  68 " =    1.657
peak=   -3.472 closest distance to " O   HOH Z  61 " =    1.460
peak=   -3.470 closest distance to " NH1 ARG A  56 " =    2.503
peak=   -3.470 closest distance to " CG  PRO A 163 " =    2.590
peak=   -3.468 closest distance to " O   HOH Z 120 " =    0.885
peak=   -3.463 closest distance to " O   HOH Z 164 " =    5.886
peak=   -3.462 closest distance to " OG1 THR A 246 " =    1.427
peak=   -3.459 closest distance to " CD2 HIS A 115 " =    2.063
peak=   -3.457 closest distance to " O   GLU A  44 " =    1.766
peak=   -3.455 closest distance to " O   SER A  22 " =    1.329
peak=   -3.451 closest distance to " O   HOH Z 125 " =    2.985
peak=   -3.450 closest distance to " CG  ASN A  60 " =    1.138
peak=   -3.442 closest distance to " OG  SER A  87 " =    1.611
peak=   -3.441 closest distance to " CG  ASP A  50 " =    0.970
peak=   -3.439 closest distance to " N   GLN A  58 " =    2.035
peak=   -3.437 closest distance to " CB  PHE A  38 " =    2.932
peak=   -3.434 closest distance to " CG  GLN A  88 " =    0.826
peak=   -3.432 closest distance to " O   HOH Z 139 " =    2.896
peak=   -3.430 closest distance to " O   HOH Z 420 " =    3.949
peak=   -3.429 closest distance to " CZ  PHE A  16 " =    0.964
peak=   -3.429 closest distance to " O   HOH Z 138 " =    1.030
peak=   -3.425 closest distance to " O   HOH Z 385 " =    2.407
peak=   -3.415 closest distance to " CD1 TRP A 179 " =    1.104
peak=   -3.412 closest distance to " O   HOH Z 268 " =    0.800
peak=   -3.412 closest distance to " O   HOH Z 286 " =    1.581
peak=   -3.411 closest distance to " OE1 GLN A 223 " =    2.504
peak=   -3.403 closest distance to " N   GLN A  58 " =    1.126
peak=   -3.403 closest distance to " O   HOH Z 402 " =    1.422
peak=   -3.396 closest distance to " O   HOH Z 298 " =    1.157
peak=   -3.395 closest distance to " OG  SER A  26 " =    1.063
peak=   -3.392 closest distance to " O   HOH Z 395 " =    0.759
peak=   -3.392 closest distance to " C   ASP A 231 " =    2.335
peak=   -3.386 closest distance to " O   PRO A 243 " =    2.394
peak=   -3.385 closest distance to " OD1 ASP A 200 " =    1.147
peak=   -3.383 closest distance to " OD2 ASP A 171 " =    1.398
peak=   -3.380 closest distance to " N   HIS A 115 " =    1.911
peak=   -3.376 closest distance to " O   HOH Z 377 " =    2.065
peak=   -3.374 closest distance to " O   HOH Z  61 " =    0.885
peak=   -3.371 closest distance to " CE2 TYR A  30 " =    2.818
peak=   -3.369 closest distance to " CG BLYS A 290 " =    1.171
peak=   -3.365 closest distance to " CG  ARG A 138 " =    0.924
peak=   -3.360 closest distance to " NH1 ARG A 138 " =    1.109
peak=   -3.358 closest distance to " O   HOH Z 221 " =    0.928
peak=   -3.357 closest distance to " O   HOH Z 166 " =    1.788
peak=   -3.354 closest distance to " CD  ARG A 219 " =    2.488
peak=   -3.352 closest distance to " O   HOH Z 103 " =    1.315
peak=   -3.351 closest distance to " O   HOH Z 211 " =    1.434
peak=   -3.347 closest distance to " OG  SER A 206 " =    1.769
peak=   -3.338 closest distance to " ND2 ASN A  60 " =    1.410
peak=   -3.336 closest distance to " O   HOH Z 406 " =    0.861
peak=   -3.335 closest distance to " O   HOH Z 385 " =    1.167
peak=   -3.335 closest distance to " OG1 THR A  82 " =    1.506
peak=   -3.330 closest distance to " O   ILE A 106 " =    2.227
peak=   -3.328 closest distance to " CD1AILE A 234 " =    2.505
peak=   -3.319 closest distance to " OD2 ASP A 171 " =    1.743
peak=   -3.317 closest distance to " CB  ALA A 248 " =    1.928
peak=   -3.316 closest distance to " O   GLN A  73 " =    1.381
peak=   -3.311 closest distance to " O   PRO A 198 " =    1.349
peak=   -3.311 closest distance to " O   HOH Z  93 " =    1.773
peak=   -3.310 closest distance to " CB  PHE A  61 " =    1.382
peak=   -3.304 closest distance to " CG  HIS A 108 " =    0.903
peak=   -3.300 closest distance to " CZ3 TRP A 274 " =    1.967
peak=   -3.295 closest distance to " CG  PRO A 213 " =    1.213
peak=   -3.290 closest distance to " O   HOH Z  43 " =    1.845
peak=   -3.290 closest distance to " N   ASN A  60 " =    1.175
peak=   -3.289 closest distance to " CE3 TRP A 274 " =    2.568
peak=   -3.287 closest distance to " CG2 THR A  31 " =    2.199
peak=   -3.286 closest distance to " O   HOH Z  54 " =    0.728
peak=   -3.284 closest distance to " CG1 VAL A 257 " =    2.329
peak=   -3.283 closest distance to " OE2 GLU A 152 " =    2.102
peak=   -3.283 closest distance to " O   ASP A  65 " =    1.082
peak=   -3.277 closest distance to " O   GLY A  80 " =    2.439
peak=   -3.276 closest distance to " OD1 ASN A 301 " =    2.004
peak=   -3.273 closest distance to " O   HOH Z 265 " =    5.023
peak=   -3.270 closest distance to " O   HOH Z 347 " =    0.704
peak=   -3.269 closest distance to " CD1 PHE A  59 " =    2.115
peak=   -3.267 closest distance to " CD  ARG A 259 " =    2.649
peak=   -3.267 closest distance to " O   LYS A 289 " =    1.365
peak=   -3.260 closest distance to " O   HOH Z 100 " =    1.152
peak=   -3.257 closest distance to " O   HOH Z 126 " =    1.674
peak=   -3.257 closest distance to " O   HOH Z 143 " =    0.730
peak=   -3.254 closest distance to " O   HOH Z 404 " =    1.218
peak=   -3.254 closest distance to " O   LEU A 143 " =    1.515
peak=   -3.248 closest distance to " O   HOH Z 416 " =    0.741
peak=   -3.246 closest distance to " O   HOH Z 279 " =    1.370
peak=   -3.241 closest distance to " O   HOH Z 258 " =    4.800
peak=   -3.240 closest distance to " O   HOH Z 158 " =    2.024
peak=   -3.238 closest distance to " O   HOH Z 368 " =    1.525
peak=   -3.234 closest distance to " O   HOH Z 168 " =    1.217
peak=   -3.233 closest distance to " N   VAL A  72 " =    2.029
peak=   -3.229 closest distance to " O   GLY A 118 " =    2.026
peak=   -3.223 closest distance to " OG  SER A   3 " =    1.194
peak=   -3.223 closest distance to " O   HOH Z  63 " =    1.520
peak=   -3.216 closest distance to " O   HOH Z 418 " =    1.405
peak=   -3.215 closest distance to " OE1 GLN A 278 " =    1.708
peak=   -3.212 closest distance to " N   ALA A 248 " =    1.793
peak=   -3.206 closest distance to " CB  ALA A 227 " =    2.233
peak=   -3.201 closest distance to " O   HOH Z  77 " =    1.230
peak=   -3.196 closest distance to " O   SER A  97 " =    1.204
peak=   -3.191 closest distance to " O   TRP A  92 " =    1.886
peak=   -3.191 closest distance to " O   HOH Z 336 " =    5.149
peak=   -3.190 closest distance to " OD2 ASP A  27 " =    1.552
peak=   -3.189 closest distance to " O   HOH Z 111 " =    1.046
peak=   -3.185 closest distance to " CD2 LEU A 297 " =    1.135
peak=   -3.185 closest distance to " CB  TRP A  85 " =    2.592
peak=   -3.182 closest distance to " O   HOH Z  15 " =    0.740
peak=   -3.179 closest distance to " O   HOH Z  12 " =    1.736
peak=   -3.177 closest distance to " CA  ARG A  56 " =    1.231
peak=   -3.169 closest distance to " CD2 LEU A 237 " =    2.561
peak=   -3.165 closest distance to " OD1 ASN A 249 " =    1.553
peak=   -3.162 closest distance to " O   GLN A 194 " =    1.389
peak=   -3.162 closest distance to " ND2 ASN A 285 " =    2.242
peak=   -3.158 closest distance to " CZ3 TRP A  92 " =    1.064
peak=   -3.157 closest distance to " CA  TYR A  68 " =    2.529
peak=   -3.157 closest distance to " NE  ARG A 269 " =    1.716
peak=   -3.153 closest distance to " CG  LEU A 281 " =    1.527
peak=   -3.133 closest distance to " N   SER A  28 " =    1.096
peak=   -3.133 closest distance to " C   LEU A 143 " =    1.290
peak=   -3.130 closest distance to " CB  ALA A 244 " =    1.923
peak=   -3.130 closest distance to " O   HOH Z 205 " =    1.234
peak=   -3.125 closest distance to " O   HOH Z 158 " =    1.605
peak=   -3.125 closest distance to " CB  PHE A 283 " =    2.289
peak=   -3.124 closest distance to " O   HOH Z 137 " =    1.490
peak=   -3.121 closest distance to " O   HOH Z  58 " =    0.947
peak=   -3.120 closest distance to " CA  VAL A 296 " =    1.032
peak=   -3.111 closest distance to " OD1 ASN A  39 " =    2.099
peak=   -3.104 closest distance to " O   HOH Z  92 " =    1.519
peak=   -3.094 closest distance to " O   HOH Z 426 " =    1.588
peak=   -3.088 closest distance to " O   HOH Z 345 " =    2.288
peak=   -3.083 closest distance to " O   HOH Z 109 " =    3.922
peak=   -3.067 closest distance to " O   ASN A 301 " =    1.224
peak=   -3.064 closest distance to " O   HOH Z 165 " =    2.346
peak=   -3.064 closest distance to " O   HOH Z 231 " =    1.140
peak=   -3.059 closest distance to " CD  ARG A 156 " =    1.857
peak=   -3.045 closest distance to " O   HOH Z 392 " =    3.169
peak=   -3.034 closest distance to " CG  ASN A  45 " =    1.748
peak=   -3.010 closest distance to " O   HOH Z  40 " =    4.230
peak=   -3.004 closest distance to " O   HOH Z 220 " =    1.369

================= 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    :  0.5097 0.5114   6.305656e+00   6.303035e+00
   1_bss:  0.5020 0.4991   6.300942e+00   6.295579e+00
   1_xyz:  0.4517 0.4728   6.250417e+00   6.271816e+00
   1_adp:  0.4162 0.4729   6.214761e+00   6.271231e+00
   1_occ:  0.4162 0.4737   6.214832e+00   6.271374e+00
   2_bss:  0.4140 0.4697   6.215785e+00   6.269602e+00
   2_xyz:  0.3638 0.4349   6.119912e+00   6.222882e+00
   2_adp:  0.3473 0.4211   6.095729e+00   6.205959e+00
   2_occ:  0.3471 0.4211   6.095514e+00   6.206070e+00
   3_bss:  0.3458 0.4207   6.096854e+00   6.206718e+00
   3_xyz:  0.2875 0.3590   5.950811e+00   6.096333e+00
   3_adp:  0.2616 0.3452   5.890700e+00   6.068401e+00
   3_occ:  0.2613 0.3452   5.890396e+00   6.068309e+00
   4_bss:  0.2606 0.3442   5.889519e+00   6.067186e+00
   4_xyz:  0.2048 0.2748   5.686768e+00   5.898512e+00
   4_adp:  0.1811 0.2523   5.586382e+00   5.815104e+00
   4_occ:  0.1808 0.2519   5.585051e+00   5.813514e+00
   5_bss:  0.1806 0.2507   5.580774e+00   5.809970e+00
   5_xyz:  0.1512 0.2091   5.412926e+00   5.652521e+00
   5_adp:  0.1412 0.1960   5.349764e+00   5.585805e+00
   5_occ:  0.1410 0.1955   5.348582e+00   5.584084e+00
   5_bss:  0.1417 0.1953   5.348945e+00   5.583580e+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:  0.360   0.000   6.394   8.802   8.606   0.000   0.000   0.000
   1_xyz:  0.360   0.000   6.394   8.802   8.606   0.000   0.000   0.000
   1_adp:  0.360   0.000   6.394   8.802   8.606   0.000   0.000   0.000
   1_occ:  0.360   0.000   6.394   8.802   8.606   0.000   0.000   0.000
   2_bss:  0.359  33.670   2.892   4.343   5.115   0.000   0.000   0.000
   2_xyz:  0.359  33.670   2.892   4.343   5.115   0.000   0.000   0.000
   2_adp:  0.359  33.670   2.892   4.343   5.115   0.000   0.000   0.000
   2_occ:  0.359  33.670   2.892   4.343   5.115   0.000   0.000   0.000
   3_bss:  0.335  37.292   1.630   2.175   2.847   0.000   0.000   0.000
   3_xyz:  0.335  37.292   1.630   2.175   2.847   0.000   0.000   0.000
   3_adp:  0.335  37.292   1.630   2.175   2.847   0.000   0.000   0.000
   3_occ:  0.335  37.292   1.630   2.175   2.847   0.000   0.000   0.000
   4_bss:  0.338  46.987   0.660   0.679   1.488   0.000   0.000   0.000
   4_xyz:  0.338  46.987   0.660   0.679   1.488   0.000   0.000   0.000
   4_adp:  0.338  46.987   0.660   0.679   1.488   0.000   0.000   0.000
   4_occ:  0.338  46.987   0.660   0.679   1.488   0.000   0.000   0.000
   5_bss:  0.321  45.050   0.158  -0.224   0.765  -0.000   0.000   0.000
   5_xyz:  0.321  45.050   0.158  -0.224   0.765  -0.000   0.000   0.000
   5_adp:  0.321  45.050   0.158  -0.224   0.765  -0.000   0.000   0.000
   5_occ:  0.321  45.050   0.158  -0.224   0.765  -0.000   0.000   0.000
   5_bss:  0.311  39.160  -0.230  -0.554   0.383  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.848 0.3180  0.3889    85293.058
   1_bss:  65.281 0.3242  0.4896    81985.298
   1_xyz:  59.995 0.3917  0.5800    71231.902
   1_adp:  59.767 0.3944  0.6556    70891.592
   1_occ:  59.920 0.3925  0.6525    71358.910
   2_bss:  59.698 0.3952  0.5863    70784.831
   2_xyz:  51.648 0.4975  0.7424    56355.378
   2_adp:  48.118 0.5428  0.8238    52217.516
   2_occ:  48.138 0.5425  0.8232    52223.650
   3_bss:  48.075 0.5433  0.7716    52299.067
   3_xyz:  38.186 0.6634  0.9208    35095.030
   3_adp:  35.922 0.6898  0.9432    31556.168
   3_occ:  35.952 0.6895  0.9421    31574.928
   4_bss:  35.919 0.6899  0.9002    31570.602
   4_xyz:  28.296 0.7758  0.9760    20162.525
   4_adp:  24.962 0.8122  0.9835    16710.162
   4_occ:  24.918 0.8126  0.9833    16628.625
   5_bss:  24.784 0.8136  0.9588    16375.222
   5_xyz:  20.277 0.8587  0.9906    11402.711
   5_adp:  18.394 0.8773  0.9930     9958.456
   5_occ:  18.355 0.8776  0.9930     9918.044
   5_bss:  18.354 0.8776  0.9792     9897.073
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2901e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2901e+01
   1_xyz:   1.681  0.013  0.105 18.475  0.007  4.105   1.4345e-01
   1_adp:   1.681  0.013  0.105 18.475  0.007  4.105   1.4345e-01
   1_occ:   1.681  0.013  0.105 18.475  0.007  4.105   1.4345e-01
   2_bss:   1.681  0.013  0.105 18.475  0.007  4.105   1.4345e-01
   2_xyz:   1.224  0.009  0.087 16.909  0.005  4.102   1.0138e-01
   2_adp:   1.224  0.009  0.087 16.909  0.005  4.102   1.0138e-01
   2_occ:   1.224  0.009  0.087 16.909  0.005  4.102   1.0138e-01
   3_bss:   1.224  0.009  0.087 16.909  0.005  4.102   1.0138e-01
   3_xyz:   1.157  0.008  0.085 16.153  0.004  4.106   7.8412e-02
   3_adp:   1.157  0.008  0.085 16.153  0.004  4.106   7.8412e-02
   3_occ:   1.157  0.008  0.085 16.153  0.004  4.106   7.8412e-02
   4_bss:   1.157  0.008  0.085 16.153  0.004  4.106   7.8412e-02
   4_xyz:   1.076  0.008  0.076 15.678  0.005  4.113   7.8614e-02
   4_adp:   1.076  0.008  0.076 15.678  0.005  4.113   7.8614e-02
   4_occ:   1.076  0.008  0.076 15.678  0.005  4.113   7.8614e-02
   5_bss:   1.076  0.008  0.076 15.678  0.005  4.113   7.8614e-02
   5_xyz:   1.005  0.006  0.071 15.348  0.003  4.106   6.1388e-02
   5_adp:   1.005  0.006  0.071 15.348  0.003  4.106   6.1388e-02
   5_occ:   1.005  0.006  0.071 15.348  0.003  4.106   6.1388e-02
   5_bss:   1.005  0.006  0.071 15.348  0.003  4.106   6.1388e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8542e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8542e+00
   1_xyz:  12.875  0.172  0.426 85.049  0.053  2.064   9.4020e-02
   1_adp:  12.875  0.172  0.426 85.049  0.053  2.064   9.4020e-02
   1_occ:  12.875  0.172  0.426 85.049  0.053  2.064   9.4020e-02
   2_bss:  12.875  0.172  0.426 85.049  0.053  2.064   9.4020e-02
   2_xyz:   7.839  0.080  0.366 75.511  0.044  2.135   5.5765e-02
   2_adp:   7.839  0.080  0.366 75.511  0.044  2.135   5.5765e-02
   2_occ:   7.839  0.080  0.366 75.511  0.044  2.135   5.5765e-02
   3_bss:   7.839  0.080  0.366 75.511  0.044  2.135   5.5765e-02
   3_xyz:   8.034  0.062  0.298 69.996  0.043  2.281   7.1209e-02
   3_adp:   8.034  0.062  0.298 69.996  0.043  2.281   7.1209e-02
   3_occ:   8.034  0.062  0.298 69.996  0.043  2.281   7.1209e-02
   4_bss:   8.034  0.062  0.298 69.996  0.043  2.281   7.1209e-02
   4_xyz:   6.939  0.061  0.299 84.742  0.037  2.290   1.6602e-01
   4_adp:   6.939  0.061  0.299 84.742  0.037  2.290   1.6602e-01
   4_occ:   6.939  0.061  0.299 84.742  0.037  2.290   1.6602e-01
   5_bss:   6.939  0.061  0.299 84.742  0.037  2.290   1.6602e-01
   5_xyz:   6.712  0.042  0.387 82.273  0.026  2.338   3.8796e-02
   5_adp:   6.712  0.042  0.387 82.273  0.026  2.338   3.8796e-02
   5_occ:   6.712  0.042  0.387 82.273  0.026  2.338   3.8796e-02
   5_bss:   6.712  0.042  0.387 82.273  0.026  2.338   3.8796e-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: 116.10   0.00  17.47  92.84   0.00  16.33 116.10   0.00  23.71
   1_occ: 116.10   0.00  17.47  92.84   0.00  16.33 116.10   0.00  23.71
   2_bss: 116.10   0.00  17.47  92.84   0.00  16.33 116.10   0.00  23.71
   2_xyz: 116.10   0.00  17.47  92.84   0.00  16.33 116.10   0.00  23.71
   2_adp: 112.41   0.00  16.42  95.39   0.00  14.63 112.41   0.00  26.15
   2_occ: 112.41   0.00  16.42  95.39   0.00  14.63 112.41   0.00  26.15
   3_bss: 112.41   0.00  16.42  95.39   0.00  14.63 112.41   0.00  26.15
   3_xyz: 112.41   0.00  16.42  95.39   0.00  14.63 112.41   0.00  26.15
   3_adp: 116.61   0.00  17.42 107.95   0.00  13.97 116.61   0.00  36.18
   3_occ: 116.61   0.00  17.42 107.95   0.00  13.97 116.61   0.00  36.18
   4_bss: 116.61   0.00  17.42 107.95   0.00  13.97 116.61   0.00  36.18
   4_xyz: 116.61   0.00  17.42 107.95   0.00  13.97 116.61   0.00  36.18
   4_adp: 122.67   0.00  17.05 108.08   0.00  12.03 122.67   3.20  44.39
   4_occ: 122.67   0.00  17.05 108.08   0.00  12.03 122.67   3.20  44.39
   5_bss: 122.67   0.00  17.05 108.08   0.00  12.03 122.67   3.20  44.39
   5_xyz: 122.67   0.00  17.05 108.08   0.00  12.03 122.67   3.20  44.39
   5_adp: 121.51   0.00  16.42 109.08   0.00  11.32 121.51   4.41  44.22
   5_occ: 121.51   0.00  16.42 109.08   0.00  11.32 121.51   4.41  44.22
   5_bss: 121.51   0.00  16.42 109.08   0.00  11.32 121.51   4.42  44.23
------------------------------------------------------------------------
 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:    1.259    0.023    0.406
   1_adp:    1.259    0.023    0.406
   1_occ:    1.259    0.023    0.406
   2_bss:    1.259    0.023    0.406
   2_xyz:    1.682    0.038    0.575
   2_adp:    1.682    0.038    0.575
   2_occ:    1.682    0.038    0.575
   3_bss:    1.682    0.038    0.575
   3_xyz:    1.698    0.053    0.695
   3_adp:    1.698    0.053    0.695
   3_occ:    1.698    0.053    0.695
   4_bss:    1.698    0.053    0.695
   4_xyz:    1.897    0.036    0.825
   4_adp:    1.897    0.036    0.825
   4_occ:    1.897    0.036    0.825
   5_bss:    1.897    0.036    0.825
   5_xyz:    2.148    0.069    0.887
   5_adp:    2.148    0.069    0.887
   5_occ:    2.148    0.069    0.887
   5_bss:    2.148    0.069    0.887
------------------------------------------------------------------------

CPU time actual refinement: 356.33


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_737/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_737/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_737/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_737/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_737/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.17 
  Macro-tasks:
    bulk solvent and scale       = 42.69  
    individual site refinement   = 149.14 
    weights calculation          = 32.80  
    collect and process          = 6.32   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 231.10 
  Micro-tasks:
    mask                            = 3.06   
    f_calc                          = 114.55 
    alpha_beta                      = 8.21   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 121.98 
    fmodel                         = 7.05   
    r_factors                      = 0.21   
    phase_errors                   = 9.65   
    foms                           = 0.37   
    TOTAL for micro-tasks          = 266.22 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.082 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    618 calls, 114.23 s
gradients_fft:          562 calls, 109.66 s

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

# Date 2008-01-16 Time 02:19:33 PST -0800 (1200478773.93 s)
Start R-work = 0.5097, R-free = 0.5114 (no bulk solvent and anisotropic scale)
Final R-work = 0.1563, R-free = 0.2107 (no bulk solvent and anisotropic scale)

Start R-work = 0.5020, R-free = 0.4991
Final R-work = 0.1417, R-free = 0.1953