# Date 2008-01-16 Time 01:50:45 PST -0800 (1200477045.35 s)
#phil __OFF__

Command line arguments: "../581.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 = 7610
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 581

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.6339, 88.1178, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99077
Completeness in resolution range: 0.944458
Completeness with d_max=infinity: 0.941553

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9908

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99077
Completeness in resolution range: 0.944458
Completeness with d_max=infinity: 0.941553

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2594 [2183/2211]  1962   221  10.1%
  bin  2:  4.2594 -  3.3937 [2078/2097]  1870   208  10.0%
  bin  3:  3.3937 -  2.9684 [2078/2098]  1874   204   9.8%
  bin  4:  2.9684 -  2.6987 [2040/2065]  1833   207  10.1%
  bin  5:  2.6987 -  2.5063 [2022/2041]  1822   200   9.9%
  bin  6:  2.5063 -  2.3591 [2015/2061]  1811   204  10.1%
  bin  7:  2.3591 -  2.2413 [2016/2050]  1819   197   9.8%
  bin  8:  2.2413 -  2.1441 [2009/2044]  1799   210  10.5%
  bin  9:  2.1441 -  2.0617 [2005/2035]  1812   193   9.6%
  bin 10:  2.0617 -  1.9908 [1143/2039]  1028   115  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_581/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:
        1.58 -     2.25: 11
        2.25 -     2.91: 1411
        2.91 -     3.57: 4389
        3.57 -     4.24: 9047
        4.24 -     4.90: 13032
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.585 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.840 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.896 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.913 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27885 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_581/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_581/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.63395 88.1178 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: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4892   r_free= 0.4769   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.289887                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7506 0.99   1414  157 0.3915 0.3831      6.6003      6.5736|
|  2:  4.7506 -  3.7906 0.99   1363  153 0.4130 0.4663      6.7963      6.9443|
|  3:  3.7906 -  3.3173 0.99   1334  150 0.4569 0.4178      6.6988      6.6378|
|  4:  3.3173 -  3.0167 0.99   1327  138 0.4779 0.4402      6.5277      6.4812|
|  5:  3.0167 -  2.8020 0.99   1311  150 0.5244 0.4724      6.3848      6.3993|
|  6:  2.8020 -  2.6377 0.98   1307  147 0.5208 0.5519      6.2829      6.1987|
|  7:  2.6377 -  2.5063 0.99   1305  145 0.5035 0.4492      6.2308      6.1294|
|  8:  2.5063 -  2.3976 0.98   1303  146 0.5367 0.4674      6.2015      6.1621|
|  9:  2.3976 -  2.3057 0.98   1304  143 0.5344 0.5941      6.1228      6.1923|
| 10:  2.3057 -  2.2264 0.98   1279  141 0.5577 0.4707      6.1216      6.0715|
| 11:  2.2264 -  2.1569 0.99   1309  146 0.5230 0.5380      6.0253      6.0588|
| 12:  2.1569 -  2.0955 0.98   1279  145 0.5384 0.5509      5.9636      6.0027|
| 13:  2.0955 -  2.0404 0.97   1280  131 0.5445 0.5074      5.8925      5.8173|
| 14:  2.0404 -  1.9908 0.40    515   67 0.5464 0.5254      5.8867      5.7664|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7506  1414   157  0.70  34.65   0.80     0.70      71130.51|
|  2:  4.7506 -  3.7906  1363   153  0.68  36.57   0.87     0.73     111615.96|
|  3:  3.7906 -  3.3173  1334   150  0.59  44.92   0.80     0.69     117979.39|
|  4:  3.3173 -  3.0167  1327   138  0.50  51.74   0.78     0.58     101092.20|
|  5:  3.0167 -  2.8020  1311   150  0.42  57.99   0.72     0.49      80334.38|
|  6:  2.8020 -  2.6377  1307   147  0.40  60.12   0.71     0.46      70086.51|
|  7:  2.6377 -  2.5063  1305   145  0.41  59.03   0.74     0.46      61843.69|
|  8:  2.5063 -  2.3976  1303   146  0.42  58.03   0.72     0.49      53641.63|
|  9:  2.3976 -  2.3057  1304   143  0.39  60.34   0.69     0.47      51647.76|
| 10:  2.3057 -  2.2264  1279   141  0.35  63.64   0.71     0.42      49635.30|
| 11:  2.2264 -  2.1569  1309   146  0.30  67.38   0.74     0.38      49138.24|
| 12:  2.1569 -  2.0955  1279   145  0.29  68.61   0.74     0.37      44905.28|
| 13:  2.0955 -  2.0404  1280   131  0.28  68.79   0.70     0.35      38427.67|
| 14:  2.0404 -  1.9908   515    67  0.30  67.58   0.72     0.32      30001.10|
|alpha:            min =        0.32 max =            0.73 mean =         0.50|
|beta:             min =    30001.10 max =       117979.39 mean =     68575.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.36|
|phase err.(test): min =        0.00 max =           89.84 mean =        56.63|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.862114             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.880   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.323102              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.924   (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:       31 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1490 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2576 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3855 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4997 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6498 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7653 |
|-----------------------------------------------------------------------------|
|-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 |       54.308 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.801 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    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 = 12.179)------------------------------------------|
|    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: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4952   r_free= 0.4801   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.291760                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4808   r_free= 0.4704   ksol= 0.29   Bsol= 0.00   scale= 0.990    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.61,10.27,11.15,0.00,0.00,0.00); trace/3= 9.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.281624                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.522787             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.039   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.250599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.810   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4808      final r-factor (work) = 0.3998          |
| start r-factor (free) = 0.4704      final r-factor (free) = 0.4205          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.8350 = 13.52 * 0.50 * 6.2897 + 1.00 * 54.3081                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.0721 = 13.52 * 0.50 * 6.2006 + 1.00 * 0.1476                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3998      final r-factor (work) = 0.3550          |
| start r-factor (free) = 0.4205      final r-factor (free) = 0.4076          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7688 = 1.25 * 1.00 * 6.2006 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6691 = 1.25 * 1.00 * 6.1166 + 1.00 * 0.0197                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.87   14.17    None  None   None       |
|    all(noH): 2823   0      0.00    99.87   14.17    None  None   None       |
|    Sol.    : 438    0      0.00    99.87   27.30    None  None   None       |
|    Mac.    : 2385   0      0.00    77.57   11.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.987: 1376   |   5:    49.933 -  59.919:   39        |
|      1:     9.987 -  19.973:  743   |   6:    59.919 -  69.906:   13        |
|      2:    19.973 -  29.960:  384   |   7:    69.906 -  79.892:    8        |
|      3:    29.960 -  39.946:  173   |   8:    79.892 -  89.879:    4        |
|      4:    39.946 -  49.933:   81   |   9:    89.879 -  99.865:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3550 r_free = 0.4076             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3543 r_free = 0.4079             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3543   r_free= 0.4079   ksol= 0.29   Bsol= 0.00   scale= 1.106    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.61,10.27,11.15,0.00,0.00,0.00); trace/3= 9.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.100122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3507   r_free= 0.4003   ksol= 0.33   Bsol= 50.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,6.16,6.97,0.00,0.00,0.00); trace/3= 5.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.099962                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.157101             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.575   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.476273              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.506  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3507      final r-factor (work) = 0.2546          |
| start r-factor (free) = 0.4003      final r-factor (free) = 0.3075          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.2483 = 11.16 * 0.50 * 6.1128 + 1.00 * 0.1476                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.3809 = 11.16 * 0.50 * 5.9651 + 1.00 * 0.1042                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2546      final r-factor (work) = 0.2252          |
| start r-factor (free) = 0.3075      final r-factor (free) = 0.2754          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8612 = 0.48 * 1.00 * 5.9651 + 1.00 * 0.0202                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7636 = 0.48 * 1.00 * 5.7774 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.11   13.29    None  None   None       |
|    all(noH): 2823   0      0.00    91.11   13.29    None  None   None       |
|    Sol.    : 438    0      0.00    91.11   33.01    None  None   None       |
|    Mac.    : 2385   0      0.00    70.19   9.66     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.112: 1457   |   5:    45.557 -  54.669:   72        |
|      1:     9.112 -  18.223:  732   |   6:    54.669 -  63.780:   23        |
|      2:    18.223 -  27.334:  247   |   7:    63.780 -  72.891:    9        |
|      3:    27.334 -  36.446:  183   |   8:    72.891 -  82.003:    5        |
|      4:    36.446 -  45.557:   93   |   9:    82.003 -  91.114:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2252 r_free = 0.2754             target_work(ml) = 5.734         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2249 r_free = 0.2756             target_work(ml) = 5.733         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2249   r_free= 0.2756   ksol= 0.33   Bsol= 50.00   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,6.16,6.97,0.00,0.00,0.00); trace/3= 5.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.733190                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2228   r_free= 0.2751   ksol= 0.31   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,3.51,4.32,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.733591                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.531334              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.150  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.193710              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.718  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2228      final r-factor (work) = 0.1633          |
| start r-factor (free) = 0.2751      final r-factor (free) = 0.2046          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2110 = 4.53 * 0.50 * 5.7849 + 1.00 * 0.1042                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8005 = 4.53 * 0.50 * 5.6170 + 1.00 * 0.0743                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1633      final r-factor (work) = 0.1521          |
| start r-factor (free) = 0.2046      final r-factor (free) = 0.1915          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1022 = 0.19 * 1.00 * 5.6170 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0903 = 0.19 * 1.00 * 5.4171 + 1.00 * 0.0410                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.90   12.93    None  None   None       |
|    all(noH): 2823   0      0.00    85.90   12.93    None  None   None       |
|    Sol.    : 438    0      1.90    85.90   34.08    None  None   None       |
|    Mac.    : 2385   0      0.00    70.98   9.05     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.590: 1513   |   5:    42.952 -  51.542:   87        |
|      1:     8.590 -  17.181:  724   |   6:    51.542 -  60.132:   40        |
|      2:    17.181 -  25.771:  177   |   7:    60.132 -  68.723:   13        |
|      3:    25.771 -  34.361:  129   |   8:    68.723 -  77.313:    4        |
|      4:    34.361 -  42.952:  134   |   9:    77.313 -  85.903:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1521 r_free = 0.1915             target_work(ml) = 5.388         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1518 r_free = 0.1917             target_work(ml) = 5.388         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1518   r_free= 0.1917   ksol= 0.31   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,3.51,4.32,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.387648                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1512   r_free= 0.1913   ksol= 0.33   Bsol= 50.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.00,2.30,3.41,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.386483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.481703              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.954  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.053648              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.576   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1512      final r-factor (work) = 0.1318          |
| start r-factor (free) = 0.1913      final r-factor (free) = 0.1738          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8025 = 2.48 * 0.50 * 5.4222 + 1.00 * 0.0743                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6818 = 2.48 * 0.50 * 5.3278 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1318      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1738      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6339 = 1.05 * 1.00 * 5.3278 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5486 = 1.05 * 1.00 * 5.2532 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.97   13.58    None  None   None       |
|    all(noH): 2823   0      0.00    87.97   13.58    None  None   None       |
|    Sol.    : 438    0      2.01    87.97   38.36    None  None   None       |
|    Mac.    : 2385   0      0.00    81.95   9.03     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 -   8.797: 1569   |   5:    43.985 -  52.783:   90        |
|      1:     8.797 -  17.594:  666   |   6:    52.783 -  61.580:   64        |
|      2:    17.594 -  26.391:  164   |   7:    61.580 -  70.377:   42        |
|      3:    26.391 -  35.188:  113   |   8:    70.377 -  79.174:   13        |
|      4:    35.188 -  43.985:   99   |   9:    79.174 -  87.971:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1260 r_free = 0.1727             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1259 r_free = 0.1725             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1725   ksol= 0.33   Bsol= 50.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.00,2.30,3.41,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250585                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1727   ksol= 0.33   Bsol= 64.98   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.19,2.18,3.40,0.00,0.00,0.00); trace/3= 2.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250588                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.564465              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.964  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.003269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.228  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1260      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1727      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8060 = 2.56 * 0.50 * 5.2528 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7781 = 2.56 * 0.50 * 5.2298 + 1.00 * 0.0723                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2604 = 1.00 * 1.00 * 5.2298 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2403 = 1.00 * 1.00 * 5.2092 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.09   13.43    None  None   None       |
|    all(noH): 2823   0      0.00    90.09   13.43    None  None   None       |
|    Sol.    : 438    0      1.58    90.09   38.30    None  None   None       |
|    Mac.    : 2385   0      0.00    84.30   8.87     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.009: 1640   |   5:    45.045 -  54.054:   91        |
|      1:     9.009 -  18.018:  603   |   6:    54.054 -  63.063:   57        |
|      2:    18.018 -  27.027:  172   |   7:    63.063 -  72.071:   37        |
|      3:    27.027 -  36.036:  109   |   8:    72.071 -  81.080:   13        |
|      4:    36.036 -  45.045:   99   |   9:    81.080 -  90.089:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1675             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1193 r_free = 0.1675             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1675   ksol= 0.33   Bsol= 64.98   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.19,2.18,3.40,0.00,0.00,0.00); trace/3= 2.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209483                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7506 0.99   1414  157 0.1002 0.1322      5.4068      5.5587|
|  2:  4.7506 -  3.7906 0.99   1363  153 0.0871 0.1069      5.4435      5.6464|
|  3:  3.7906 -  3.3173 0.99   1334  150 0.1105 0.1539      5.5041      5.8562|
|  4:  3.3173 -  3.0167 0.99   1327  138 0.1276 0.1728      5.4946       5.673|
|  5:  3.0167 -  2.8020 0.99   1311  150 0.1441 0.1744      5.4096      5.5756|
|  6:  2.8020 -  2.6377 0.98   1307  147 0.1370 0.2311      5.2997      5.6097|
|  7:  2.6377 -  2.5063 0.99   1305  145 0.1392 0.1664      5.2529      5.3854|
|  8:  2.5063 -  2.3976 0.98   1303  146 0.1226 0.1828      5.1499      5.3924|
|  9:  2.3976 -  2.3057 0.98   1304  143 0.1287 0.2147       5.098      5.4519|
| 10:  2.3057 -  2.2264 0.98   1279  141 0.1240 0.1664      5.0446      5.1761|
| 11:  2.2264 -  2.1569 0.99   1309  146 0.1232 0.1937      4.9922      5.3235|
| 12:  2.1569 -  2.0955 0.98   1279  145 0.1193 0.1842      4.9328      5.2393|
| 13:  2.0955 -  2.0404 0.97   1280  131 0.1186 0.1749      4.8314      5.0412|
| 14:  2.0404 -  1.9908 0.40    515   67 0.1046 0.1956      4.7234       5.014|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7506  1414   157  0.94   9.37   0.96     0.94       7632.43|
|  2:  4.7506 -  3.7906  1363   153  0.95   8.40   1.00     0.99       9251.78|
|  3:  3.7906 -  3.3173  1334   150  0.93  11.72   1.02     1.01      10908.29|
|  4:  3.3173 -  3.0167  1327   138  0.92  14.20   1.00     0.98      11163.40|
|  5:  3.0167 -  2.8020  1311   150  0.89  17.63   0.99     0.96       9814.27|
|  6:  2.8020 -  2.6377  1307   147  0.88  18.56   0.97     0.94       8712.04|
|  7:  2.6377 -  2.5063  1305   145  0.89  17.09   0.98     0.94       7322.94|
|  8:  2.5063 -  2.3976  1303   146  0.89  16.85   0.98     0.94       6452.76|
|  9:  2.3976 -  2.3057  1304   143  0.89  17.37   0.99     0.95       5776.73|
| 10:  2.3057 -  2.2264  1279   141  0.88  17.75   0.98     0.93       5343.45|
| 11:  2.2264 -  2.1569  1309   146  0.89  17.75   0.97     0.93       4951.15|
| 12:  2.1569 -  2.0955  1279   145  0.90  16.93   0.99     0.98       4510.43|
| 13:  2.0955 -  2.0404  1280   131  0.89  17.30   0.97     0.95       3713.66|
| 14:  2.0404 -  1.9908   515    67  0.91  15.41   0.94     0.90       2894.71|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     2894.71 max =        11163.40 mean =      7251.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.38|
|phase err.(test): min =        0.00 max =           87.40 mean =        14.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1673   ksol= 0.32   Bsol= 64.71   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,-0.11,1.12,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209549                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1673   ksol= 0.32   Bsol= 64.71   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,-0.11,1.12,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209549                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7506 0.99   1414  157 0.1001 0.1322      5.4055      5.5582|
|  2:  4.7506 -  3.7906 0.99   1363  153 0.0870 0.1067      5.4429       5.645|
|  3:  3.7906 -  3.3173 0.99   1334  150 0.1105 0.1539      5.5039      5.8568|
|  4:  3.3173 -  3.0167 0.99   1327  138 0.1277 0.1729      5.4951      5.6734|
|  5:  3.0167 -  2.8020 0.99   1311  150 0.1442 0.1744      5.4102      5.5759|
|  6:  2.8020 -  2.6377 0.98   1307  147 0.1370 0.2313         5.3      5.6101|
|  7:  2.6377 -  2.5063 0.99   1305  145 0.1392 0.1667      5.2534      5.3862|
|  8:  2.5063 -  2.3976 0.98   1303  146 0.1226 0.1828      5.1505      5.3928|
|  9:  2.3976 -  2.3057 0.98   1304  143 0.1287 0.2147      5.0984      5.4521|
| 10:  2.3057 -  2.2264 0.98   1279  141 0.1240 0.1664      5.0449      5.1765|
| 11:  2.2264 -  2.1569 0.99   1309  146 0.1232 0.1935      4.9922      5.3231|
| 12:  2.1569 -  2.0955 0.98   1279  145 0.1193 0.1841      4.9326      5.2389|
| 13:  2.0955 -  2.0404 0.97   1280  131 0.1186 0.1748      4.8314      5.0412|
| 14:  2.0404 -  1.9908 0.40    515   67 0.1046 0.1954      4.7241      5.0139|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7506  1414   157  0.94   9.36   0.96     0.94       7611.63|
|  2:  4.7506 -  3.7906  1363   153  0.95   8.39   1.01     0.99       9235.69|
|  3:  3.7906 -  3.3173  1334   150  0.93  11.72   1.02     1.02      10900.61|
|  4:  3.3173 -  3.0167  1327   138  0.92  14.21   1.01     0.98      11172.80|
|  5:  3.0167 -  2.8020  1311   150  0.89  17.64   1.00     0.97       9825.84|
|  6:  2.8020 -  2.6377  1307   147  0.88  18.57   0.98     0.94       8718.53|
|  7:  2.6377 -  2.5063  1305   145  0.89  17.10   0.99     0.95       7331.32|
|  8:  2.5063 -  2.3976  1303   146  0.89  16.86   0.99     0.95       6459.23|
|  9:  2.3976 -  2.3057  1304   143  0.89  17.38   1.00     0.96       5783.32|
| 10:  2.3057 -  2.2264  1279   141  0.88  17.76   0.99     0.94       5343.68|
| 11:  2.2264 -  2.1569  1309   146  0.89  17.75   0.98     0.94       4949.95|
| 12:  2.1569 -  2.0955  1279   145  0.90  16.93   1.00     0.99       4509.76|
| 13:  2.0955 -  2.0404  1280   131  0.89  17.30   0.98     0.96       3712.86|
| 14:  2.0404 -  1.9908   515    67  0.91  15.43   0.96     0.91       2894.40|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2894.40 max =        11172.80 mean =      7251.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.38|
|phase err.(test): min =        0.00 max =           87.63 mean =        14.80|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.179)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.49    92.57   15.92    None  None   None       |
|    all(noH): 2823   0      2.49    92.57   15.92    None  None   None       |
|    Sol.    : 438    0      4.07    92.57   40.78    None  None   None       |
|    Mac.    : 2385   0      2.49    86.78   11.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.486 -  11.494: 1640   |   5:    47.530 -  56.539:   91        |
|      1:    11.494 -  20.503:  603   |   6:    56.539 -  65.548:   57        |
|      2:    20.503 -  29.512:  172   |   7:    65.548 -  74.557:   37        |
|      3:    29.512 -  38.521:  109   |   8:    74.557 -  83.566:   13        |
|      4:    38.521 -  47.530:   99   |   9:    83.566 -  92.575:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.213 - 5.365
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 319
   mapped sites are within: 0.717 - 5.365

peak=   10.623 closest distance to " CB  VAL A 230 " =    1.433
peak=    6.050 closest distance to " NH2 ARG A  56 " =    2.200
peak=    5.902 closest distance to " CG  LEU A   5 " =    1.199
peak=    5.883 closest distance to " O   HOH Z 210 " =    1.213
peak=    5.442 closest distance to " CB  GLN A 223 " =    1.449
peak=    5.270 closest distance to " CB  VAL A 296 " =    1.077
peak=    5.016 closest distance to " CB  SER A  63 " =    1.165
peak=    4.967 closest distance to " CG  LEU A 228 " =    1.206
peak=    4.886 closest distance to " CG2 VAL A 296 " =    1.014
peak=    4.817 closest distance to " O   HOH Z 403 " =    1.798
peak=    4.798 closest distance to " CG  PRO A  54 " =    1.352
peak=    4.795 closest distance to " CG  PRO A 280 " =    0.863
peak=    4.789 closest distance to " O   HOH Z 248 " =    1.507
peak=    4.752 closest distance to " O   HOH Z 128 " =    1.503
peak=    4.731 closest distance to " CB  PRO A  54 " =    0.977
peak=    4.633 closest distance to " CD2 LEU A   5 " =    1.116
peak=    4.622 closest distance to " CG1 VAL A 296 " =    1.169
peak=    4.581 closest distance to " CB  GLN A 183 " =    1.296
peak=    4.561 closest distance to " CB  ARG A 190 " =    1.757
peak=    4.544 closest distance to " CB  ARG A 275 " =    0.922
peak=    4.530 closest distance to " O   HOH Z 232 " =    2.281
peak=    4.511 closest distance to " NE2 GLN A  11 " =    1.111
peak=    4.483 closest distance to " O   HOH Z 251 " =    1.697
peak=    4.439 closest distance to " O   HOH Z 265 " =    2.004
peak=    4.421 closest distance to " CA  ALA A  51 " =    0.991
peak=    4.410 closest distance to " CA  TYR A  30 " =    0.950
peak=    4.390 closest distance to " CG  PRO A 198 " =    1.337
peak=    4.364 closest distance to " O   HOH Z 126 " =    1.623
peak=    4.353 closest distance to " O   HOH Z 142 " =    1.691
peak=    4.332 closest distance to " CZ  PHE A 218 " =    1.194
peak=    4.331 closest distance to " O   HOH Z 154 " =    1.669
peak=    4.292 closest distance to " CB  ASN A 142 " =    1.212
peak=    4.292 closest distance to " CD2 LEU A 228 " =    1.283
peak=    4.255 closest distance to " CG  PRO A 213 " =    1.204
peak=    4.242 closest distance to " CB  TRP A 179 " =    1.383
peak=    4.217 closest distance to " O   HOH Z 359 " =    1.857
peak=    4.190 closest distance to " O   SER A  87 " =    2.358
peak=    4.184 closest distance to " O   HOH Z 412 " =    3.817
peak=    4.183 closest distance to " O   HOH Z 365 " =    2.425
peak=    4.171 closest distance to " O   HOH Z 214 " =    1.359
peak=    4.169 closest distance to " O   HOH Z  43 " =    2.022
peak=    4.164 closest distance to " O   HOH Z  49 " =    1.290
peak=    4.155 closest distance to " O   HOH Z  76 " =    1.143
peak=    4.144 closest distance to " CD1AILE A 234 " =    0.933
peak=    4.142 closest distance to " CB  VAL A 230 " =    1.231
peak=    4.096 closest distance to " O   PRO A 198 " =    1.526
peak=    4.085 closest distance to " CD2 TRP A 179 " =    1.291
peak=    4.080 closest distance to " CB  GLU A 277 " =    3.762
peak=    4.074 closest distance to " CB  ARG A  79 " =    1.461
peak=    4.070 closest distance to " O   HOH Z 402 " =    1.488
peak=    4.062 closest distance to " O   HOH Z 238 " =    1.051
peak=    4.038 closest distance to " OG BSER A 164 " =    2.224
peak=    4.038 closest distance to " O   HOH Z 130 " =    2.641
peak=    4.034 closest distance to " CB  ASN A 148 " =    1.367
peak=    4.034 closest distance to " O   HOH Z 425 " =    1.482
peak=    4.028 closest distance to " CB  GLU A 128 " =    1.181
peak=    4.022 closest distance to " O   HOH Z 234 " =    3.652
peak=    4.003 closest distance to " O   HOH Z 369 " =    2.198
peak=    3.999 closest distance to " CG  PRO A 243 " =    1.143
peak=    3.990 closest distance to " O   HOH Z 346 " =    1.504
peak=    3.966 closest distance to " O   HOH Z 422 " =    2.638
peak=    3.960 closest distance to " CA  ALA A 295 " =    1.050
peak=    3.957 closest distance to " O   HOH Z  44 " =    2.240
peak=    3.945 closest distance to " O   HOH Z 303 " =    2.259
peak=    3.944 closest distance to " O   HOH Z 189 " =    2.866
peak=    3.933 closest distance to " CB  TRP A 266 " =    1.062
peak=    3.914 closest distance to " O   HOH Z 316 " =    3.186
peak=    3.911 closest distance to " CZ3 TRP A 266 " =    1.118
peak=    3.907 closest distance to " O   HOH Z 126 " =    2.018
peak=    3.905 closest distance to " CD  LYS A 166 " =    1.450
peak=    3.900 closest distance to " O   HOH Z  40 " =    1.911
peak=    3.882 closest distance to " CB  GLU A 152 " =    1.135
peak=    3.879 closest distance to " O   HOH Z  63 " =    1.944
peak=    3.867 closest distance to " O   ASP A 124 " =    1.279
peak=    3.861 closest distance to " ND2 ASN A 187 " =    1.653
peak=    3.860 closest distance to " O   ALA A 165 " =    1.399
peak=    3.860 closest distance to " O   HOH Z 199 " =    1.628
peak=    3.860 closest distance to " NZ  LYS A  48 " =    1.299
peak=    3.844 closest distance to " O   HOH Z 214 " =    2.571
peak=    3.809 closest distance to " CA  ARG A 195 " =    1.185
peak=    3.805 closest distance to " CB  TYR A 169 " =    0.799
peak=    3.803 closest distance to " O   HOH Z 261 " =    2.451
peak=    3.798 closest distance to " O   HOH Z 154 " =    2.285
peak=    3.793 closest distance to " O   HOH Z 427 " =    2.982
peak=    3.787 closest distance to " CE  LYS A  76 " =    0.866
peak=    3.782 closest distance to " CD  ARG A 269 " =    1.029
peak=    3.778 closest distance to " CB  GLU A  46 " =    0.974
peak=    3.776 closest distance to " O   HOH Z 280 " =    2.867
peak=    3.772 closest distance to " O   HOH Z 287 " =    1.820
peak=    3.771 closest distance to " CA  ARG A  36 " =    1.053
peak=    3.768 closest distance to " CD1 LEU A  96 " =    0.758
peak=    3.764 closest distance to " O   HOH Z 423 " =    1.814
peak=    3.761 closest distance to " O   HOH Z  80 " =    1.952
peak=    3.758 closest distance to " NH1AARG A 145 " =    1.372
peak=    3.754 closest distance to " CZ  PHE A  38 " =    1.157
peak=    3.739 closest distance to " CG  MET A 185 " =    1.173
peak=    3.719 closest distance to " O   HOH Z 298 " =    1.786
peak=    3.714 closest distance to " CB  SER A  26 " =    1.810
peak=    3.707 closest distance to " CB AVAL A  41 " =    1.203
peak=    3.686 closest distance to " NE2 GLN A  77 " =    3.319
peak=    3.686 closest distance to " CB  THR A  52 " =    0.846
peak=    3.683 closest distance to " ND2 ASN A 249 " =    0.898
peak=    3.662 closest distance to " CD  ARG A 159 " =    0.762
peak=    3.657 closest distance to " O   HOH Z  61 " =    1.632
peak=    3.654 closest distance to " OD1 ASN A  69 " =    2.507
peak=    3.650 closest distance to " CD1 ILE A 199 " =    1.075
peak=    3.646 closest distance to " NH2 ARG A 156 " =    1.182
peak=    3.645 closest distance to " CB  ALA A   9 " =    1.644
peak=    3.632 closest distance to " CD2 LEU A 297 " =    0.981
peak=    3.631 closest distance to " CG1 VAL A 153 " =    1.034
peak=    3.627 closest distance to " N   ASN A  39 " =    1.225
peak=    3.627 closest distance to " CB  PRO A  90 " =    1.182
peak=    3.626 closest distance to " CB  ASN A  39 " =    0.856
peak=    3.625 closest distance to " CA  ILE A 106 " =    0.776
peak=    3.625 closest distance to " O  BHOH Z 338 " =    2.228
peak=    3.620 closest distance to " CB  SER A   3 " =    1.343
peak=    3.619 closest distance to " CB  ARG A  79 " =    0.938
peak=    3.611 closest distance to " CA  ALA A 160 " =    0.963
peak=    3.603 closest distance to " O   HOH Z 285 " =    2.210
peak=    3.597 closest distance to " CA  VAL A  41 " =    0.743
peak=    3.595 closest distance to " O   TRP A 274 " =    1.838
peak=    3.593 closest distance to " O   HOH Z 353 " =    2.696
peak=    3.592 closest distance to " CE1 TYR A 186 " =    1.233
peak=    3.590 closest distance to " O   HOH Z 371 " =    2.760
peak=    3.588 closest distance to " CA  TYR A 116 " =    1.349
peak=    3.584 closest distance to " O   HOH Z 189 " =    2.959
peak=    3.584 closest distance to " O   HOH Z 433 " =    1.512
peak=    3.567 closest distance to " CB  THR A  31 " =    1.450
peak=    3.565 closest distance to " CB  VAL A 265 " =    1.294
peak=    3.562 closest distance to " O   HOH Z 130 " =    1.107
peak=    3.556 closest distance to " O   HOH Z  48 " =    1.705
peak=    3.555 closest distance to " O   HOH Z 193 " =    1.468
peak=    3.548 closest distance to " CB  VAL A 202 " =    1.518
peak=    3.548 closest distance to " CG2 ILE A 234 " =    1.099
peak=    3.539 closest distance to " O   HOH Z 247 " =    1.339
peak=    3.529 closest distance to " CB  GLN A  89 " =    1.149
peak=    3.525 closest distance to " O   ASN A  74 " =    2.031
peak=    3.519 closest distance to " CG1 ILE A  49 " =    1.602
peak=    3.514 closest distance to " CG AARG A 275 " =    1.277
peak=    3.513 closest distance to " O   HOH Z 361 " =    3.375
peak=    3.512 closest distance to " CB  ASP A 298 " =    1.177
peak=    3.512 closest distance to " O   HOH Z 258 " =    2.108
peak=    3.510 closest distance to " O   HOH Z 203 " =    1.753
peak=    3.504 closest distance to " CA  ALA A  21 " =    1.189
peak=    3.501 closest distance to " CG1 ILE A  33 " =    1.199
peak=    3.498 closest distance to " ND2 ASN A 249 " =    1.908
peak=    3.495 closest distance to " CB  LEU A  83 " =    0.751
peak=    3.493 closest distance to " CA  GLY A 267 " =    0.862
peak=    3.492 closest distance to " O   HOH Z  78 " =    1.670
peak=    3.484 closest distance to " CA  SER A  87 " =    1.039
peak=    3.480 closest distance to " O   HOH Z 393 " =    3.369
peak=    3.477 closest distance to " O   ASP A 200 " =    1.644
peak=    3.477 closest distance to " O   HOH Z 365 " =    2.701
peak=    3.476 closest distance to " OG  SER A 245 " =    1.560
peak=    3.470 closest distance to " O   HOH Z 391 " =    2.941
peak=    3.468 closest distance to " O   HOH Z 327 " =    2.645
peak=    3.460 closest distance to " CB  MET A  40 " =    0.876
peak=    3.459 closest distance to " CB  ASN A 285 " =    1.003
peak=    3.458 closest distance to " O   HOH Z 337 " =    1.842
peak=    3.458 closest distance to " O   HOH Z 406 " =    1.493
peak=    3.448 closest distance to " O   HOH Z 431 " =    1.061
peak=    3.446 closest distance to " O   HOH Z 417 " =    3.157
peak=    3.442 closest distance to " O   HOH Z  83 " =    1.485
peak=    3.433 closest distance to " O   HOH Z 383 " =    2.008
peak=    3.430 closest distance to " O   HOH Z 146 " =    1.544
peak=    3.429 closest distance to " O   HOH Z 124 " =    1.135
peak=    3.427 closest distance to " O   HOH Z  54 " =    1.629
peak=    3.423 closest distance to " O   ASP A 124 " =    1.780
peak=    3.422 closest distance to " O   HOH Z 407 " =    2.660
peak=    3.409 closest distance to " O   HOH Z   4 " =    1.702
peak=    3.399 closest distance to " CG2 ILE A  20 " =    1.336
peak=    3.397 closest distance to " CA  ASP A 191 " =    1.159
peak=    3.397 closest distance to " OG BSER A 134 " =    2.817
peak=    3.396 closest distance to " CZ3 TRP A  85 " =    0.930
peak=    3.393 closest distance to " O   HOH Z 158 " =    3.174
peak=    3.389 closest distance to " O   HOH Z 299 " =    4.297
peak=    3.387 closest distance to " CG1 ILE A  20 " =    1.229
peak=    3.386 closest distance to " CD  PRO A  54 " =    0.994
peak=    3.382 closest distance to " O   HOH Z 394 " =    1.488
peak=    3.377 closest distance to " O   HOH Z 145 " =    2.308
peak=    3.376 closest distance to " CD  ARG A 195 " =    1.019
peak=    3.376 closest distance to " O   HOH Z   3 " =    1.866
peak=    3.372 closest distance to " O   HOH Z 438 " =    2.901
peak=    3.372 closest distance to " O   HOH Z  35 " =    2.355
peak=    3.369 closest distance to " O   HOH Z 162 " =    1.476
peak=    3.367 closest distance to " O   HOH Z 437 " =    1.702
peak=    3.367 closest distance to " CB  ASP A 140 " =    1.126
peak=    3.365 closest distance to " CD1 LEU A   5 " =    1.357
peak=    3.364 closest distance to " O   HOH Z 313 " =    1.653
peak=    3.356 closest distance to " O   HOH Z 313 " =    1.714
peak=    3.352 closest distance to " CG  GLN A  58 " =    2.958
peak=    3.349 closest distance to " O   HOH Z 272 " =    1.873
peak=    3.344 closest distance to " CG  LEU A 167 " =    1.134
peak=    3.343 closest distance to " CB  GLN A  88 " =    1.214
peak=    3.343 closest distance to " O   HOH Z 102 " =    1.306
peak=    3.341 closest distance to " CA  LYS A 117 " =    1.279
peak=    3.340 closest distance to " CB  ALA A 248 " =    1.370
peak=    3.337 closest distance to " O   HOH Z 393 " =    3.772
peak=    3.336 closest distance to " CG2 THR A 221 " =    1.147
peak=    3.332 closest distance to " CB  ALA A  43 " =    0.887
peak=    3.332 closest distance to " CA  VAL A 125 " =    1.276
peak=    3.330 closest distance to " O   HOH Z 357 " =    2.189
peak=    3.322 closest distance to " O   HOH Z 435 " =    1.983
peak=    3.319 closest distance to " O   HOH Z 271 " =    2.349
peak=    3.319 closest distance to " OG  SER A 276 " =    1.340
peak=    3.319 closest distance to " CG  PHE A 204 " =    0.891
peak=    3.319 closest distance to " O   HOH Z 420 " =    5.365
peak=    3.315 closest distance to " OE1 GLU A   2 " =    1.814
peak=    3.314 closest distance to " O   HOH Z  19 " =    1.901
peak=    3.313 closest distance to " N   ASP A 162 " =    1.284
peak=    3.313 closest distance to " O   HOH Z 361 " =    3.679
peak=    3.307 closest distance to " CA  ALA A 158 " =    1.370
peak=    3.304 closest distance to " O   HOH Z 117 " =    1.981
peak=    3.303 closest distance to " O   HOH Z 245 " =    1.374
peak=    3.302 closest distance to " O   HOH Z  85 " =    1.295
peak=    3.299 closest distance to " O   HOH Z 187 " =    2.366
peak=    3.297 closest distance to " O   HOH Z 361 " =    2.644
peak=    3.292 closest distance to " O   HOH Z 148 " =    3.339
peak=    3.290 closest distance to " CG  ARG A 138 " =    1.306
peak=    3.287 closest distance to " CG  GLU A  37 " =    0.908
peak=    3.287 closest distance to " OD2 ASP A 298 " =    3.840
peak=    3.285 closest distance to " CB  SER A  62 " =    0.799
peak=    3.277 closest distance to " O   HOH Z 193 " =    1.663
peak=    3.277 closest distance to " CB  LYS A 117 " =    1.203
peak=    3.273 closest distance to " CA  LEU A 282 " =    1.151
peak=    3.272 closest distance to " CB  PHE A 204 " =    0.989
peak=    3.270 closest distance to " CG2AVAL A 121 " =    2.157
peak=    3.269 closest distance to " CG  MET A 185 " =    0.970
peak=    3.269 closest distance to " O   HOH Z 134 " =    1.320
peak=    3.268 closest distance to " OD1 ASN A 217 " =    1.805
peak=    3.267 closest distance to " NZ  LYS A 117 " =    3.012
peak=    3.266 closest distance to " O   HOH Z 185 " =    1.748
peak=    3.264 closest distance to " CD2 TYR A 186 " =    1.025
peak=    3.264 closest distance to " O   HOH Z 329 " =    4.152
peak=    3.263 closest distance to " O   HOH Z 327 " =    1.567
peak=    3.262 closest distance to " CB  THR A 235 " =    1.253
peak=    3.261 closest distance to " CA  ASN A 217 " =    1.219
peak=    3.261 closest distance to " O   HOH Z  97 " =    2.246
peak=    3.260 closest distance to " CB  PRO A 243 " =    1.265
peak=    3.258 closest distance to " O   HOH Z  21 " =    1.784
peak=    3.257 closest distance to " O   HOH Z 147 " =    1.784
peak=    3.257 closest distance to " CB  PHE A  16 " =    1.040
peak=    3.255 closest distance to " CB  MET A 105 " =    1.155
peak=    3.251 closest distance to " NH1 ARG A  14 " =    1.139
peak=    3.250 closest distance to " CA  ALA A 100 " =    0.914
peak=    3.247 closest distance to " CG  MET A 188 " =    0.821
peak=    3.245 closest distance to " CB  ASN A 215 " =    1.195
peak=    3.243 closest distance to " CB  SER A 273 " =    0.912
peak=    3.241 closest distance to " O   HOH Z  85 " =    1.826
peak=    3.234 closest distance to " CZ3 TRP A 274 " =    4.419
peak=    3.233 closest distance to " CA  LYS A 290 " =    1.178
peak=    3.225 closest distance to " O   HOH Z 357 " =    2.511
peak=    3.225 closest distance to " CB  PRO A 198 " =    1.070
peak=    3.224 closest distance to " O   HOH Z 345 " =    1.702
peak=    3.224 closest distance to " O   HOH Z 193 " =    1.743
peak=    3.221 closest distance to " O   HOH Z 180 " =    2.186
peak=    3.221 closest distance to " O   THR A 182 " =    1.473
peak=    3.219 closest distance to " O   HOH Z 301 " =    1.845
peak=    3.218 closest distance to " O   PRO A 213 " =    1.423
peak=    3.218 closest distance to " O   HOH Z 125 " =    3.936
peak=    3.216 closest distance to " CB  TYR A 247 " =    0.985
peak=    3.215 closest distance to " CB  SER A  62 " =    1.046
peak=    3.214 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.208 closest distance to " CB  GLU A 236 " =    1.164
peak=    3.208 closest distance to " CB  SER A 288 " =    1.427
peak=    3.208 closest distance to " O   HOH Z 133 " =    2.560
peak=    3.207 closest distance to " ND2 ASN A 301 " =    1.835
peak=    3.206 closest distance to " CB  SER A 210 " =    0.816
peak=    3.205 closest distance to " CA  MET A 105 " =    1.069
peak=    3.201 closest distance to " O   HOH Z 293 " =    1.925
peak=    3.200 closest distance to " CG2 ILE A 120 " =    1.231
peak=    3.200 closest distance to " O   ALA A 158 " =    1.240
peak=    3.197 closest distance to " CG2 THR A 220 " =    0.803
peak=    3.195 closest distance to " C   ILE A 106 " =    1.893
peak=    3.187 closest distance to " N   SER A 164 " =    0.913
peak=    3.186 closest distance to " O   HOH Z 213 " =    1.710
peak=    3.185 closest distance to " CG  GLN A  11 " =    1.498
peak=    3.183 closest distance to " O   HOH Z 193 " =    1.151
peak=    3.183 closest distance to " O   HOH Z 156 " =    2.501
peak=    3.174 closest distance to " CA  ARG A 139 " =    1.169
peak=    3.173 closest distance to " O   HOH Z 305 " =    3.544
peak=    3.172 closest distance to " CE3 TRP A 150 " =    1.104
peak=    3.171 closest distance to " CZ  PHE A 192 " =    1.111
peak=    3.162 closest distance to " O   HOH Z 109 " =    2.511
peak=    3.156 closest distance to " O   LEU A 228 " =    1.868
peak=    3.145 closest distance to " O   ASN A 284 " =    1.809
peak=    3.141 closest distance to " N   CYS A 260 " =    0.806
peak=    3.140 closest distance to " NE2 HIS A 207 " =    1.150
peak=    3.137 closest distance to " O   HOH Z 419 " =    1.755
peak=    3.135 closest distance to " CG2 ILE A 106 " =    0.879
peak=    3.133 closest distance to " CA  ALA A 154 " =    1.035
peak=    3.129 closest distance to " CA  THR A 264 " =    0.717
peak=    3.126 closest distance to " O   HOH Z  88 " =    3.479
peak=    3.121 closest distance to " OH  TYR A 169 " =    0.972
peak=    3.120 closest distance to " CD  LYS A 119 " =    1.917
peak=    3.113 closest distance to " OG  SER A  62 " =    2.879
peak=    3.110 closest distance to " C   ALA A 299 " =    0.913
peak=    3.104 closest distance to " O   GLY A  91 " =    1.286
peak=    3.100 closest distance to " CD1 ILE A  33 " =    1.707
peak=    3.099 closest distance to " O   ALA A 292 " =    1.004
peak=    3.092 closest distance to " CB  GLN A 103 " =    0.940
peak=    3.089 closest distance to " CA  ARG A 102 " =    1.129
peak=    3.071 closest distance to " O   HOH Z 344 " =    3.003
peak=    3.063 closest distance to " CB  ARG A 219 " =    1.021
peak=    3.057 closest distance to " N   VAL A 126 " =    1.598
peak=    3.054 closest distance to " O   HOH Z 302 " =    1.921
peak=    3.052 closest distance to " O   HOH Z   9 " =    2.142
peak=    3.039 closest distance to " O   HOH Z 394 " =    1.759
peak=    3.039 closest distance to " CD ALYS A 290 " =    0.998
peak=    3.026 closest distance to " CB  ALA A   1 " =    4.943
peak=    3.023 closest distance to " O   HOH Z 151 " =    1.633
peak=    3.006 closest distance to " O   HOH Z 189 " =    3.599

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.778 - 5.648
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 211
   mapped sites are within: 0.778 - 5.648

peak=   -5.158 closest distance to " CG2 VAL A 230 " =    0.778
peak=   -4.553 closest distance to " SG  CYS A 254 " =    3.352
peak=   -4.495 closest distance to " CD  GLN A  58 " =    0.997
peak=   -4.333 closest distance to " CG2BVAL A  41 " =    2.737
peak=   -4.327 closest distance to " CG1 VAL A 250 " =    2.760
peak=   -4.236 closest distance to " O   HOH Z 266 " =    5.595
peak=   -4.218 closest distance to " CD  ARG A 156 " =    2.111
peak=   -4.208 closest distance to " O   HOH Z 196 " =    2.278
peak=   -4.157 closest distance to " O   HOH Z  10 " =    1.629
peak=   -4.082 closest distance to " CA  ASP A 298 " =    1.078
peak=   -4.074 closest distance to " O   HOH Z 166 " =    1.595
peak=   -4.025 closest distance to " CE3 TRP A 150 " =    2.348
peak=   -3.992 closest distance to " O   PRO A 163 " =    2.210
peak=   -3.981 closest distance to " O   SER A 271 " =    2.109
peak=   -3.971 closest distance to " CE2 TYR A  30 " =    2.723
peak=   -3.955 closest distance to " O   HOH Z 193 " =    1.136
peak=   -3.952 closest distance to " CG2 ILE A  49 " =    2.788
peak=   -3.944 closest distance to " CG1 VAL A 296 " =    1.102
peak=   -3.939 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.936 closest distance to " O   HOH Z 231 " =    2.232
peak=   -3.935 closest distance to " O   HOH Z  13 " =    1.735
peak=   -3.920 closest distance to " CD2 TYR A 293 " =    1.933
peak=   -3.905 closest distance to " OG BSER A 134 " =    1.352
peak=   -3.898 closest distance to " CB  PRO A 243 " =    2.763
peak=   -3.894 closest distance to " O   HOH Z 283 " =    2.357
peak=   -3.891 closest distance to " O   ILE A 109 " =    2.602
peak=   -3.874 closest distance to " OE1 GLN A 223 " =    2.228
peak=   -3.870 closest distance to " OXT GLY A 302 " =    2.914
peak=   -3.866 closest distance to " CG1 VAL A 112 " =    2.675
peak=   -3.862 closest distance to " O   HOH Z 351 " =    1.563
peak=   -3.856 closest distance to " CG  ARG A 269 " =    2.275
peak=   -3.851 closest distance to " CE2 PHE A  61 " =    2.657
peak=   -3.842 closest distance to " O   HOH Z 394 " =    1.689
peak=   -3.814 closest distance to " CB  PHE A 208 " =    2.396
peak=   -3.808 closest distance to " CG2BVAL A  41 " =    1.774
peak=   -3.774 closest distance to " CD1 LEU A 101 " =    2.399
peak=   -3.766 closest distance to " CG  GLU A 277 " =    1.190
peak=   -3.762 closest distance to " CD1 PHE A  59 " =    2.030
peak=   -3.761 closest distance to " CG2 ILE A  20 " =    3.017
peak=   -3.750 closest distance to " CE2 TRP A  70 " =    2.147
peak=   -3.748 closest distance to " C   HIS A 108 " =    1.145
peak=   -3.746 closest distance to " CG2 VAL A 189 " =    2.091
peak=   -3.738 closest distance to " O   HOH Z  37 " =    1.910
peak=   -3.732 closest distance to " CG  GLN A 103 " =    2.509
peak=   -3.730 closest distance to " CB  ALA A 248 " =    2.197
peak=   -3.711 closest distance to " CH2 TRP A 179 " =    1.228
peak=   -3.693 closest distance to " ND2 ASN A 187 " =    1.619
peak=   -3.692 closest distance to " ND2BASN A 224 " =    1.856
peak=   -3.686 closest distance to " OG  SER A  97 " =    2.337
peak=   -3.682 closest distance to " CB  ALA A  10 " =    2.261
peak=   -3.672 closest distance to " O   HOH Z 211 " =    1.377
peak=   -3.654 closest distance to " O   HOH Z 285 " =    2.008
peak=   -3.640 closest distance to " CZ  TYR A 169 " =    1.827
peak=   -3.640 closest distance to " O   HOH Z 133 " =    1.198
peak=   -3.624 closest distance to " O   HOH Z 301 " =    2.554
peak=   -3.622 closest distance to " O   HOH Z 177 " =    1.859
peak=   -3.620 closest distance to " O   HOH Z 384 " =    2.136
peak=   -3.613 closest distance to " CG  GLU A  53 " =    1.586
peak=   -3.606 closest distance to " CD2 PHE A  61 " =    2.134
peak=   -3.601 closest distance to " OD1 ASN A 148 " =    1.447
peak=   -3.599 closest distance to " CD  LYS A 289 " =    2.416
peak=   -3.596 closest distance to " O   HOH Z 407 " =    2.907
peak=   -3.593 closest distance to " CG2 ILE A 263 " =    2.372
peak=   -3.590 closest distance to " O   SER A 210 " =    1.729
peak=   -3.567 closest distance to " CD  PRO A 243 " =    1.986
peak=   -3.563 closest distance to " O   HOH Z  19 " =    2.392
peak=   -3.559 closest distance to " O   HOH Z 136 " =    2.502
peak=   -3.552 closest distance to " CG  PRO A 243 " =    1.696
peak=   -3.547 closest distance to " O   HOH Z 216 " =    1.081
peak=   -3.538 closest distance to " O   HOH Z 290 " =    1.116
peak=   -3.537 closest distance to " O   HOH Z 264 " =    1.778
peak=   -3.532 closest distance to " CD2 PHE A 192 " =    2.110
peak=   -3.520 closest distance to " O   GLY A  17 " =    1.160
peak=   -3.515 closest distance to " NE  ARG A  66 " =    4.344
peak=   -3.512 closest distance to " O   HOH Z 431 " =    2.191
peak=   -3.510 closest distance to " O   HOH Z 426 " =    1.719
peak=   -3.509 closest distance to " O   HOH Z 114 " =    3.232
peak=   -3.506 closest distance to " O   HOH Z 154 " =    1.412
peak=   -3.502 closest distance to " CA  GLY A 241 " =    2.400
peak=   -3.491 closest distance to " O   HOH Z 165 " =    1.944
peak=   -3.491 closest distance to " O   HOH Z 210 " =    0.911
peak=   -3.477 closest distance to " N   ALA A  43 " =    2.688
peak=   -3.473 closest distance to " O   HOH Z 198 " =    1.939
peak=   -3.465 closest distance to " OG  SER A  63 " =    1.129
peak=   -3.461 closest distance to " N   SER A 276 " =    1.499
peak=   -3.460 closest distance to " O   HOH Z 102 " =    1.598
peak=   -3.456 closest distance to " CZ  PHE A  38 " =    2.389
peak=   -3.456 closest distance to " CG1 VAL A 112 " =    2.655
peak=   -3.450 closest distance to " O   HOH Z 200 " =    1.648
peak=   -3.445 closest distance to " NE2 GLN A 194 " =    1.978
peak=   -3.436 closest distance to " O   HOH Z  52 " =    1.735
peak=   -3.433 closest distance to " CG2 THR A   4 " =    1.963
peak=   -3.430 closest distance to " O   GLY A  80 " =    2.572
peak=   -3.427 closest distance to " CE3 TRP A 274 " =    2.456
peak=   -3.427 closest distance to " O   ALA A  34 " =    2.520
peak=   -3.418 closest distance to " O   HOH Z 191 " =    5.648
peak=   -3.418 closest distance to " O   HOH Z 166 " =    1.594
peak=   -3.416 closest distance to " CD2 LEU A 167 " =    1.862
peak=   -3.408 closest distance to " ND2 ASN A 249 " =    2.376
peak=   -3.386 closest distance to " CG  GLN A  11 " =    1.717
peak=   -3.384 closest distance to " NH2 ARG A  36 " =    2.434
peak=   -3.382 closest distance to " O   HOH Z 128 " =    2.592
peak=   -3.381 closest distance to " O   ALA A 227 " =    1.387
peak=   -3.380 closest distance to " O   MET A  40 " =    2.893
peak=   -3.380 closest distance to " O   HOH Z 340 " =    1.591
peak=   -3.377 closest distance to " O   HOH Z 421 " =    3.594
peak=   -3.376 closest distance to " O   HOH Z 185 " =    2.485
peak=   -3.365 closest distance to " O   HOH Z 423 " =    2.366
peak=   -3.362 closest distance to " C   ASN A 285 " =    2.317
peak=   -3.361 closest distance to " O   ARG A  24 " =    2.134
peak=   -3.360 closest distance to " O   HOH Z 150 " =    1.761
peak=   -3.351 closest distance to " CD  GLN A 223 " =    1.294
peak=   -3.336 closest distance to " N   ALA A 226 " =    2.037
peak=   -3.330 closest distance to " O   HOH Z 174 " =    2.175
peak=   -3.328 closest distance to " CB  SER A 210 " =    1.099
peak=   -3.324 closest distance to " CG  TRP A 266 " =    1.782
peak=   -3.321 closest distance to " OD1 ASN A 173 " =    1.417
peak=   -3.321 closest distance to " O   HOH Z 131 " =    4.153
peak=   -3.320 closest distance to " O   HOH Z 378 " =    1.454
peak=   -3.315 closest distance to " CE1 TYR A 247 " =    2.666
peak=   -3.313 closest distance to " ND2 ASN A  45 " =    1.231
peak=   -3.311 closest distance to " CG  ASP A 231 " =    0.882
peak=   -3.311 closest distance to " O   VAL A 189 " =    2.666
peak=   -3.310 closest distance to " O   HOH Z 252 " =    3.520
peak=   -3.308 closest distance to " O   HOH Z 377 " =    2.114
peak=   -3.303 closest distance to " C   LEU A 143 " =    1.058
peak=   -3.295 closest distance to " CB  PRO A 163 " =    2.532
peak=   -3.293 closest distance to " CA  LYS A 166 " =    2.178
peak=   -3.292 closest distance to " CG  LEU A   5 " =    1.424
peak=   -3.290 closest distance to " O   HOH Z 251 " =    4.952
peak=   -3.288 closest distance to " CD1 ILE A 199 " =    2.482
peak=   -3.288 closest distance to " O   GLN A 240 " =    2.453
peak=   -3.286 closest distance to " O   HOH Z 236 " =    1.511
peak=   -3.284 closest distance to " CA  GLY A 133 " =    2.386
peak=   -3.283 closest distance to " CG  LEU A   5 " =    0.981
peak=   -3.282 closest distance to " O   HOH Z 265 " =    2.472
peak=   -3.271 closest distance to " CD2 LEU A 300 " =    2.562
peak=   -3.270 closest distance to " CB  ASP A 171 " =    2.281
peak=   -3.267 closest distance to " O   HOH Z 111 " =    1.711
peak=   -3.267 closest distance to " O   HOH Z  44 " =    2.424
peak=   -3.267 closest distance to " CG  ASP A 286 " =    1.581
peak=   -3.264 closest distance to " CG  HIS A  86 " =    1.199
peak=   -3.264 closest distance to " O   GLY A 203 " =    2.330
peak=   -3.254 closest distance to " CG1 VAL A  78 " =    2.522
peak=   -3.253 closest distance to " O   HOH Z 116 " =    1.333
peak=   -3.252 closest distance to " CG  MET A 105 " =    0.915
peak=   -3.249 closest distance to " CB  ALA A 129 " =    2.468
peak=   -3.249 closest distance to " CA  GLY A 203 " =    2.467
peak=   -3.248 closest distance to " C   THR A 279 " =    1.128
peak=   -3.246 closest distance to " O   PHE A 218 " =    1.472
peak=   -3.245 closest distance to " ND2 ASN A  69 " =    1.906
peak=   -3.244 closest distance to " CD1 ILE A 109 " =    2.824
peak=   -3.242 closest distance to " O   HOH Z   6 " =    1.701
peak=   -3.240 closest distance to " O   HOH Z 140 " =    1.275
peak=   -3.240 closest distance to " O   TRP A  70 " =    1.634
peak=   -3.240 closest distance to " O   HOH Z 110 " =    1.450
peak=   -3.239 closest distance to " ND2 ASN A  45 " =    2.124
peak=   -3.238 closest distance to " C   MET A 188 " =    1.437
peak=   -3.236 closest distance to " NE2 GLN A 223 " =    1.437
peak=   -3.236 closest distance to " N   SER A   3 " =    2.328
peak=   -3.233 closest distance to " CE3 TRP A  70 " =    1.797
peak=   -3.233 closest distance to " CG2 VAL A 296 " =    1.435
peak=   -3.227 closest distance to " O   HOH Z 171 " =    2.267
peak=   -3.224 closest distance to " O   VAL A 189 " =    1.825
peak=   -3.217 closest distance to " O   SER A 276 " =    1.710
peak=   -3.216 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.214 closest distance to " O   HOH Z 106 " =    1.934
peak=   -3.214 closest distance to " O   ALA A 299 " =    2.306
peak=   -3.210 closest distance to " O   HOH Z 232 " =    1.683
peak=   -3.207 closest distance to " CG1BVAL A  72 " =    2.485
peak=   -3.204 closest distance to " NH2AARG A 275 " =    5.040
peak=   -3.201 closest distance to " O   HOH Z 139 " =    3.411
peak=   -3.201 closest distance to " O   HOH Z 156 " =    3.648
peak=   -3.193 closest distance to " O   HOH Z 231 " =    2.208
peak=   -3.192 closest distance to " O   ILE A 234 " =    1.248
peak=   -3.190 closest distance to " O   HOH Z 174 " =    3.699
peak=   -3.183 closest distance to " CE BMET A  47 " =    1.962
peak=   -3.178 closest distance to " CH2 TRP A 150 " =    1.112
peak=   -3.176 closest distance to " CG  ASP A  50 " =    2.156
peak=   -3.173 closest distance to " O   HOH Z 396 " =    2.123
peak=   -3.166 closest distance to " CA  GLY A 241 " =    3.133
peak=   -3.164 closest distance to " NE2 GLN A  88 " =    1.036
peak=   -3.164 closest distance to " O   HOH Z 149 " =    2.133
peak=   -3.146 closest distance to " CD2 PHE A 225 " =    1.138
peak=   -3.145 closest distance to " O   HOH Z  60 " =    2.027
peak=   -3.142 closest distance to " CD1 LEU A  25 " =    2.567
peak=   -3.141 closest distance to " C   ALA A 158 " =    1.313
peak=   -3.140 closest distance to " O   GLY A  75 " =    2.094
peak=   -3.136 closest distance to " O   SER A   3 " =    1.131
peak=   -3.134 closest distance to " CD  ARG A 139 " =    1.682
peak=   -3.133 closest distance to " O   ALA A   1 " =    1.683
peak=   -3.129 closest distance to " O   TYR A 186 " =    1.803
peak=   -3.116 closest distance to " CD2 LEU A 237 " =    2.642
peak=   -3.114 closest distance to " O   HOH Z  71 " =    2.451
peak=   -3.110 closest distance to " C   VAL A 265 " =    0.892
peak=   -3.107 closest distance to " OE1 GLN A  88 " =    0.950
peak=   -3.104 closest distance to " O   HOH Z 259 " =    1.935
peak=   -3.103 closest distance to " CB  TRP A  85 " =    2.641
peak=   -3.102 closest distance to " O   HOH Z 313 " =    1.228
peak=   -3.091 closest distance to " O   HOH Z 435 " =    2.640
peak=   -3.083 closest distance to " O   HOH Z 357 " =    2.069
peak=   -3.082 closest distance to " ND2 ASN A  39 " =    1.260
peak=   -3.081 closest distance to " C   PHE A  59 " =    1.275
peak=   -3.079 closest distance to " CB  ASP A 132 " =    2.327
peak=   -3.079 closest distance to " CD  ARG A 195 " =    5.075
peak=   -3.072 closest distance to " CZ  TYR A  68 " =    1.155
peak=   -3.063 closest distance to " CA  VAL A 197 " =    0.959
peak=   -3.060 closest distance to " O   HOH Z 145 " =    2.553
peak=   -3.034 closest distance to " O   HOH Z 340 " =    2.136
peak=   -3.027 closest distance to " O   PRO A 198 " =    1.323

================= 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    :  0.4892 0.4769   6.289887e+00   6.273157e+00
   1_bss:  0.4808 0.4704   6.281624e+00   6.269409e+00
   1_xyz:  0.3998 0.4205   6.176960e+00   6.202544e+00
   1_adp:  0.3550 0.4076   6.100449e+00   6.177411e+00
   1_occ:  0.3543 0.4079   6.100122e+00   6.178172e+00
   2_bss:  0.3507 0.4003   6.099962e+00   6.175604e+00
   2_xyz:  0.2546 0.3075   5.830826e+00   5.985754e+00
   2_adp:  0.2252 0.2754   5.733586e+00   5.902197e+00
   2_occ:  0.2249 0.2756   5.733190e+00   5.902881e+00
   3_bss:  0.2228 0.2751   5.733591e+00   5.901564e+00
   3_xyz:  0.1633 0.2046   5.452944e+00   5.643175e+00
   3_adp:  0.1521 0.1915   5.387847e+00   5.582498e+00
   3_occ:  0.1518 0.1917   5.387648e+00   5.583390e+00
   4_bss:  0.1512 0.1913   5.386483e+00   5.581518e+00
   4_xyz:  0.1318 0.1738   5.276746e+00   5.484004e+00
   4_adp:  0.1260 0.1727   5.251055e+00   5.474888e+00
   4_occ:  0.1259 0.1725   5.250585e+00   5.474367e+00
   5_bss:  0.1260 0.1727   5.250588e+00   5.474341e+00
   5_xyz:  0.1201 0.1676   5.213142e+00   5.447017e+00
   5_adp:  0.1193 0.1675   5.209652e+00   5.446602e+00
   5_occ:  0.1193 0.1675   5.209483e+00   5.446544e+00
   5_bss:  0.1191 0.1673   5.209549e+00   5.446589e+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:  0.294   0.000   6.608  10.268  11.154   0.000   0.000   0.000
   1_xyz:  0.294   0.000   6.608  10.268  11.154   0.000   0.000   0.000
   1_adp:  0.294   0.000   6.608  10.268  11.154   0.000   0.000   0.000
   1_occ:  0.294   0.000   6.608  10.268  11.154   0.000   0.000   0.000
   2_bss:  0.328  50.001   2.952   6.164   6.969   0.000   0.000   0.000
   2_xyz:  0.328  50.001   2.952   6.164   6.969   0.000   0.000   0.000
   2_adp:  0.328  50.001   2.952   6.164   6.969   0.000   0.000   0.000
   2_occ:  0.328  50.001   2.952   6.164   6.969   0.000   0.000   0.000
   3_bss:  0.314  50.001   1.676   3.511   4.318   0.000   0.000   0.000
   3_xyz:  0.314  50.001   1.676   3.511   4.318   0.000   0.000   0.000
   3_adp:  0.314  50.001   1.676   3.511   4.318   0.000   0.000   0.000
   3_occ:  0.314  50.001   1.676   3.511   4.318   0.000   0.000   0.000
   4_bss:  0.325  50.001   0.999   2.297   3.411   0.000   0.000   0.000
   4_xyz:  0.325  50.001   0.999   2.297   3.411   0.000   0.000   0.000
   4_adp:  0.325  50.001   0.999   2.297   3.411   0.000   0.000   0.000
   4_occ:  0.325  50.001   0.999   2.297   3.411   0.000   0.000   0.000
   5_bss:  0.330  64.981   1.192   2.182   3.402   0.000   0.000   0.000
   5_xyz:  0.330  64.981   1.192   2.182   3.402   0.000   0.000   0.000
   5_adp:  0.330  64.981   1.192   2.182   3.402   0.000   0.000   0.000
   5_occ:  0.330  64.981   1.192   2.182   3.402   0.000   0.000   0.000
   5_bss:  0.325  64.712  -1.008  -0.110   1.118  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.384 0.4407  0.5045    68566.617
   1_bss:  56.490 0.4383  0.6593    68270.239
   1_xyz:  47.970 0.5445  0.7991    50543.434
   1_adp:  44.885 0.5832  0.9049    46602.935
   1_occ:  44.986 0.5820  0.9019    46755.459
   2_bss:  44.437 0.5888  0.8006    46128.623
   2_xyz:  32.661 0.7273  0.9637    25669.388
   2_adp:  28.591 0.7734  0.9960    20794.126
   2_occ:  28.608 0.7732  0.9957    20808.908
   3_bss:  28.455 0.7749  0.9236    20719.641
   3_xyz:  20.207 0.8593  0.9830    11127.774
   3_adp:  18.496 0.8761  0.9881     9874.397
   3_occ:  18.519 0.8759  0.9879     9897.377
   4_bss:  18.424 0.8767  0.9564     9802.773
   4_xyz:  16.171 0.8970  0.9651     7917.316
   4_adp:  15.980 0.8987  0.9575     7771.625
   4_occ:  15.964 0.8988  0.9575     7762.661
   5_bss:  15.975 0.8988  0.9586     7781.368
   5_xyz:  15.375 0.9039  0.9615     7293.091
   5_adp:  15.327 0.9044  0.9548     7251.922
   5_occ:  15.320 0.9044  0.9548     7250.541
   5_bss:  15.323 0.9044  0.9624     7250.493
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4308e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4308e+01
   1_xyz:   1.739  0.014  0.109 18.157  0.007  4.112   1.4760e-01
   1_adp:   1.739  0.014  0.109 18.157  0.007  4.112   1.4760e-01
   1_occ:   1.739  0.014  0.109 18.157  0.007  4.112   1.4760e-01
   2_bss:   1.739  0.014  0.109 18.157  0.007  4.112   1.4760e-01
   2_xyz:   1.378  0.011  0.086 16.368  0.005  4.115   1.0421e-01
   2_adp:   1.378  0.011  0.086 16.368  0.005  4.115   1.0421e-01
   2_occ:   1.378  0.011  0.086 16.368  0.005  4.115   1.0421e-01
   3_bss:   1.378  0.011  0.086 16.368  0.005  4.115   1.0421e-01
   3_xyz:   1.113  0.009  0.081 15.754  0.004  4.141   7.4310e-02
   3_adp:   1.113  0.009  0.081 15.754  0.004  4.141   7.4310e-02
   3_occ:   1.113  0.009  0.081 15.754  0.004  4.141   7.4310e-02
   4_bss:   1.113  0.009  0.081 15.754  0.004  4.141   7.4310e-02
   4_xyz:   1.083  0.009  0.083 15.577  0.004  4.119   7.0753e-02
   4_adp:   1.083  0.009  0.083 15.577  0.004  4.119   7.0753e-02
   4_occ:   1.083  0.009  0.083 15.577  0.004  4.119   7.0753e-02
   5_bss:   1.083  0.009  0.083 15.577  0.004  4.119   7.0753e-02
   5_xyz:   1.096  0.009  0.087 15.484  0.004  4.124   7.2329e-02
   5_adp:   1.096  0.009  0.087 15.484  0.004  4.124   7.2329e-02
   5_occ:   1.096  0.009  0.087 15.484  0.004  4.124   7.2329e-02
   5_bss:   1.096  0.009  0.087 15.484  0.004  4.124   7.2329e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0404e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0404e+00
   1_xyz:  15.220  0.172  0.476 86.734  0.050  2.224   1.0963e-01
   1_adp:  15.220  0.172  0.476 86.734  0.050  2.224   1.0963e-01
   1_occ:  15.220  0.172  0.476 86.734  0.050  2.224   1.0963e-01
   2_bss:  15.220  0.172  0.476 86.734  0.050  2.224   1.0963e-01
   2_xyz:   9.288  0.100  0.344 89.240  0.037  2.053   7.9915e-02
   2_adp:   9.288  0.100  0.344 89.240  0.037  2.053   7.9915e-02
   2_occ:   9.288  0.100  0.344 89.240  0.037  2.053   7.9915e-02
   3_bss:   9.288  0.100  0.344 89.240  0.037  2.053   7.9915e-02
   3_xyz:   7.081  0.050  0.313 83.534  0.048  2.275   6.8571e-02
   3_adp:   7.081  0.050  0.313 83.534  0.048  2.275   6.8571e-02
   3_occ:   7.081  0.050  0.313 83.534  0.048  2.275   6.8571e-02
   4_bss:   7.081  0.050  0.313 83.534  0.048  2.275   6.8571e-02
   4_xyz:   7.603  0.043  0.413 86.792  0.030  2.253   5.8739e-02
   4_adp:   7.603  0.043  0.413 86.792  0.030  2.253   5.8739e-02
   4_occ:   7.603  0.043  0.413 86.792  0.030  2.253   5.8739e-02
   5_bss:   7.603  0.043  0.413 86.792  0.030  2.253   5.8739e-02
   5_xyz:   7.948  0.047  0.473 89.262  0.031  2.336   5.0074e-02
   5_adp:   7.948  0.047  0.473 89.262  0.031  2.336   5.0074e-02
   5_occ:   7.948  0.047  0.473 89.262  0.031  2.336   5.0074e-02
   5_bss:   7.948  0.047  0.473 89.262  0.031  2.336   5.0074e-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:  99.87   0.00  14.17  77.57   0.00  11.75  99.87   0.00  27.30
   1_occ:  99.87   0.00  14.17  77.57   0.00  11.75  99.87   0.00  27.30
   2_bss:  99.87   0.00  14.17  77.57   0.00  11.75  99.87   0.00  27.30
   2_xyz:  99.87   0.00  14.17  77.57   0.00  11.75  99.87   0.00  27.30
   2_adp:  91.11   0.00  13.29  70.19   0.00   9.66  91.11   0.00  33.01
   2_occ:  91.11   0.00  13.29  70.19   0.00   9.66  91.11   0.00  33.01
   3_bss:  91.11   0.00  13.29  70.19   0.00   9.66  91.11   0.00  33.01
   3_xyz:  91.11   0.00  13.29  70.19   0.00   9.66  91.11   0.00  33.01
   3_adp:  85.90   0.00  12.93  70.98   0.00   9.05  85.90   1.90  34.08
   3_occ:  85.90   0.00  12.93  70.98   0.00   9.05  85.90   1.90  34.08
   4_bss:  85.90   0.00  12.93  70.98   0.00   9.05  85.90   1.90  34.08
   4_xyz:  85.90   0.00  12.93  70.98   0.00   9.05  85.90   1.90  34.08
   4_adp:  87.97   0.00  13.58  81.95   0.00   9.03  87.97   2.01  38.36
   4_occ:  87.97   0.00  13.58  81.95   0.00   9.03  87.97   2.01  38.36
   5_bss:  87.97   0.00  13.58  81.95   0.00   9.03  87.97   2.01  38.36
   5_xyz:  87.97   0.00  13.58  81.95   0.00   9.03  87.97   2.01  38.36
   5_adp:  90.09   0.00  13.43  84.30   0.00   8.87  90.09   1.58  38.30
   5_occ:  90.09   0.00  13.43  84.30   0.00   8.87  90.09   1.58  38.30
   5_bss:  92.57   2.49  15.92  86.78   2.49  11.35  92.57   4.07  40.78
------------------------------------------------------------------------
 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:    1.277    0.005    0.415
   1_adp:    1.277    0.005    0.415
   1_occ:    1.277    0.005    0.415
   2_bss:    1.277    0.005    0.415
   2_xyz:    1.813    0.018    0.628
   2_adp:    1.813    0.018    0.628
   2_occ:    1.813    0.018    0.628
   3_bss:    1.813    0.018    0.628
   3_xyz:    1.868    0.037    0.711
   3_adp:    1.868    0.037    0.711
   3_occ:    1.868    0.037    0.711
   4_bss:    1.868    0.037    0.711
   4_xyz:    1.992    0.041    0.752
   4_adp:    1.992    0.041    0.752
   4_occ:    1.992    0.041    0.752
   5_bss:    1.992    0.041    0.752
   5_xyz:    2.145    0.038    0.765
   5_adp:    2.145    0.038    0.765
   5_occ:    2.145    0.038    0.765
   5_bss:    2.145    0.038    0.765
------------------------------------------------------------------------

CPU time actual refinement: 356.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_581/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_581/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_581/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_581/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_581/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.69 
  Macro-tasks:
    bulk solvent and scale       = 43.32  
    individual site refinement   = 155.40 
    weights calculation          = 32.39  
    collect and process          = 6.69   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 237.95 
  Micro-tasks:
    mask                            = 2.30   
    f_calc                          = 109.97 
    alpha_beta                      = 8.36   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 123.12 
    fmodel                         = 7.65   
    r_factors                      = 0.24   
    phase_errors                   = 10.54  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 263.54 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.860 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    681 calls, 109.56 s
gradients_fft:          626 calls, 108.20 s

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

# Date 2008-01-16 Time 01:56:54 PST -0800 (1200477414.62 s)
Start R-work = 0.4892, R-free = 0.4769 (no bulk solvent and anisotropic scale)
Final R-work = 0.1361, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4808, R-free = 0.4704
Final R-work = 0.1191, R-free = 0.1673