# Date 2008-01-16 Time 03:32:29 PST -0800 (1200483149.49 s)
#phil __OFF__

Command line arguments: "../1277.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3425
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1277

-------------------------------------------------------------------------------
  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: (72.0062, 47.1647, 84.6622, 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: 3.30, per 1000 atoms: 1.17


================================== 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: (72.0062, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96133
Completeness in resolution range: 0.921965
Completeness with d_max=infinity: 0.919283

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1768
                             d_min =   1.9613

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: (72.0062, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96133
Completeness in resolution range: 0.921965
Completeness with d_max=infinity: 0.919283

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1772 -  4.1986 [2237/2267]  2017   220   9.8%
  bin  2:  4.1986 -  3.3442 [2131/2154]  1918   213  10.0%
  bin  3:  3.3442 -  2.9249 [2106/2128]  1886   220  10.4%
  bin  4:  2.9249 -  2.6591 [2104/2123]  1903   201   9.6%
  bin  5:  2.6591 -  2.4693 [2074/2103]  1866   208  10.0%
  bin  6:  2.4693 -  2.3243 [2070/2112]  1857   213  10.3%
  bin  7:  2.3243 -  2.2083 [2055/2091]  1847   208  10.1%
  bin  8:  2.2083 -  2.1124 [2054/2091]  1855   199   9.7%
  bin  9:  2.1124 -  2.0313 [2015/2102]  1812   203  10.1%
  bin 10:  2.0313 -  1.9613 [ 743/2076]   669    74  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1277/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 31
        2.35 -     2.99: 1831
        2.99 -     3.62: 4593
        3.62 -     4.26: 9127
        4.26 -     4.90: 12670
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.711 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.793 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.796 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.833 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28247 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_1277/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1277/model_refine_001.geo

CPU time processing inputs: 9.30


============================ 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 = 72.00625 47.16465 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4861   r_free= 0.4907   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.287321                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6837 0.99   1444  162 0.3981 0.4011       6.603      6.5976|
|  2:  4.6837 -  3.7358 0.99   1394  154 0.4039 0.4110      6.7937      6.8478|
|  3:  3.7358 -  3.2690 0.99   1369  151 0.4512 0.4358      6.6761      6.6633|
|  4:  3.2690 -  2.9725 0.99   1359  154 0.4727 0.4967       6.512      6.5208|
|  5:  2.9725 -  2.7608 0.99   1340  149 0.5212 0.5420      6.3715      6.3565|
|  6:  2.7608 -  2.5989 0.98   1350  148 0.5169 0.5374        6.28       6.252|
|  7:  2.5989 -  2.4693 0.99   1334  144 0.5357 0.4626      6.2541      6.1568|
|  8:  2.4693 -  2.3623 0.99   1329  156 0.5359 0.5423      6.1524       6.193|
|  9:  2.3623 -  2.2716 0.98   1325  151 0.5246 0.5237      6.1391      6.1104|
| 10:  2.2716 -  2.1935 0.98   1319  149 0.5261 0.5259      6.0752      6.0861|
| 11:  2.1935 -  2.1251 0.98   1332  133 0.5274 0.5808      6.0301      6.0381|
| 12:  2.1251 -  2.0645 0.99   1304  152 0.5368 0.5524      5.9512      5.9751|
| 13:  2.0645 -  2.0103 0.82   1110  131 0.5410 0.5002      5.8642      5.8352|
| 14:  2.0103 -  1.9613 0.23    321   25 0.5597 0.5937      5.8145      5.8568|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6837  1444   162  0.70  34.59   0.79     0.73      72320.96|
|  2:  4.6837 -  3.7358  1394   154  0.69  36.48   0.87     0.76     111024.14|
|  3:  3.7358 -  3.2690  1369   151  0.55  47.50   0.82     0.67     125363.17|
|  4:  3.2690 -  2.9725  1359   154  0.43  57.31   0.79     0.55     118750.07|
|  5:  2.9725 -  2.7608  1340   149  0.33  65.08   0.72     0.42      96397.40|
|  6:  2.7608 -  2.5989  1350   148  0.33  65.35   0.73     0.41      80229.45|
|  7:  2.5989 -  2.4693  1334   144  0.34  64.18   0.72     0.39      66341.67|
|  8:  2.4693 -  2.3623  1329   156  0.35  64.07   0.71     0.42      59916.79|
|  9:  2.3623 -  2.2716  1325   151  0.33  65.56   0.74     0.39      54577.53|
| 10:  2.2716 -  2.1935  1319   149  0.29  68.38   0.74     0.35      53793.77|
| 11:  2.1935 -  2.1251  1332   133  0.24  71.94   0.76     0.31      51155.74|
| 12:  2.1251 -  2.0645  1304   152  0.20  74.80   0.72     0.27      48080.45|
| 13:  2.0645 -  2.0103  1110   131  0.20  74.97   0.71     0.26      41016.92|
| 14:  2.0103 -  1.9613   321    25  0.22  73.41   0.69     0.28      33895.32|
|alpha:            min =        0.26 max =            0.76 mean =         0.46|
|beta:             min =    33895.32 max =       125363.17 mean =     75344.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.53|
|phase err.(test): min =        0.00 max =           89.97 mean =        60.64|
|-----------------------------------------------------------------------------|

============================== 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 = 17.844330             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.758   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.617287              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.214   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      708 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1491 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2631 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3932 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5033 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6572 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7704 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.813 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.866 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    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 = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4913   r_free= 0.4954   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.288698                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4786   r_free= 0.4768   ksol= 0.32   Bsol= 7.62   scale= 0.987    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.89,7.68,8.50,0.00,0.00,0.00); trace/3= 8.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.285023                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.143805             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.765   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.360547              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.885   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4786      final r-factor (work) = 0.4051          |
| start r-factor (free) = 0.4768      final r-factor (free) = 0.4378          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 98.2583 = 14.14 * 0.50 * 6.2848 + 1.00 * 53.8129                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.0601 = 14.14 * 0.50 * 6.2090 + 1.00 * 0.1507                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4051      final r-factor (work) = 0.3660          |
| start r-factor (free) = 0.4378      final r-factor (free) = 0.4222          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4620 = 1.36 * 1.00 * 6.2090 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3790 = 1.36 * 1.00 * 6.1464 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.52   13.48    None  None   None       |
|    all(noH): 2823   0      0.00    83.52   13.48    None  None   None       |
|    Sol.    : 438    0      0.00    83.44   25.69    None  None   None       |
|    Mac.    : 2385   0      0.00    83.52   11.24    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 -   8.352: 1238   |   5:    41.759 -  50.111:   48        |
|      1:     8.352 -  16.704:  749   |   6:    50.111 -  58.463:   29        |
|      2:    16.704 -  25.056:  410   |   7:    58.463 -  66.815:   15        |
|      3:    25.056 -  33.407:  214   |   8:    66.815 -  75.166:    6        |
|      4:    33.407 -  41.759:  108   |   9:    75.166 -  83.518:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3660 r_free = 0.4222             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3656 r_free = 0.4228             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3656   r_free= 0.4228   ksol= 0.32   Bsol= 7.62   scale= 1.094    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.89,7.68,8.50,0.00,0.00,0.00); trace/3= 8.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.128676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3636   r_free= 0.4200   ksol= 0.33   Bsol= 34.60   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.03,4.45,5.85,0.00,0.00,0.00); trace/3= 5.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.128599                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.788584              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.307  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.708393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.796  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3636      final r-factor (work) = 0.2781          |
| start r-factor (free) = 0.4200      final r-factor (free) = 0.3476          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.2110 = 9.79 * 0.50 * 6.1419 + 1.00 * 0.1507                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.6337 = 9.79 * 0.50 * 6.0363 + 1.00 * 0.0902                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2781      final r-factor (work) = 0.2553          |
| start r-factor (free) = 0.3476      final r-factor (free) = 0.3215          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2927 = 0.71 * 1.00 * 6.0363 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1911 = 0.71 * 1.00 * 5.8982 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.43   13.55    None  None   None       |
|    all(noH): 2823   0      0.00    77.43   13.55    None  None   None       |
|    Sol.    : 438    0      0.00    74.49   32.22    None  None   None       |
|    Mac.    : 2385   0      0.00    77.43   10.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.743: 1209   |   5:    38.715 -  46.458:   94        |
|      1:     7.743 -  15.486:  786   |   6:    46.458 -  54.201:   48        |
|      2:    15.486 -  23.229:  328   |   7:    54.201 -  61.944:   24        |
|      3:    23.229 -  30.972:  183   |   8:    61.944 -  69.687:   10        |
|      4:    30.972 -  38.715:  133   |   9:    69.687 -  77.430:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2553 r_free = 0.3215             target_work(ml) = 5.864         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2552 r_free = 0.3213             target_work(ml) = 5.863         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2552   r_free= 0.3213   ksol= 0.33   Bsol= 34.60   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.03,4.45,5.85,0.00,0.00,0.00); trace/3= 5.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.863103                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2535   r_free= 0.3171   ksol= 0.32   Bsol= 34.60   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.83,2.83,3.43,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.861376                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.609143              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.030  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.848763              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.754  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2535      final r-factor (work) = 0.1912          |
| start r-factor (free) = 0.3171      final r-factor (free) = 0.2470          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6882 = 4.61 * 0.50 * 5.9004 + 1.00 * 0.0902                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3445 = 4.61 * 0.50 * 5.7607 + 1.00 * 0.0686                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1912      final r-factor (work) = 0.1726          |
| start r-factor (free) = 0.2470      final r-factor (free) = 0.2318          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6629 = 1.85 * 1.00 * 5.7607 + 1.00 * 0.0127                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3015 = 1.85 * 1.00 * 5.5630 + 1.00 * 0.0168                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.98   14.82    None  None   None       |
|    all(noH): 2823   0      0.00    99.98   14.82    None  None   None       |
|    Sol.    : 438    0      1.65    98.42   41.02    None  None   None       |
|    Mac.    : 2385   0      0.00    99.98   10.01    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 -   9.998: 1579   |   5:    49.989 -  59.986:   98        |
|      1:     9.998 -  19.996:  656   |   6:    59.986 -  69.984:   52        |
|      2:    19.996 -  29.993:  169   |   7:    69.984 -  79.982:   23        |
|      3:    29.993 -  39.991:  128   |   8:    79.982 -  89.980:    8        |
|      4:    39.991 -  49.989:  106   |   9:    89.980 -  99.977:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1726 r_free = 0.2318             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1725 r_free = 0.2316             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1725   r_free= 0.2316   ksol= 0.32   Bsol= 34.60   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.83,2.83,3.43,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.530999                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1720   r_free= 0.2319   ksol= 0.31   Bsol= 54.74   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,1.82,2.09,0.00,0.00,0.00); trace/3= 2.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.530368                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.524638              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.528  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.653377              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.850  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1720      final r-factor (work) = 0.1425          |
| start r-factor (free) = 0.2319      final r-factor (free) = 0.1983          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8857 = 3.52 * 0.50 * 5.5706 + 1.00 * 0.0686                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6866 = 3.52 * 0.50 * 5.4588 + 1.00 * 0.0665                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1425      final r-factor (work) = 0.1352          |
| start r-factor (free) = 0.1983      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5835 = 0.65 * 1.00 * 5.4588 + 1.00 * 0.0168                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5090 = 0.65 * 1.00 * 5.3493 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.39  14.51    None  None   None       |
|    all(noH): 2823   0      0.00    104.39  14.51    None  None   None       |
|    Sol.    : 438    0      2.21    95.61   41.06    None  None   None       |
|    Mac.    : 2385   0      0.00    104.39  9.64     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.439: 1727   |   5:    52.197 -  62.636:   77        |
|      1:    10.439 -  20.879:  560   |   6:    62.636 -  73.076:   49        |
|      2:    20.879 -  31.318:  151   |   7:    73.076 -  83.515:   15        |
|      3:    31.318 -  41.757:  116   |   8:    83.515 -  93.954:    5        |
|      4:    41.757 -  52.197:  118   |   9:    93.954 - 104.394:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1352 r_free = 0.1891             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1350 r_free = 0.1888             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1350   r_free= 0.1888   ksol= 0.31   Bsol= 54.74   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,1.82,2.09,0.00,0.00,0.00); trace/3= 2.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322581                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1353   r_free= 0.1891   ksol= 0.33   Bsol= 54.74   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,1.48,1.81,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323758                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.493820              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.072  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.397538              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.586  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1353      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1891      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0892 = 4.49 * 0.50 * 5.3508 + 1.00 * 0.0665                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9499 = 4.49 * 0.50 * 5.2796 + 1.00 * 0.0872                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1727      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1125 = 0.40 * 1.00 * 5.2796 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0871 = 0.40 * 1.00 * 5.2207 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.30  13.97    None  None   None       |
|    all(noH): 2823   0      0.00    105.30  13.97    None  None   None       |
|    Sol.    : 438    0      2.34    93.72   38.84    None  None   None       |
|    Mac.    : 2385   0      0.00    105.30  9.41     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.530: 1757   |   5:    52.648 -  63.178:   54        |
|      1:    10.530 -  21.059:  562   |   6:    63.178 -  73.708:   45        |
|      2:    21.059 -  31.589:  147   |   7:    73.708 -  84.237:    9        |
|      3:    31.589 -  42.119:  132   |   8:    84.237 -  94.767:    3        |
|      4:    42.119 -  52.648:  110   |   9:    94.767 - 105.297:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1692             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1689             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1689   ksol= 0.33   Bsol= 54.74   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,1.48,1.81,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207360                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6837 0.99   1444  162 0.0948 0.1347      5.3586      5.5871|
|  2:  4.6837 -  3.7358 0.99   1394  154 0.0859 0.1142      5.4445      5.6985|
|  3:  3.7358 -  3.2690 0.99   1369  151 0.1102 0.1802       5.512      5.9324|
|  4:  3.2690 -  2.9725 0.99   1359  154 0.1345 0.1654      5.5278      5.6715|
|  5:  2.9725 -  2.7608 0.99   1340  149 0.1406 0.1935      5.3984      5.6143|
|  6:  2.7608 -  2.5989 0.98   1350  148 0.1360 0.1958      5.2933      5.5046|
|  7:  2.5989 -  2.4693 0.99   1334  144 0.1313 0.1831      5.2261      5.4555|
|  8:  2.4693 -  2.3623 0.99   1329  156 0.1213 0.1760      5.0953      5.3178|
|  9:  2.3623 -  2.2716 0.98   1325  151 0.1208 0.2008      5.0578      5.3504|
| 10:  2.2716 -  2.1935 0.98   1319  149 0.1222 0.1804      5.0268      5.2732|
| 11:  2.1935 -  2.1251 0.98   1332  133 0.1257 0.1936      5.0051      5.3627|
| 12:  2.1251 -  2.0645 0.99   1304  152 0.1203 0.1909      4.9471      5.1813|
| 13:  2.0645 -  2.0103 0.82   1110  131 0.1207 0.1783      4.8173      5.0426|
| 14:  2.0103 -  1.9613 0.23    321   25 0.1108 0.1796      4.6729      4.9594|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6837  1444   162  0.94   9.14   0.97     0.96       7369.06|
|  2:  4.6837 -  3.7358  1394   154  0.95   8.50   1.01     0.99       9605.30|
|  3:  3.7358 -  3.2690  1369   151  0.92  12.66   1.03     1.02      11752.58|
|  4:  3.2690 -  2.9725  1359   154  0.90  16.46   1.00     0.98      12626.22|
|  5:  2.9725 -  2.7608  1340   149  0.88  17.85   1.00     0.97      10029.81|
|  6:  2.7608 -  2.5989  1350   148  0.88  18.20   0.99     0.96       8660.43|
|  7:  2.5989 -  2.4693  1334   144  0.89  17.19   0.99     0.96       7233.23|
|  8:  2.4693 -  2.3623  1329   156  0.90  16.52   0.99     0.95       5842.56|
|  9:  2.3623 -  2.2716  1325   151  0.89  17.41   1.00     0.96       5449.75|
| 10:  2.2716 -  2.1935  1319   149  0.90  16.68   1.00     0.97       5080.88|
| 11:  2.1935 -  2.1251  1332   133  0.88  18.20   0.99     0.95       5132.81|
| 12:  2.1251 -  2.0645  1304   152  0.89  17.81   1.01     1.01       4791.26|
| 13:  2.0645 -  2.0103  1110   131  0.89  17.78   0.99     0.98       3683.26|
| 14:  2.0103 -  1.9613   321    25  0.90  16.13   0.98     0.97       2682.66|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2682.66 max =        12626.22 mean =      7474.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.63|
|phase err.(test): min =        0.00 max =           89.71 mean =        14.97|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1689   ksol= 0.32   Bsol= 52.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.12,-0.22,0.10,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207309                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1689   ksol= 0.32   Bsol= 52.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.12,-0.22,0.10,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207309                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6837 0.99   1444  162 0.0947 0.1343      5.3575      5.5841|
|  2:  4.6837 -  3.7358 0.99   1394  154 0.0855 0.1138      5.4416       5.695|
|  3:  3.7358 -  3.2690 0.99   1369  151 0.1101 0.1802      5.5102      5.9317|
|  4:  3.2690 -  2.9725 0.99   1359  154 0.1345 0.1655      5.5279      5.6718|
|  5:  2.9725 -  2.7608 0.99   1340  149 0.1407 0.1936      5.3991      5.6153|
|  6:  2.7608 -  2.5989 0.98   1350  148 0.1361 0.1959      5.2942       5.505|
|  7:  2.5989 -  2.4693 0.99   1334  144 0.1314 0.1830      5.2268      5.4559|
|  8:  2.4693 -  2.3623 0.99   1329  156 0.1214 0.1762      5.0959      5.3187|
|  9:  2.3623 -  2.2716 0.98   1325  151 0.1209 0.2007      5.0584      5.3505|
| 10:  2.2716 -  2.1935 0.98   1319  149 0.1223 0.1806      5.0274       5.274|
| 11:  2.1935 -  2.1251 0.98   1332  133 0.1257 0.1936      5.0056      5.3628|
| 12:  2.1251 -  2.0645 0.99   1304  152 0.1203 0.1910      4.9474      5.1817|
| 13:  2.0645 -  2.0103 0.82   1110  131 0.1208 0.1784      4.8177       5.043|
| 14:  2.0103 -  1.9613 0.23    321   25 0.1108 0.1796      4.6731      4.9589|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6837  1444   162  0.94   9.12   0.97     0.96       7341.02|
|  2:  4.6837 -  3.7358  1394   154  0.95   8.48   1.01     1.00       9553.37|
|  3:  3.7358 -  3.2690  1369   151  0.92  12.61   1.03     1.02      11690.43|
|  4:  3.2690 -  2.9725  1359   154  0.90  16.45   1.00     0.98      12620.85|
|  5:  2.9725 -  2.7608  1340   149  0.88  17.86   1.00     0.97      10039.16|
|  6:  2.7608 -  2.5989  1350   148  0.88  18.22   0.99     0.96       8674.06|
|  7:  2.5989 -  2.4693  1334   144  0.89  17.20   0.99     0.96       7243.13|
|  8:  2.4693 -  2.3623  1329   156  0.90  16.53   0.99     0.95       5849.12|
|  9:  2.3623 -  2.2716  1325   151  0.89  17.42   1.00     0.96       5454.62|
| 10:  2.2716 -  2.1935  1319   149  0.90  16.69   1.00     0.97       5085.28|
| 11:  2.1935 -  2.1251  1332   133  0.88  18.22   0.99     0.95       5138.66|
| 12:  2.1251 -  2.0645  1304   152  0.89  17.82   1.01     1.01       4796.14|
| 13:  2.0645 -  2.0103  1110   131  0.89  17.80   0.99     0.98       3686.62|
| 14:  2.0103 -  1.9613   321    25  0.90  16.14   0.98     0.97       2684.02|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2684.02 max =        12620.85 mean =      7467.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.63|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    107.01  15.68    None  None   None       |
|    all(noH): 2823   0      1.71    107.01  15.68    None  None   None       |
|    Sol.    : 438    0      4.04    95.43   40.55    None  None   None       |
|    Mac.    : 2385   0      1.71    107.01  11.11    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:     1.709 -  12.238: 1757   |   5:    54.357 -  64.887:   54        |
|      1:    12.238 -  22.768:  562   |   6:    64.887 -  75.416:   45        |
|      2:    22.768 -  33.298:  147   |   7:    75.416 -  85.946:    9        |
|      3:    33.298 -  43.827:  132   |   8:    85.946 -  96.476:    3        |
|      4:    43.827 -  54.357:  110   |   9:    96.476 - 107.005:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.546 - 5.892
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 341
   mapped sites are within: 0.705 - 5.892

peak=    9.869 closest distance to " CB  VAL A 230 " =    1.450
peak=    8.683 closest distance to " CG2 VAL A 296 " =    1.240
peak=    6.074 closest distance to " O   HOH Z 278 " =    1.197
peak=    5.913 closest distance to " O   HOH Z  37 " =    1.423
peak=    5.868 closest distance to " O   HOH Z 111 " =    1.970
peak=    5.813 closest distance to " CG  LEU A   5 " =    1.257
peak=    5.772 closest distance to " O   HOH Z 112 " =    1.527
peak=    5.523 closest distance to " CD2 LEU A   5 " =    1.167
peak=    5.496 closest distance to " O   HOH Z 186 " =    1.569
peak=    5.352 closest distance to " CB  GLN A 223 " =    1.490
peak=    5.269 closest distance to " O   HOH Z 179 " =    0.955
peak=    5.185 closest distance to " CB  SER A  63 " =    1.367
peak=    4.979 closest distance to " CG  ARG A 138 " =    1.013
peak=    4.955 closest distance to " NH2BARG A 102 " =    0.943
peak=    4.847 closest distance to " O   HOH Z 102 " =    1.051
peak=    4.847 closest distance to " CG  LEU A 228 " =    1.220
peak=    4.813 closest distance to " CB  GLN A 183 " =    1.228
peak=    4.784 closest distance to " O   HOH Z 247 " =    1.542
peak=    4.749 closest distance to " O   HOH Z  80 " =    1.881
peak=    4.745 closest distance to " CG  PRO A  54 " =    1.254
peak=    4.711 closest distance to " O   HOH Z 126 " =    1.635
peak=    4.692 closest distance to " CB  VAL A 230 " =    1.288
peak=    4.644 closest distance to " NE2 GLN A  11 " =    1.115
peak=    4.561 closest distance to " O   HOH Z 108 " =    1.714
peak=    4.531 closest distance to " O   HOH Z 193 " =    1.720
peak=    4.524 closest distance to " O   HOH Z 260 " =    1.350
peak=    4.521 closest distance to " O   HOH Z 236 " =    1.893
peak=    4.509 closest distance to " O   HOH Z  48 " =    1.824
peak=    4.504 closest distance to " CD1AILE A 234 " =    1.031
peak=    4.500 closest distance to " O   HOH Z 369 " =    1.969
peak=    4.494 closest distance to " O   HOH Z 368 " =    1.970
peak=    4.453 closest distance to " O   HOH Z 124 " =    1.394
peak=    4.439 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.414 closest distance to " O   HOH Z 132 " =    1.054
peak=    4.393 closest distance to " NH1 ARG A  56 " =    1.087
peak=    4.362 closest distance to " O   HOH Z 277 " =    1.116
peak=    4.359 closest distance to " CB  PRO A  54 " =    0.771
peak=    4.345 closest distance to " CG2 THR A 221 " =    0.934
peak=    4.307 closest distance to " O   HOH Z  68 " =    1.714
peak=    4.301 closest distance to " CB  GLU A 152 " =    1.187
peak=    4.293 closest distance to " CD2 LEU A 228 " =    1.213
peak=    4.267 closest distance to " O   HOH Z 427 " =    3.395
peak=    4.261 closest distance to " CB  SER A   3 " =    1.470
peak=    4.259 closest distance to " O   HOH Z  11 " =    1.209
peak=    4.246 closest distance to " O   PRO A 198 " =    1.501
peak=    4.238 closest distance to " O   HOH Z 232 " =    2.150
peak=    4.237 closest distance to " O   HOH Z 303 " =    2.178
peak=    4.228 closest distance to " OD1 ASN A  69 " =    2.572
peak=    4.186 closest distance to " O   HOH Z 403 " =    1.861
peak=    4.179 closest distance to " O   HOH Z 193 " =    2.172
peak=    4.168 closest distance to " OE1 GLN A  58 " =    1.284
peak=    4.147 closest distance to " CB  LEU A 228 " =    1.320
peak=    4.147 closest distance to " CA  ALA A  21 " =    1.196
peak=    4.146 closest distance to " CB  ASN A 148 " =    1.221
peak=    4.145 closest distance to " CB  TYR A 169 " =    0.930
peak=    4.139 closest distance to " O   HOH Z  97 " =    1.893
peak=    4.136 closest distance to " O   HOH Z 298 " =    1.790
peak=    4.124 closest distance to " O   HOH Z 316 " =    2.899
peak=    4.109 closest distance to " O   HOH Z  58 " =    1.646
peak=    4.099 closest distance to " O   HOH Z  92 " =    1.063
peak=    4.089 closest distance to " CD1 LEU A 300 " =    1.189
peak=    4.076 closest distance to " CB  VAL A 202 " =    1.572
peak=    4.059 closest distance to " O   HOH Z  63 " =    1.873
peak=    4.048 closest distance to " O   SER A  87 " =    2.322
peak=    4.048 closest distance to " CB  GLU A 128 " =    1.159
peak=    4.036 closest distance to " O   HOH Z  15 " =    2.087
peak=    4.027 closest distance to " O   HOH Z 184 " =    1.644
peak=    4.023 closest distance to " O   HOH Z  78 " =    2.163
peak=    4.022 closest distance to " O   HOH Z 183 " =    1.470
peak=    3.993 closest distance to " O   HOH Z 116 " =    1.711
peak=    3.990 closest distance to " O   HOH Z 371 " =    3.442
peak=    3.986 closest distance to " O   HOH Z 272 " =    1.961
peak=    3.984 closest distance to " O   HOH Z 295 " =    1.552
peak=    3.979 closest distance to " O   HOH Z 271 " =    2.106
peak=    3.976 closest distance to " OD2 ASP A 286 " =    2.877
peak=    3.958 closest distance to " CB  VAL A 265 " =    1.270
peak=    3.958 closest distance to " OG BSER A 164 " =    2.148
peak=    3.949 closest distance to " O   HOH Z  88 " =    3.404
peak=    3.930 closest distance to " OD1 ASN A 217 " =    1.586
peak=    3.912 closest distance to " ND2 ASN A 249 " =    1.949
peak=    3.908 closest distance to " O   HOH Z  54 " =    1.501
peak=    3.907 closest distance to " NH1 ARG A 138 " =    1.132
peak=    3.905 closest distance to " O   HOH Z 284 " =    3.102
peak=    3.895 closest distance to " O   HOH Z 411 " =    3.386
peak=    3.895 closest distance to " O   HOH Z 243 " =    1.173
peak=    3.882 closest distance to " O   ASP A 132 " =    3.746
peak=    3.878 closest distance to " CD2 LEU A 255 " =    1.549
peak=    3.873 closest distance to " CB  GLU A 277 " =    3.639
peak=    3.845 closest distance to " O   HOH Z 134 " =    1.400
peak=    3.845 closest distance to " CB  TRP A 179 " =    1.382
peak=    3.833 closest distance to " O   HOH Z 355 " =    1.970
peak=    3.824 closest distance to " O   HOH Z 127 " =    1.236
peak=    3.819 closest distance to " O   HOH Z 128 " =    2.085
peak=    3.817 closest distance to " CB  ARG A 275 " =    0.818
peak=    3.813 closest distance to " O   HOH Z 425 " =    1.488
peak=    3.813 closest distance to " O   HOH Z 313 " =    1.896
peak=    3.809 closest distance to " O   HOH Z 163 " =    1.632
peak=    3.807 closest distance to " O   HOH Z   4 " =    1.891
peak=    3.805 closest distance to " O   HOH Z 263 " =    1.529
peak=    3.802 closest distance to " O   HOH Z 182 " =    1.419
peak=    3.800 closest distance to " O   HOH Z 281 " =    4.184
peak=    3.782 closest distance to " O   HOH Z 394 " =    1.834
peak=    3.769 closest distance to " CB  TYR A  30 " =    1.401
peak=    3.763 closest distance to " CG1BVAL A  72 " =    1.624
peak=    3.759 closest distance to " O   HOH Z  63 " =    1.134
peak=    3.756 closest distance to " O   HOH Z  99 " =    2.509
peak=    3.743 closest distance to " CB  TRP A 266 " =    0.998
peak=    3.731 closest distance to " O   HOH Z 180 " =    2.122
peak=    3.727 closest distance to " O   HOH Z  20 " =    2.341
peak=    3.725 closest distance to " O   HOH Z 332 " =    1.618
peak=    3.722 closest distance to " O   HOH Z 423 " =    1.764
peak=    3.721 closest distance to " O   HOH Z  61 " =    1.547
peak=    3.711 closest distance to " CG  PRO A 243 " =    1.178
peak=    3.701 closest distance to " O   HOH Z 255 " =    1.672
peak=    3.701 closest distance to " O   HOH Z 344 " =    2.972
peak=    3.701 closest distance to " CA  THR A 221 " =    0.924
peak=    3.694 closest distance to " O   HOH Z 118 " =    1.919
peak=    3.685 closest distance to " O   MET A 105 " =    1.841
peak=    3.683 closest distance to " O   HOH Z 437 " =    2.265
peak=    3.675 closest distance to " O   HOH Z 276 " =    1.363
peak=    3.666 closest distance to " CG  ARG A  66 " =    2.441
peak=    3.662 closest distance to " O   HOH Z 109 " =    2.651
peak=    3.658 closest distance to " O   HOH Z 193 " =    1.896
peak=    3.647 closest distance to " O   ALA A 291 " =    1.681
peak=    3.647 closest distance to " CG1 ILE A  33 " =    1.269
peak=    3.643 closest distance to " O   HOH Z 126 " =    1.946
peak=    3.635 closest distance to " O   HOH Z 203 " =    1.659
peak=    3.634 closest distance to " NH2 ARG A 156 " =    1.159
peak=    3.634 closest distance to " CD  LYS A 119 " =    1.688
peak=    3.628 closest distance to " O   HOH Z  30 " =    1.438
peak=    3.626 closest distance to " O   HOH Z 133 " =    2.349
peak=    3.622 closest distance to " O   HOH Z 374 " =    1.095
peak=    3.620 closest distance to " O   HOH Z 175 " =    3.696
peak=    3.620 closest distance to " O   HOH Z 410 " =    1.497
peak=    3.603 closest distance to " O   HOH Z  93 " =    2.856
peak=    3.598 closest distance to " CB  LEU A 143 " =    1.153
peak=    3.595 closest distance to " CA  TYR A  30 " =    1.006
peak=    3.580 closest distance to " CB  ARG A  79 " =    1.532
peak=    3.576 closest distance to " O   HOH Z 236 " =    1.635
peak=    3.576 closest distance to " O   HOH Z  49 " =    2.039
peak=    3.572 closest distance to " OE1 GLN A  11 " =    1.786
peak=    3.565 closest distance to " CD1 ILE A  33 " =    1.608
peak=    3.564 closest distance to " NE2 GLN A  58 " =    5.732
peak=    3.561 closest distance to " O   HOH Z 290 " =    1.233
peak=    3.547 closest distance to " O   HOH Z 420 " =    2.215
peak=    3.546 closest distance to " CG1 VAL A 153 " =    1.042
peak=    3.541 closest distance to " CB  ALA A 100 " =    1.329
peak=    3.538 closest distance to " CB  SER A 216 " =    0.837
peak=    3.531 closest distance to " O   HOH Z 132 " =    2.582
peak=    3.523 closest distance to " CD ALYS A 290 " =    1.057
peak=    3.516 closest distance to " CB  ASP A 140 " =    0.739
peak=    3.515 closest distance to " CA  LEU A 282 " =    1.058
peak=    3.514 closest distance to " O   HOH Z 202 " =    1.311
peak=    3.514 closest distance to " CG1 ILE A  49 " =    1.589
peak=    3.510 closest distance to " O   HOH Z  54 " =    2.398
peak=    3.508 closest distance to " O   HOH Z 171 " =    3.857
peak=    3.507 closest distance to " O   HOH Z  53 " =    2.580
peak=    3.506 closest distance to " O   HOH Z 387 " =    3.113
peak=    3.504 closest distance to " NZ  LYS A 117 " =    3.285
peak=    3.501 closest distance to " CA  MET A  40 " =    1.126
peak=    3.498 closest distance to " O   HOH Z 177 " =    1.188
peak=    3.498 closest distance to " CG  PRO A 198 " =    1.433
peak=    3.496 closest distance to " O   HOH Z 426 " =    1.451
peak=    3.496 closest distance to " CA  ALA A 295 " =    1.090
peak=    3.491 closest distance to " O   HOH Z 261 " =    1.743
peak=    3.483 closest distance to " CB  ALA A 161 " =    0.957
peak=    3.480 closest distance to " CD  ARG A 138 " =    1.151
peak=    3.479 closest distance to " O   HOH Z 227 " =    1.826
peak=    3.474 closest distance to " CA  VAL A 126 " =    0.869
peak=    3.473 closest distance to " CD  ARG A 269 " =    0.811
peak=    3.471 closest distance to " CG  GLN A  88 " =    1.069
peak=    3.471 closest distance to " O   HOH Z 108 " =    2.182
peak=    3.470 closest distance to " CA  ALA A  51 " =    1.001
peak=    3.468 closest distance to " OD1 ASP A 231 " =    1.880
peak=    3.466 closest distance to " CG2 THR A  42 " =    0.880
peak=    3.465 closest distance to " NH1 ARG A  14 " =    1.021
peak=    3.462 closest distance to " CA  ALA A 158 " =    1.093
peak=    3.461 closest distance to " NH2BARG A 145 " =    2.126
peak=    3.457 closest distance to " CG  PRO A 280 " =    0.705
peak=    3.455 closest distance to " O   HOH Z 282 " =    1.471
peak=    3.451 closest distance to " O   HOH Z 345 " =    3.535
peak=    3.444 closest distance to " CB  TRP A 150 " =    1.453
peak=    3.442 closest distance to " O   GLN A 278 " =    1.082
peak=    3.439 closest distance to " NH1AARG A 145 " =    1.014
peak=    3.438 closest distance to " O   HOH Z 422 " =    2.673
peak=    3.437 closest distance to " NZ  LYS A  48 " =    1.509
peak=    3.433 closest distance to " O   ALA A 158 " =    1.317
peak=    3.432 closest distance to " ND1 HIS A  81 " =    1.575
peak=    3.429 closest distance to " O   HOH Z 327 " =    2.236
peak=    3.427 closest distance to " CA  LYS A 117 " =    1.225
peak=    3.423 closest distance to " CB  ALA A 248 " =    0.949
peak=    3.423 closest distance to " O   HOH Z 346 " =    1.384
peak=    3.422 closest distance to " CG BARG A 102 " =    1.913
peak=    3.421 closest distance to " CB  GLU A 152 " =    1.379
peak=    3.414 closest distance to " CG2 THR A 264 " =    0.880
peak=    3.411 closest distance to " O   HOH Z 329 " =    3.867
peak=    3.407 closest distance to " CB  ASN A 187 " =    1.057
peak=    3.406 closest distance to " CG  MET A 185 " =    1.393
peak=    3.405 closest distance to " CA  ALA A 160 " =    0.872
peak=    3.403 closest distance to " CB  MET A  40 " =    0.788
peak=    3.400 closest distance to " O   HOH Z 280 " =    1.547
peak=    3.398 closest distance to " O   HOH Z  21 " =    1.850
peak=    3.393 closest distance to " O   HOH Z 155 " =    1.669
peak=    3.392 closest distance to " O   HOH Z 374 " =    3.030
peak=    3.390 closest distance to " CA  ASN A  74 " =    1.229
peak=    3.386 closest distance to " O   HOH Z 197 " =    2.432
peak=    3.382 closest distance to " CG BARG A 275 " =    1.535
peak=    3.375 closest distance to " O   HOH Z 374 " =    2.505
peak=    3.374 closest distance to " CB  MET A  47 " =    1.138
peak=    3.374 closest distance to " CB  LYS A 117 " =    1.160
peak=    3.372 closest distance to " O   HOH Z 174 " =    1.221
peak=    3.370 closest distance to " NE AARG A 275 " =    1.476
peak=    3.366 closest distance to " O   HOH Z  44 " =    2.318
peak=    3.366 closest distance to " O   HOH Z   7 " =    1.175
peak=    3.365 closest distance to " CG AARG A 275 " =    1.107
peak=    3.361 closest distance to " N   ASN A  39 " =    1.310
peak=    3.358 closest distance to " CD1 ILE A 106 " =    1.086
peak=    3.357 closest distance to " O   HOH Z 215 " =    1.575
peak=    3.354 closest distance to " O   HOH Z 214 " =    1.882
peak=    3.354 closest distance to " O   HOH Z 279 " =    2.386
peak=    3.347 closest distance to " CB  GLN A  88 " =    1.232
peak=    3.344 closest distance to " O   HOH Z 174 " =    2.557
peak=    3.343 closest distance to " O   HOH Z 197 " =    2.178
peak=    3.340 closest distance to " O   HOH Z 287 " =    1.680
peak=    3.337 closest distance to " O   ALA A  71 " =    0.944
peak=    3.335 closest distance to " N   PHE A 130 " =    1.380
peak=    3.320 closest distance to " CZ  PHE A 218 " =    1.055
peak=    3.319 closest distance to " CG  LEU A 167 " =    1.167
peak=    3.313 closest distance to " CB  LEU A 237 " =    1.003
peak=    3.306 closest distance to " CG2AVAL A 121 " =    2.360
peak=    3.305 closest distance to " O   HOH Z 189 " =    2.776
peak=    3.303 closest distance to " ND1 HIS A  86 " =    1.672
peak=    3.299 closest distance to " O   HOH Z 148 " =    3.654
peak=    3.298 closest distance to " CA  TYR A 186 " =    1.523
peak=    3.298 closest distance to " CZ  PHE A 192 " =    1.143
peak=    3.295 closest distance to " NE AARG A 102 " =    1.194
peak=    3.294 closest distance to " CD  ARG A  14 " =    1.279
peak=    3.291 closest distance to " O   HOH Z  57 " =    1.355
peak=    3.290 closest distance to " CB  ALA A   9 " =    1.597
peak=    3.290 closest distance to " O   HOH Z  38 " =    2.218
peak=    3.284 closest distance to " O   HOH Z 128 " =    2.239
peak=    3.282 closest distance to " O   HOH Z 151 " =    1.802
peak=    3.281 closest distance to " O   HOH Z 144 " =    1.386
peak=    3.281 closest distance to " O   HOH Z  43 " =    2.185
peak=    3.280 closest distance to " O   HOH Z 277 " =    2.358
peak=    3.279 closest distance to " CA  ASP A 140 " =    1.264
peak=    3.278 closest distance to " CB  GLU A 236 " =    1.187
peak=    3.276 closest distance to " CA  GLY A 196 " =    0.874
peak=    3.275 closest distance to " O   HOH Z 172 " =    4.076
peak=    3.274 closest distance to " CD1 LEU A 101 " =    1.195
peak=    3.274 closest distance to " CA  LEU A 101 " =    1.634
peak=    3.273 closest distance to " OG  SER A  22 " =    2.922
peak=    3.271 closest distance to " CA  GLU A 152 " =    0.815
peak=    3.268 closest distance to " CB  ARG A 139 " =    0.909
peak=    3.267 closest distance to " O   HOH Z  78 " =    1.647
peak=    3.266 closest distance to " O   TRP A 274 " =    1.807
peak=    3.264 closest distance to " CB  ALA A 291 " =    1.453
peak=    3.263 closest distance to " O   HOH Z 419 " =    1.649
peak=    3.261 closest distance to " NH1BARG A 275 " =    1.323
peak=    3.259 closest distance to " CG  MET A 188 " =    1.366
peak=    3.259 closest distance to " CB  SER A  62 " =    1.289
peak=    3.258 closest distance to " CD  LYS A 166 " =    1.358
peak=    3.257 closest distance to " O   HOH Z 345 " =    1.602
peak=    3.255 closest distance to " CE  LYS A  76 " =    0.867
peak=    3.255 closest distance to " O   HOH Z 217 " =    1.390
peak=    3.254 closest distance to " O   HOH Z 207 " =    2.445
peak=    3.253 closest distance to " O   ALA A 165 " =    1.338
peak=    3.250 closest distance to " O   HOH Z 145 " =    1.721
peak=    3.249 closest distance to " CB  THR A  31 " =    1.594
peak=    3.247 closest distance to " CA  ILE A  33 " =    1.640
peak=    3.244 closest distance to " O   HOH Z 383 " =    2.176
peak=    3.240 closest distance to " NH2 ARG A  79 " =    1.325
peak=    3.239 closest distance to " O   HOH Z 131 " =    2.469
peak=    3.236 closest distance to " O   HOH Z 114 " =    1.598
peak=    3.235 closest distance to " O   HOH Z  30 " =    2.154
peak=    3.231 closest distance to " O   HOH Z  49 " =    2.683
peak=    3.230 closest distance to " CB  SER A 271 " =    0.975
peak=    3.225 closest distance to " CA  ASN A 215 " =    1.198
peak=    3.222 closest distance to " O   HOH Z  87 " =    2.484
peak=    3.222 closest distance to " CE  LYS A 166 " =    2.006
peak=    3.222 closest distance to " CD  ARG A 159 " =    0.834
peak=    3.219 closest distance to " CB  ASN A  39 " =    0.846
peak=    3.219 closest distance to " O   HOH Z 404 " =    1.464
peak=    3.207 closest distance to " O   HOH Z 147 " =    1.620
peak=    3.202 closest distance to " O   HOH Z 420 " =    5.883
peak=    3.200 closest distance to " O   HOH Z 434 " =    3.085
peak=    3.200 closest distance to " O   HOH Z 158 " =    3.122
peak=    3.195 closest distance to " O   HOH Z 407 " =    2.178
peak=    3.194 closest distance to " CA  ALA A 154 " =    1.314
peak=    3.193 closest distance to " O   HOH Z 284 " =    1.468
peak=    3.189 closest distance to " O   HOH Z 407 " =    3.328
peak=    3.188 closest distance to " O   HOH Z 149 " =    1.917
peak=    3.187 closest distance to " O   GLN A  58 " =    1.785
peak=    3.185 closest distance to " O   HOH Z 244 " =    1.593
peak=    3.184 closest distance to " O   HOH Z 133 " =    1.785
peak=    3.181 closest distance to " CD1 LEU A 228 " =    1.308
peak=    3.177 closest distance to " NH2BARG A 190 " =    1.665
peak=    3.171 closest distance to " O   HOH Z 302 " =    2.042
peak=    3.171 closest distance to " O   HOH Z 359 " =    1.909
peak=    3.170 closest distance to " O   HOH Z 172 " =    5.892
peak=    3.170 closest distance to " CA  ASP A 191 " =    0.775
peak=    3.162 closest distance to " O   HOH Z 130 " =    1.294
peak=    3.160 closest distance to " O   HOH Z 273 " =    2.617
peak=    3.153 closest distance to " CB  LYS A 193 " =    1.276
peak=    3.152 closest distance to " CZ3 TRP A  92 " =    1.210
peak=    3.152 closest distance to " CA  GLY A 211 " =    1.142
peak=    3.151 closest distance to " O   HOH Z 130 " =    2.199
peak=    3.143 closest distance to " O   HOH Z  71 " =    1.178
peak=    3.143 closest distance to " NH2 ARG A 219 " =    1.862
peak=    3.137 closest distance to " CB  SER A 212 " =    1.125
peak=    3.137 closest distance to " O   HOH Z  63 " =    1.762
peak=    3.131 closest distance to " O   HOH Z  59 " =    2.036
peak=    3.126 closest distance to " O   HOH Z 136 " =    1.078
peak=    3.114 closest distance to " O   HOH Z 305 " =    3.563
peak=    3.113 closest distance to " NH1BARG A 145 " =    1.265
peak=    3.109 closest distance to " CB  THR A 235 " =    0.994
peak=    3.109 closest distance to " NE1 TRP A  85 " =    2.109
peak=    3.104 closest distance to " C   ALA A 299 " =    0.973
peak=    3.103 closest distance to " O   HOH Z 139 " =    3.312
peak=    3.100 closest distance to " CB  ALA A  84 " =    0.965
peak=    3.098 closest distance to " CE1 PHE A 208 " =    1.019
peak=    3.097 closest distance to " O   HOH Z   1 " =    1.946
peak=    3.095 closest distance to " O   VAL A 232 " =    1.960
peak=    3.089 closest distance to " CG1 VAL A 296 " =    1.176
peak=    3.088 closest distance to " O   HOH Z  88 " =    2.738
peak=    3.078 closest distance to " CB  ALA A 256 " =    1.490
peak=    3.078 closest distance to " O   HOH Z 189 " =    1.518
peak=    3.076 closest distance to " CA  GLY A 267 " =    0.962
peak=    3.076 closest distance to " O   HOH Z 116 " =    3.152
peak=    3.066 closest distance to " CA  THR A 264 " =    0.784
peak=    3.048 closest distance to " NH2AARG A 190 " =    1.262
peak=    3.048 closest distance to " O   HOH Z 175 " =    2.304
peak=    3.041 closest distance to " O   HOH Z  48 " =    1.788
peak=    3.002 closest distance to " O   HOH Z 334 " =    1.600

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.793 - 5.551
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 219
   mapped sites are within: 0.793 - 5.551

peak=   -5.394 closest distance to " CG2 VAL A 230 " =    0.909
peak=   -4.915 closest distance to " O   HOH Z 231 " =    1.391
peak=   -4.482 closest distance to " O   ILE A 109 " =    2.689
peak=   -4.332 closest distance to " O   HOH Z  92 " =    1.521
peak=   -4.180 closest distance to " OG ASER A 134 " =    1.325
peak=   -4.155 closest distance to " CD2 LEU A 143 " =    2.541
peak=   -4.152 closest distance to " CA  SER A 271 " =    2.420
peak=   -4.140 closest distance to " O   HOH Z 290 " =    1.134
peak=   -4.112 closest distance to " OG  SER A  87 " =    1.551
peak=   -4.093 closest distance to " O   HOH Z  13 " =    1.363
peak=   -4.091 closest distance to " O   HOH Z 266 " =    4.388
peak=   -4.085 closest distance to " O   HOH Z 377 " =    1.522
peak=   -4.070 closest distance to " O   HOH Z  19 " =    2.219
peak=   -4.007 closest distance to " O   HOH Z  52 " =    1.674
peak=   -4.005 closest distance to " CD2 LEU A 237 " =    2.711
peak=   -4.002 closest distance to " O   HOH Z 177 " =    1.211
peak=   -3.961 closest distance to " O   HOH Z  17 " =    1.367
peak=   -3.959 closest distance to " NH1 ARG A  56 " =    2.329
peak=   -3.942 closest distance to " CG  ASN A  45 " =    1.759
peak=   -3.932 closest distance to " CD  GLN A  88 " =    2.322
peak=   -3.908 closest distance to " O   HOH Z 184 " =    1.276
peak=   -3.897 closest distance to " CD1 PHE A  59 " =    1.834
peak=   -3.896 closest distance to " NH2 ARG A  66 " =    1.789
peak=   -3.858 closest distance to " CG  ASP A 231 " =    0.825
peak=   -3.836 closest distance to " N   THR A 157 " =    1.655
peak=   -3.835 closest distance to " O   HOH Z 151 " =    1.408
peak=   -3.823 closest distance to " O   HOH Z  43 " =    1.553
peak=   -3.820 closest distance to " N   GLN A  58 " =    1.571
peak=   -3.816 closest distance to " CD  ARG A 156 " =    1.994
peak=   -3.795 closest distance to " O   HOH Z 243 " =    1.564
peak=   -3.787 closest distance to " CB  TYR A  15 " =    2.210
peak=   -3.785 closest distance to " CD  LYS A 289 " =    2.480
peak=   -3.779 closest distance to " N   ALA A 226 " =    2.057
peak=   -3.778 closest distance to " O   HOH Z 103 " =    1.984
peak=   -3.772 closest distance to " C   ALA A 158 " =    1.292
peak=   -3.766 closest distance to " C   ASN A 187 " =    1.788
peak=   -3.753 closest distance to " O   HOH Z 275 " =    1.565
peak=   -3.745 closest distance to " CB  SER A 134 " =    1.906
peak=   -3.739 closest distance to " OE1 GLN A  88 " =    1.000
peak=   -3.736 closest distance to " CD  ARG A  14 " =    3.191
peak=   -3.735 closest distance to " C   ASN A 285 " =    2.544
peak=   -3.729 closest distance to " CD2 LEU A 167 " =    1.822
peak=   -3.712 closest distance to " CG  GLN A 223 " =    2.307
peak=   -3.706 closest distance to " O   HOH Z 407 " =    3.501
peak=   -3.689 closest distance to " O   HOH Z 388 " =    1.870
peak=   -3.669 closest distance to " CB  CYS A 254 " =    2.221
peak=   -3.661 closest distance to " CG1 VAL A 296 " =    1.399
peak=   -3.661 closest distance to " O   HOH Z  97 " =    1.708
peak=   -3.652 closest distance to " OG1 THR A 178 " =    1.304
peak=   -3.648 closest distance to " O   HOH Z 166 " =    1.912
peak=   -3.636 closest distance to " O   HOH Z 292 " =    4.484
peak=   -3.627 closest distance to " CD  ARG A 138 " =    1.431
peak=   -3.605 closest distance to " O   HOH Z  15 " =    1.721
peak=   -3.604 closest distance to " O   HOH Z 221 " =    1.423
peak=   -3.593 closest distance to " CD2 LEU A 300 " =    2.968
peak=   -3.587 closest distance to " OG  SER A  26 " =    1.169
peak=   -3.585 closest distance to " CB  TRP A  85 " =    2.562
peak=   -3.584 closest distance to " CG  GLU A   2 " =    1.835
peak=   -3.580 closest distance to " O   HOH Z 120 " =    4.128
peak=   -3.580 closest distance to " CG  PRO A 163 " =    2.492
peak=   -3.578 closest distance to " O   HOH Z 221 " =    1.347
peak=   -3.576 closest distance to " CD1 LEU A 228 " =    2.457
peak=   -3.573 closest distance to " O   HOH Z 124 " =    1.354
peak=   -3.560 closest distance to " CG  GLU A 152 " =    2.341
peak=   -3.560 closest distance to " O   HOH Z 389 " =    1.731
peak=   -3.555 closest distance to " NH1 ARG A 195 " =    2.712
peak=   -3.554 closest distance to " CB  ALA A 227 " =    2.374
peak=   -3.535 closest distance to " OG BSER A 134 " =    1.392
peak=   -3.523 closest distance to " CG  GLU A  53 " =    1.589
peak=   -3.517 closest distance to " O   HOH Z  98 " =    1.857
peak=   -3.515 closest distance to " O   HOH Z 353 " =    2.371
peak=   -3.513 closest distance to " O   HOH Z 396 " =    1.592
peak=   -3.513 closest distance to " O   HOH Z 189 " =    2.316
peak=   -3.508 closest distance to " C   HIS A 108 " =    1.146
peak=   -3.507 closest distance to " CG  MET A 105 " =    0.992
peak=   -3.504 closest distance to " N   ALA A   9 " =    1.462
peak=   -3.501 closest distance to " CD  GLN A  88 " =    0.802
peak=   -3.498 closest distance to " CB  GLN A  55 " =    1.410
peak=   -3.493 closest distance to " CD2 LEU A 237 " =    2.769
peak=   -3.485 closest distance to " CH2 TRP A 179 " =    1.232
peak=   -3.481 closest distance to " CD1 LEU A 101 " =    2.788
peak=   -3.477 closest distance to " OD2 ASP A  65 " =    1.649
peak=   -3.476 closest distance to " CG  ARG A 138 " =    1.066
peak=   -3.476 closest distance to " CE2 TYR A  30 " =    2.810
peak=   -3.471 closest distance to " O   HOH Z  38 " =    1.447
peak=   -3.469 closest distance to " O   HOH Z  98 " =    1.476
peak=   -3.466 closest distance to " O   HOH Z  88 " =    2.093
peak=   -3.458 closest distance to " O   PRO A 163 " =    2.024
peak=   -3.452 closest distance to " C   GLN A 240 " =    2.288
peak=   -3.452 closest distance to " O   SER A 135 " =    1.435
peak=   -3.450 closest distance to " CD  ARG A 139 " =    1.653
peak=   -3.446 closest distance to " CG2 VAL A 112 " =    2.559
peak=   -3.444 closest distance to " OG  SER A  97 " =    2.246
peak=   -3.443 closest distance to " OD1 ASN A 148 " =    1.660
peak=   -3.439 closest distance to " O   HOH Z 211 " =    1.579
peak=   -3.438 closest distance to " N   ALA A  43 " =    2.490
peak=   -3.429 closest distance to " N   GLN A 122 " =    1.590
peak=   -3.423 closest distance to " O   HOH Z 366 " =    1.723
peak=   -3.421 closest distance to " O   HOH Z  71 " =    1.038
peak=   -3.419 closest distance to " CH2 TRP A 177 " =    2.178
peak=   -3.419 closest distance to " O   HOH Z 274 " =    2.820
peak=   -3.414 closest distance to " O   HOH Z 166 " =    1.468
peak=   -3.410 closest distance to " CG  TRP A 266 " =    1.679
peak=   -3.408 closest distance to " CB  ALA A  43 " =    2.506
peak=   -3.402 closest distance to " O   VAL A  67 " =    2.840
peak=   -3.378 closest distance to " CG2 VAL A 296 " =    1.332
peak=   -3.375 closest distance to " CB  ASN A  39 " =    1.941
peak=   -3.374 closest distance to " O   HOH Z  11 " =    1.580
peak=   -3.371 closest distance to " CZ  TYR A 172 " =    1.629
peak=   -3.365 closest distance to " CE  MET A  93 " =    1.333
peak=   -3.362 closest distance to " NH1 ARG A 195 " =    2.290
peak=   -3.360 closest distance to " CE  MET A 105 " =    2.121
peak=   -3.359 closest distance to " O   HOH Z 336 " =    5.551
peak=   -3.354 closest distance to " O   HOH Z 252 " =    1.220
peak=   -3.350 closest distance to " O   HOH Z 431 " =    1.561
peak=   -3.350 closest distance to " N   ALA A 248 " =    2.217
peak=   -3.350 closest distance to " CB  PRO A 243 " =    2.637
peak=   -3.348 closest distance to " O   HOH Z 266 " =    4.736
peak=   -3.343 closest distance to " CB  PRO A 163 " =    2.635
peak=   -3.342 closest distance to " CG  ASP A  50 " =    2.166
peak=   -3.341 closest distance to " CA  GLY A  35 " =    2.038
peak=   -3.338 closest distance to " CA  GLY A  98 " =    2.061
peak=   -3.337 closest distance to " O   GLY A 211 " =    1.540
peak=   -3.323 closest distance to " ND2 ASN A  60 " =    1.477
peak=   -3.323 closest distance to " ND2 ASN A  60 " =    1.595
peak=   -3.321 closest distance to " O   HOH Z 345 " =    4.645
peak=   -3.317 closest distance to " CG2 THR A   4 " =    1.987
peak=   -3.314 closest distance to " CB  SER A 258 " =    2.020
peak=   -3.314 closest distance to " O   ALA A 256 " =    1.719
peak=   -3.312 closest distance to " O   HOH Z 426 " =    1.774
peak=   -3.312 closest distance to " OG ASER A 210 " =    1.424
peak=   -3.307 closest distance to " NH2 ARG A 159 " =    2.521
peak=   -3.305 closest distance to " OG1 THR A  82 " =    1.940
peak=   -3.304 closest distance to " CD2 TYR A 293 " =    2.025
peak=   -3.300 closest distance to " NH2 ARG A  79 " =    1.911
peak=   -3.299 closest distance to " O   HOH Z 292 " =    3.106
peak=   -3.299 closest distance to " O   PRO A 198 " =    1.359
peak=   -3.293 closest distance to " OXT GLY A 302 " =    3.608
peak=   -3.292 closest distance to " SG  CYS A 254 " =    3.095
peak=   -3.289 closest distance to " CA  GLY A 133 " =    1.907
peak=   -3.289 closest distance to " O   HOH Z 387 " =    3.763
peak=   -3.285 closest distance to " OD2 ASP A 171 " =    1.939
peak=   -3.283 closest distance to " NH2AARG A 275 " =    5.405
peak=   -3.278 closest distance to " O   HOH Z   9 " =    1.906
peak=   -3.276 closest distance to " O   HOH Z 241 " =    1.255
peak=   -3.275 closest distance to " O   ASN A 301 " =    1.664
peak=   -3.275 closest distance to " CB  ALA A 248 " =    1.917
peak=   -3.273 closest distance to " CD1 LEU A   5 " =    2.530
peak=   -3.270 closest distance to " CA  ASN A 127 " =    1.100
peak=   -3.268 closest distance to " O   HOH Z 295 " =    1.314
peak=   -3.260 closest distance to " O   HOH Z 198 " =    1.922
peak=   -3.255 closest distance to " O   HOH Z 377 " =    1.245
peak=   -3.250 closest distance to " O   HOH Z 317 " =    2.347
peak=   -3.248 closest distance to " CG  TYR A 172 " =    2.318
peak=   -3.247 closest distance to " CE3 TRP A  70 " =    1.744
peak=   -3.245 closest distance to " N   SER A 276 " =    1.425
peak=   -3.241 closest distance to " O   VAL A 174 " =    2.136
peak=   -3.240 closest distance to " NE2 GLN A  88 " =    0.848
peak=   -3.238 closest distance to " O   HOH Z 250 " =    1.437
peak=   -3.236 closest distance to " O   HOH Z  63 " =    0.840
peak=   -3.233 closest distance to " CG  LEU A 228 " =    0.981
peak=   -3.227 closest distance to " OH  TYR A 214 " =    1.280
peak=   -3.225 closest distance to " O   HOH Z 306 " =    2.868
peak=   -3.224 closest distance to " O   HOH Z 125 " =    2.837
peak=   -3.221 closest distance to " O   HOH Z 210 " =    1.105
peak=   -3.221 closest distance to " O   HOH Z 350 " =    1.802
peak=   -3.217 closest distance to " N   GLY A  23 " =    2.134
peak=   -3.212 closest distance to " O   HOH Z 119 " =    2.627
peak=   -3.210 closest distance to " O   HOH Z 236 " =    1.210
peak=   -3.208 closest distance to " CG  ARG A 259 " =    2.887
peak=   -3.206 closest distance to " O   HOH Z  10 " =    1.485
peak=   -3.203 closest distance to " O   GLY A  80 " =    2.546
peak=   -3.201 closest distance to " OD2 ASP A 171 " =    2.144
peak=   -3.200 closest distance to " CA  LYS A 166 " =    2.254
peak=   -3.189 closest distance to " CB  ALA A  51 " =    1.795
peak=   -3.182 closest distance to " CD  ARG A 195 " =    5.003
peak=   -3.182 closest distance to " O   ALA A 158 " =    1.047
peak=   -3.181 closest distance to " CD1 TRP A 179 " =    1.069
peak=   -3.179 closest distance to " O   TYR A  30 " =    2.647
peak=   -3.176 closest distance to " CA  GLY A 133 " =    2.206
peak=   -3.167 closest distance to " CG2 ILE A 151 " =    2.533
peak=   -3.163 closest distance to " O   GLN A 194 " =    1.249
peak=   -3.162 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.156 closest distance to " CE BMET A  47 " =    1.964
peak=   -3.154 closest distance to " CD2 LEU A   5 " =    1.280
peak=   -3.149 closest distance to " CD1 TYR A 247 " =    2.305
peak=   -3.148 closest distance to " O   HOH Z 234 " =    4.440
peak=   -3.146 closest distance to " C   LEU A 143 " =    1.309
peak=   -3.145 closest distance to " O   VAL A  67 " =    2.618
peak=   -3.140 closest distance to " CB  ALA A 114 " =    2.260
peak=   -3.139 closest distance to " O   HOH Z 186 " =    1.267
peak=   -3.139 closest distance to " O   HOH Z 179 " =    0.793
peak=   -3.137 closest distance to " CD1 ILE A 199 " =    2.492
peak=   -3.137 closest distance to " O   HOH Z 252 " =    4.196
peak=   -3.137 closest distance to " CB  PRO A  54 " =    2.407
peak=   -3.136 closest distance to " CA  VAL A 232 " =    2.278
peak=   -3.135 closest distance to " CE  LYS A  76 " =    2.735
peak=   -3.133 closest distance to " CD  ARG A 259 " =    2.543
peak=   -3.126 closest distance to " O   TYR A 186 " =    2.299
peak=   -3.118 closest distance to " O   GLY A 118 " =    2.151
peak=   -3.116 closest distance to " CB  SER A  63 " =    3.298
peak=   -3.115 closest distance to " CB  ASP A 286 " =    2.185
peak=   -3.112 closest distance to " CZ  TYR A 169 " =    1.956
peak=   -3.107 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.107 closest distance to " O   HOH Z 430 " =    1.713
peak=   -3.098 closest distance to " NH2 ARG A 156 " =    1.166
peak=   -3.097 closest distance to " CA  GLY A 203 " =    2.311
peak=   -3.091 closest distance to " CG  LYS A 193 " =    2.456
peak=   -3.090 closest distance to " OH  TYR A 169 " =    1.044
peak=   -3.087 closest distance to " O   HOH Z  60 " =    2.028
peak=   -3.081 closest distance to " O   HOH Z 108 " =    2.435
peak=   -3.080 closest distance to " O   HOH Z 426 " =    2.321
peak=   -3.068 closest distance to " NZ BLYS A 290 " =    1.278
peak=   -3.060 closest distance to " O   HOH Z 165 " =    2.068
peak=   -3.048 closest distance to " CB  PHE A 192 " =    1.784
peak=   -3.045 closest distance to " O   HOH Z 345 " =    2.104
peak=   -3.038 closest distance to " O   TRP A  92 " =    1.763
peak=   -3.036 closest distance to " NH2BARG A 145 " =    2.624

================= 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    :  0.4861 0.4907   6.287321e+00   6.284039e+00
   1_bss:  0.4786 0.4768   6.285023e+00   6.279082e+00
   1_xyz:  0.4051 0.4378   6.189877e+00   6.235816e+00
   1_adp:  0.3660 0.4222   6.129259e+00   6.215414e+00
   1_occ:  0.3656 0.4228   6.128676e+00   6.215328e+00
   2_bss:  0.3636 0.4200   6.128599e+00   6.213968e+00
   2_xyz:  0.2781 0.3476   5.931382e+00   6.088176e+00
   2_adp:  0.2553 0.3215   5.864039e+00   6.035301e+00
   2_occ:  0.2552 0.3213   5.863103e+00   6.034964e+00
   3_bss:  0.2535 0.3171   5.861376e+00   6.030739e+00
   3_xyz:  0.1912 0.2470   5.608859e+00   5.811316e+00
   3_adp:  0.1726 0.2318   5.531487e+00   5.753265e+00
   3_occ:  0.1725 0.2316   5.530999e+00   5.752706e+00
   4_bss:  0.1720 0.2319   5.530368e+00   5.753139e+00
   4_xyz:  0.1425 0.1983   5.367570e+00   5.610738e+00
   4_adp:  0.1352 0.1891   5.323178e+00   5.563320e+00
   4_occ:  0.1350 0.1888   5.322581e+00   5.562660e+00
   5_bss:  0.1353 0.1891   5.323758e+00   5.563463e+00
   5_xyz:  0.1199 0.1727   5.227051e+00   5.481004e+00
   5_adp:  0.1175 0.1692   5.208050e+00   5.461244e+00
   5_occ:  0.1174 0.1689   5.207360e+00   5.460563e+00
   5_bss:  0.1173 0.1689   5.207309e+00   5.460349e+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:  0.320   7.616   9.895   7.683   8.501   0.000   0.000   0.000
   1_xyz:  0.320   7.616   9.895   7.683   8.501   0.000   0.000   0.000
   1_adp:  0.320   7.616   9.895   7.683   8.501   0.000   0.000   0.000
   1_occ:  0.320   7.616   9.895   7.683   8.501   0.000   0.000   0.000
   2_bss:  0.328  34.598   6.034   4.450   5.849   0.000   0.000   0.000
   2_xyz:  0.328  34.598   6.034   4.450   5.849   0.000   0.000   0.000
   2_adp:  0.328  34.598   6.034   4.450   5.849   0.000   0.000   0.000
   2_occ:  0.328  34.598   6.034   4.450   5.849   0.000   0.000   0.000
   3_bss:  0.318  34.599   3.830   2.830   3.429   0.000   0.000   0.000
   3_xyz:  0.318  34.599   3.830   2.830   3.429   0.000   0.000   0.000
   3_adp:  0.318  34.599   3.830   2.830   3.429   0.000   0.000   0.000
   3_occ:  0.318  34.599   3.830   2.830   3.429   0.000   0.000   0.000
   4_bss:  0.315  54.738   2.322   1.817   2.091   0.000   0.000   0.000
   4_xyz:  0.315  54.738   2.322   1.817   2.091   0.000   0.000   0.000
   4_adp:  0.315  54.738   2.322   1.817   2.091   0.000   0.000   0.000
   4_occ:  0.315  54.738   2.322   1.817   2.091   0.000   0.000   0.000
   5_bss:  0.325  54.743   1.830   1.485   1.811   0.000   0.000   0.000
   5_xyz:  0.325  54.743   1.830   1.485   1.811   0.000   0.000   0.000
   5_adp:  0.325  54.743   1.830   1.485   1.811   0.000   0.000   0.000
   5_occ:  0.325  54.743   1.830   1.485   1.811   0.000   0.000   0.000
   5_bss:  0.322  52.451   0.122  -0.224   0.102   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.539 0.3863  0.4590    75352.817
   1_bss:  61.258 0.3744  0.5607    72755.055
   1_xyz:  54.673 0.4575  0.6708    59114.109
   1_adp:  51.060 0.5039  0.7809    54130.659
   1_occ:  51.165 0.5025  0.7777    54290.660
   2_bss:  50.858 0.5063  0.7078    53915.012
   2_xyz:  38.568 0.6578  0.9142    34829.313
   2_adp:  34.851 0.7018  0.9680    29641.359
   2_occ:  34.799 0.7024  0.9687    29574.357
   3_bss:  34.578 0.7046  0.9011    29208.412
   3_xyz:  25.009 0.8102  0.9875    16258.497
   3_adp:  23.008 0.8313  0.9981    14232.753
   3_occ:  22.996 0.8314  0.9980    14208.616
   4_bss:  22.927 0.8322  0.9548    14208.699
   4_xyz:  19.172 0.8689  0.9759    10248.059
   4_adp:  17.979 0.8805  0.9785     9333.806
   4_occ:  17.962 0.8806  0.9784     9322.254
   5_bss:  17.962 0.8806  0.9658     9334.792
   5_xyz:  16.085 0.8973  0.9745     7788.743
   5_adp:  15.582 0.9019  0.9741     7491.810
   5_occ:  15.565 0.9020  0.9740     7475.781
   5_bss:  15.565 0.9020  0.9739     7468.872
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3813e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3813e+01
   1_xyz:   1.755  0.014  0.111 18.231  0.007  4.110   1.5067e-01
   1_adp:   1.755  0.014  0.111 18.231  0.007  4.110   1.5067e-01
   1_occ:   1.755  0.014  0.111 18.231  0.007  4.110   1.5067e-01
   2_bss:   1.755  0.014  0.111 18.231  0.007  4.110   1.5067e-01
   2_xyz:   1.197  0.009  0.082 16.473  0.005  4.113   9.0222e-02
   2_adp:   1.197  0.009  0.082 16.473  0.005  4.113   9.0222e-02
   2_occ:   1.197  0.009  0.082 16.473  0.005  4.113   9.0222e-02
   3_bss:   1.197  0.009  0.082 16.473  0.005  4.113   9.0222e-02
   3_xyz:   1.098  0.007  0.079 15.353  0.005  4.112   6.8558e-02
   3_adp:   1.098  0.007  0.079 15.353  0.005  4.112   6.8558e-02
   3_occ:   1.098  0.007  0.079 15.353  0.005  4.112   6.8558e-02
   4_bss:   1.098  0.007  0.079 15.353  0.005  4.112   6.8558e-02
   4_xyz:   1.059  0.007  0.078 15.351  0.004  4.120   6.6480e-02
   4_adp:   1.059  0.007  0.078 15.351  0.004  4.120   6.6480e-02
   4_occ:   1.059  0.007  0.078 15.351  0.004  4.120   6.6480e-02
   5_bss:   1.059  0.007  0.078 15.351  0.004  4.120   6.6480e-02
   5_xyz:   1.227  0.011  0.092 15.738  0.005  4.111   8.7217e-02
   5_adp:   1.227  0.011  0.092 15.738  0.005  4.111   8.7217e-02
   5_occ:   1.227  0.011  0.092 15.738  0.005  4.111   8.7217e-02
   5_bss:   1.227  0.011  0.092 15.738  0.005  4.111   8.7217e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9759e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9759e+00
   1_xyz:  15.198  0.172  0.483 85.049  0.051  2.136   1.0427e-01
   1_adp:  15.198  0.172  0.483 85.049  0.051  2.136   1.0427e-01
   1_occ:  15.198  0.172  0.483 85.049  0.051  2.136   1.0427e-01
   2_bss:  15.198  0.172  0.483 85.049  0.051  2.136   1.0427e-01
   2_xyz:   7.594  0.074  0.288 82.294  0.039  2.165   6.0663e-02
   2_adp:   7.594  0.074  0.288 82.294  0.039  2.165   6.0663e-02
   2_occ:   7.594  0.074  0.288 82.294  0.039  2.165   6.0663e-02
   3_bss:   7.594  0.074  0.288 82.294  0.039  2.165   6.0663e-02
   3_xyz:   7.831  0.052  0.299 81.299  0.056  2.349   4.4037e-02
   3_adp:   7.831  0.052  0.299 81.299  0.056  2.349   4.4037e-02
   3_occ:   7.831  0.052  0.299 81.299  0.056  2.349   4.4037e-02
   4_bss:   7.831  0.052  0.299 81.299  0.056  2.349   4.4037e-02
   4_xyz:   8.408  0.054  0.357 83.480  0.035  2.295   4.8396e-02
   4_adp:   8.408  0.054  0.357 83.480  0.035  2.295   4.8396e-02
   4_occ:   8.408  0.054  0.357 83.480  0.035  2.295   4.8396e-02
   5_bss:   8.408  0.054  0.357 83.480  0.035  2.295   4.8396e-02
   5_xyz:   8.199  0.065  0.578 83.538  0.035  2.271   6.7946e-02
   5_adp:   8.199  0.065  0.578 83.538  0.035  2.271   6.7946e-02
   5_occ:   8.199  0.065  0.578 83.538  0.035  2.271   6.7946e-02
   5_bss:   8.199  0.065  0.578 83.538  0.035  2.271   6.7946e-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:  83.52   0.00  13.48  83.52   0.00  11.24  83.44   0.00  25.69
   1_occ:  83.52   0.00  13.48  83.52   0.00  11.24  83.44   0.00  25.69
   2_bss:  83.52   0.00  13.48  83.52   0.00  11.24  83.44   0.00  25.69
   2_xyz:  83.52   0.00  13.48  83.52   0.00  11.24  83.44   0.00  25.69
   2_adp:  77.43   0.00  13.55  77.43   0.00  10.12  74.49   0.00  32.22
   2_occ:  77.43   0.00  13.55  77.43   0.00  10.12  74.49   0.00  32.22
   3_bss:  77.43   0.00  13.55  77.43   0.00  10.12  74.49   0.00  32.22
   3_xyz:  77.43   0.00  13.55  77.43   0.00  10.12  74.49   0.00  32.22
   3_adp:  99.98   0.00  14.82  99.98   0.00  10.01  98.42   1.65  41.02
   3_occ:  99.98   0.00  14.82  99.98   0.00  10.01  98.42   1.65  41.02
   4_bss:  99.98   0.00  14.82  99.98   0.00  10.01  98.42   1.65  41.02
   4_xyz:  99.98   0.00  14.82  99.98   0.00  10.01  98.42   1.65  41.02
   4_adp: 104.39   0.00  14.51 104.39   0.00   9.64  95.61   2.21  41.06
   4_occ: 104.39   0.00  14.51 104.39   0.00   9.64  95.61   2.21  41.06
   5_bss: 104.39   0.00  14.51 104.39   0.00   9.64  95.61   2.21  41.06
   5_xyz: 104.39   0.00  14.51 104.39   0.00   9.64  95.61   2.21  41.06
   5_adp: 105.30   0.00  13.97 105.30   0.00   9.41  93.72   2.34  38.84
   5_occ: 105.30   0.00  13.97 105.30   0.00   9.41  93.72   2.34  38.84
   5_bss: 107.01   1.71  15.68 107.01   1.71  11.11  95.43   4.04  40.55
------------------------------------------------------------------------
 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:    1.236    0.042    0.414
   1_adp:    1.236    0.042    0.414
   1_occ:    1.236    0.042    0.414
   2_bss:    1.236    0.042    0.414
   2_xyz:    1.707    0.013    0.592
   2_adp:    1.707    0.013    0.592
   2_occ:    1.707    0.013    0.592
   3_bss:    1.707    0.013    0.592
   3_xyz:    1.730    0.045    0.679
   3_adp:    1.730    0.045    0.679
   3_occ:    1.730    0.045    0.679
   4_bss:    1.730    0.045    0.679
   4_xyz:    1.772    0.072    0.738
   4_adp:    1.772    0.072    0.738
   4_occ:    1.772    0.072    0.738
   5_bss:    1.772    0.072    0.738
   5_xyz:    1.867    0.074    0.771
   5_adp:    1.867    0.074    0.771
   5_occ:    1.867    0.074    0.771
   5_bss:    1.867    0.074    0.771
------------------------------------------------------------------------

CPU time actual refinement: 349.29


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1277/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_1277/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1277/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1277/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1277/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.14 
  Macro-tasks:
    bulk solvent and scale       = 40.89  
    individual site refinement   = 142.39 
    weights calculation          = 32.65  
    collect and process          = 6.43   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 222.51 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 111.51 
    alpha_beta                      = 8.15   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 119.81 
    fmodel                         = 7.07   
    r_factors                      = 0.20   
    phase_errors                   = 10.32  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 260.88 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.991 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    632 calls, 111.06 s
gradients_fft:          578 calls, 107.12 s

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

# Date 2008-01-16 Time 03:38:31 PST -0800 (1200483511.43 s)
Start R-work = 0.4861, R-free = 0.4907 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1856 (no bulk solvent and anisotropic scale)

Start R-work = 0.4786, R-free = 0.4768
Final R-work = 0.1173, R-free = 0.1689