# Date 2008-01-16 Time 01:32:11 PST -0800 (1200475931.17 s)
#phil __OFF__

Command line arguments: "../450.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7914
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 450

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.3993, 88.5498, 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: 2.81, per 1000 atoms: 1.00


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98085
Completeness in resolution range: 0.935572
Completeness with d_max=infinity: 0.932721

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9810
                             d_min =   1.9809

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98085
Completeness in resolution range: 0.935572
Completeness with d_max=infinity: 0.932721

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2384 [2201/2229]  1980   221  10.0%
  bin  2:  4.2384 -  3.3768 [2109/2128]  1895   214  10.1%
  bin  3:  3.3768 -  2.9537 [2082/2102]  1880   202   9.7%
  bin  4:  2.9537 -  2.6853 [2064/2089]  1857   207  10.0%
  bin  5:  2.6853 -  2.4938 [2047/2066]  1838   209  10.2%
  bin  6:  2.4938 -  2.3474 [2030/2078]  1825   205  10.1%
  bin  7:  2.3474 -  2.2302 [2037/2069]  1844   193   9.5%
  bin  8:  2.2302 -  2.1334 [2033/2068]  1817   216  10.6%
  bin  9:  2.1334 -  2.0515 [2024/2054]  1827   197   9.7%
  bin 10:  2.0515 -  1.9809 [ 962/2055]   867    95   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_450/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: 0.12 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:
        1.41 -     2.11: 12
        2.11 -     2.80: 755
        2.80 -     3.50: 4390
        3.50 -     4.20: 9235
        4.20 -     4.90: 13586
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.408 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.496 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.661 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.732 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.776 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27973 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_450/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_450/model_refine_001.geo

CPU time processing inputs: 8.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.3993 88.54975 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: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4890   r_free= 0.4735   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.290465                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1430  158 0.3939 0.3785      6.6113      6.5829|
|  2:  4.7272 -  3.7719 0.99   1375  153 0.4094 0.4750      6.7901      6.9517|
|  3:  3.7719 -  3.3009 0.99   1342  151 0.4624 0.4108      6.6936      6.6488|
|  4:  3.3009 -  3.0017 0.99   1351  142 0.4809 0.4452      6.5221      6.4798|
|  5:  3.0017 -  2.7881 0.99   1309  155 0.5180 0.4826      6.3721      6.4024|
|  6:  2.7881 -  2.6246 0.98   1334  144 0.5171 0.5565      6.2792      6.2036|
|  7:  2.6246 -  2.4938 0.99   1309  150 0.5201 0.4631      6.2343      6.1361|
|  8:  2.4938 -  2.3857 0.98   1324  142 0.5340 0.4502      6.1961      6.1561|
|  9:  2.3857 -  2.2942 0.98   1312  145 0.5355 0.5539      6.1346      6.1699|
| 10:  2.2942 -  2.2153 0.98   1295  143 0.5479 0.4971      6.0987      6.1079|
| 11:  2.2153 -  2.1462 0.99   1313  156 0.5214 0.5428      6.0195      6.0332|
| 12:  2.1462 -  2.0850 0.98   1295  140 0.5382 0.5205      5.9559      5.9509|
| 13:  2.0850 -  2.0303 0.93   1240  128 0.5360 0.5213      5.8891      5.8481|
| 14:  2.0303 -  1.9809 0.31    401   52 0.5281 0.4275      5.9079      5.7046|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1430   158  0.70  34.25   0.79     0.71      69903.86|
|  2:  4.7272 -  3.7719  1375   153  0.68  36.68   0.87     0.74     113690.33|
|  3:  3.7719 -  3.3009  1342   151  0.58  45.46   0.80     0.69     119168.10|
|  4:  3.3009 -  3.0017  1351   142  0.49  52.78   0.79     0.58     103204.92|
|  5:  3.0017 -  2.7881  1309   155  0.41  58.92   0.72     0.48      82037.72|
|  6:  2.7881 -  2.6246  1334   144  0.36  62.93   0.71     0.42      74647.76|
|  7:  2.6246 -  2.4938  1309   150  0.38  61.20   0.73     0.44      64035.36|
|  8:  2.4938 -  2.3857  1324   142  0.42  58.35   0.71     0.49      53798.25|
|  9:  2.3857 -  2.2942  1312   145  0.42  58.63   0.70     0.49      49742.97|
| 10:  2.2942 -  2.2153  1295   143  0.36  63.14   0.71     0.42      47592.49|
| 11:  2.2153 -  2.1462  1313   156  0.29  68.52   0.74     0.36      50096.63|
| 12:  2.1462 -  2.0850  1295   140  0.28  69.41   0.73     0.36      45397.80|
| 13:  2.0850 -  2.0303  1240   128  0.30  67.48   0.72     0.39      38859.42|
| 14:  2.0303 -  1.9809   401    52  0.40  60.14   0.75     0.41      27369.46|
|alpha:            min =        0.36 max =            0.74 mean =         0.51|
|beta:             min =    27369.46 max =       119168.10 mean =     69669.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.52|
|phase err.(test): min =        0.00 max =           89.95 mean =        56.79|
|-----------------------------------------------------------------------------|

============================== 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 = 15.213971             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.044   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.357868              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.754   (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 |  1.157 -  1.531:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.531 -  1.906:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.906 -  2.280:      153 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.280 -  2.654:      657 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.654 -  3.029:     1437 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.029 -  3.403:     2528 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.403 -  3.777:     3885 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.777 -  4.151:     5055 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.151 -  4.526:     6559 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.526 -  4.900:     7698 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.229 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.157 |       1.971 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    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 = 12.086)------------------------------------------|
|    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: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4941   r_free= 0.4771   ksol= 0.00   Bsol= 0.00   scale= 0.751    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.292768                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4794   r_free= 0.4656   ksol= 0.32   Bsol= 6.77   scale= 0.990    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.71,8.66,12.05,0.00,0.00,0.00); trace/3= 9.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.283877                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.171549             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.985   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.201786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.936   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4794      final r-factor (work) = 0.3993          |
| start r-factor (free) = 0.4656      final r-factor (free) = 0.4245          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.6446 = 13.17 * 0.50 * 6.2886 + 1.00 * 54.2292                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.9889 = 13.17 * 0.50 * 6.2014 + 1.00 * 0.1482                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3993      final r-factor (work) = 0.3560          |
| start r-factor (free) = 0.4245      final r-factor (free) = 0.4077          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4671 = 1.20 * 1.00 * 6.2014 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3741 = 1.20 * 1.00 * 6.1218 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.22   13.90    None  None   None       |
|    all(noH): 2823   0      0.00    82.22   13.90    None  None   None       |
|    Sol.    : 438    0      0.00    82.22   26.20    None  None   None       |
|    Mac.    : 2385   0      0.00    65.26   11.65    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 -   8.222: 1116   |   5:    41.109 -  49.330:   63        |
|      1:     8.222 -  16.443:  809   |   6:    49.330 -  57.552:   30        |
|      2:    16.443 -  24.665:  454   |   7:    57.552 -  65.774:   17        |
|      3:    24.665 -  32.887:  213   |   8:    65.774 -  73.995:    4        |
|      4:    32.887 -  41.109:  115   |   9:    73.995 -  82.217:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3560 r_free = 0.4077             target_work(ml) = 6.103         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3557 r_free = 0.4083             target_work(ml) = 6.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3557   r_free= 0.4083   ksol= 0.32   Bsol= 6.77   scale= 1.107    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.71,8.66,12.05,0.00,0.00,0.00); trace/3= 9.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.102160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3523   r_free= 0.4025   ksol= 0.32   Bsol= 43.64   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.54,4.43,7.58,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.102911                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.199157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.149  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553794              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.014  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3523      final r-factor (work) = 0.2747          |
| start r-factor (free) = 0.4025      final r-factor (free) = 0.3288          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1116 = 6.20 * 0.50 * 6.1181 + 1.00 * 0.1482                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.6674 = 6.20 * 0.50 * 5.9954 + 1.00 * 0.0842                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2747      final r-factor (work) = 0.2530          |
| start r-factor (free) = 0.3288      final r-factor (free) = 0.3094          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3373 = 0.55 * 1.00 * 5.9954 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2612 = 0.55 * 1.00 * 5.8646 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.27   13.82    None  None   None       |
|    all(noH): 2823   0      0.00    79.27   13.82    None  None   None       |
|    Sol.    : 438    0      0.00    79.27   32.27    None  None   None       |
|    Mac.    : 2385   0      0.00    71.90   10.43    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 -   7.927: 1205   |   5:    39.633 -  47.560:   97        |
|      1:     7.927 -  15.853:  772   |   6:    47.560 -  55.486:   42        |
|      2:    15.853 -  23.780:  362   |   7:    55.486 -  63.413:   23        |
|      3:    23.780 -  31.706:  182   |   8:    63.413 -  71.340:    8        |
|      4:    31.706 -  39.633:  128   |   9:    71.340 -  79.266:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2530 r_free = 0.3094             target_work(ml) = 5.844         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2527 r_free = 0.3093             target_work(ml) = 5.843         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2527   r_free= 0.3093   ksol= 0.32   Bsol= 43.64   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.54,4.43,7.58,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.843323                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2515   r_free= 0.3101   ksol= 0.31   Bsol= 56.80   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,2.97,5.14,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.845040                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.428420              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.382  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326098              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.509  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2515      final r-factor (work) = 0.1826          |
| start r-factor (free) = 0.3101      final r-factor (free) = 0.2351          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0057 = 5.43 * 0.50 * 5.8660 + 1.00 * 0.0842                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6090 = 5.43 * 0.50 * 5.7210 + 1.00 * 0.0809                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1826      final r-factor (work) = 0.1645          |
| start r-factor (free) = 0.2351      final r-factor (free) = 0.2139          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8793 = 0.33 * 1.00 * 5.7210 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8184 = 0.33 * 1.00 * 5.5114 + 1.00 * 0.0212                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.29  13.61    None  None   None       |
|    all(noH): 2823   0      0.00    108.29  13.61    None  None   None       |
|    Sol.    : 438    0      1.96    78.23   36.02    None  None   None       |
|    Mac.    : 2385   0      0.00    108.29  9.50     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 -  10.829: 1732   |   5:    54.146 -  64.975:   43        |
|      1:    10.829 -  21.658:  583   |   6:    64.975 -  75.804:   12        |
|      2:    21.658 -  32.487:  173   |   7:    75.804 -  86.633:    1        |
|      3:    32.487 -  43.317:  160   |   8:    86.633 -  97.462:    0        |
|      4:    43.317 -  54.146:  118   |   9:    97.462 - 108.291:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1645 r_free = 0.2139             target_work(ml) = 5.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1642 r_free = 0.2141             target_work(ml) = 5.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1642   r_free= 0.2141   ksol= 0.31   Bsol= 56.80   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,2.97,5.14,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.465975                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1633   r_free= 0.2122   ksol= 0.32   Bsol= 56.80   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.67,1.84,3.61,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.463725                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.915314              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.031  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.773227              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.597   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1633      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.2122      final r-factor (free) = 0.1796          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1244 = 2.92 * 0.50 * 5.5181 + 1.00 * 0.0809                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9272 = 2.92 * 0.50 * 5.3917 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1295          |
| start r-factor (free) = 0.1796      final r-factor (free) = 0.1768          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5856 = 1.77 * 1.00 * 5.3917 + 1.00 * 0.0250                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3851 = 1.77 * 1.00 * 5.2839 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.87  14.55    None  None   None       |
|    all(noH): 2823   0      0.00    101.87  14.55    None  None   None       |
|    Sol.    : 438    0      1.50    101.87  41.71    None  None   None       |
|    Mac.    : 2385   0      0.00    90.00   9.56     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 -  10.187: 1667   |   5:    50.937 -  61.124:   82        |
|      1:    10.187 -  20.375:  614   |   6:    61.124 -  71.312:   52        |
|      2:    20.375 -  30.562:  157   |   7:    71.312 -  81.499:   29        |
|      3:    30.562 -  40.750:  107   |   8:    81.499 -  91.687:   13        |
|      4:    40.750 -  50.937:  100   |   9:    91.687 - 101.874:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1295 r_free = 0.1768             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1294 r_free = 0.1767             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1767   ksol= 0.32   Bsol= 56.80   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.67,1.84,3.61,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.276542                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1772   ksol= 0.33   Bsol= 70.76   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,1.69,3.31,0.00,0.00,0.00); trace/3= 1.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.276303                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.653733              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.516  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.962272              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.408  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1294      final r-factor (work) = 0.1265          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1731          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4369 = 1.65 * 0.50 * 5.2836 + 1.00 * 0.0680                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4115 = 1.65 * 0.50 * 5.2665 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1265      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1731      final r-factor (free) = 0.1725          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0833 = 0.96 * 1.00 * 5.2665 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0712 = 0.96 * 1.00 * 5.2544 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.50  14.31    None  None   None       |
|    all(noH): 2823   0      0.00    102.50  14.31    None  None   None       |
|    Sol.    : 438    0      1.60    102.50  41.04    None  None   None       |
|    Mac.    : 2385   0      0.00    92.00   9.40     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 -  10.250: 1727   |   5:    51.250 -  61.500:   72        |
|      1:    10.250 -  20.500:  558   |   6:    61.500 -  71.750:   48        |
|      2:    20.500 -  30.750:  166   |   7:    71.750 -  82.000:   27        |
|      3:    30.750 -  41.000:  107   |   8:    82.000 -  92.250:   13        |
|      4:    41.000 -  51.250:  102   |   9:    92.250 - 102.500:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1255 r_free = 0.1725             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1254 r_free = 0.1725             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1725   ksol= 0.33   Bsol= 70.76   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,1.69,3.31,0.00,0.00,0.00); trace/3= 1.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252731                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1430  158 0.1005 0.1365      5.4263      5.5949|
|  2:  4.7272 -  3.7719 0.99   1375  153 0.0903 0.1127      5.4852      5.6952|
|  3:  3.7719 -  3.3009 0.99   1342  151 0.1171 0.1611      5.5514      5.8719|
|  4:  3.3009 -  3.0017 0.99   1351  142 0.1347 0.1814      5.5318      5.7183|
|  5:  3.0017 -  2.7881 0.99   1309  155 0.1518 0.1738       5.447      5.5913|
|  6:  2.7881 -  2.6246 0.98   1334  144 0.1440 0.2353      5.3326      5.6421|
|  7:  2.6246 -  2.4938 0.99   1309  150 0.1459 0.1714      5.2937      5.4153|
|  8:  2.4938 -  2.3857 0.98   1324  142 0.1328 0.1860      5.1963      5.4173|
|  9:  2.3857 -  2.2942 0.98   1312  145 0.1336 0.2160      5.1328      5.4706|
| 10:  2.2942 -  2.2153 0.98   1295  143 0.1311 0.1766      5.0717      5.2431|
| 11:  2.2153 -  2.1462 0.99   1313  156 0.1330 0.2046      5.0349      5.3732|
| 12:  2.1462 -  2.0850 0.98   1295  140 0.1305 0.1756      4.9832      5.1983|
| 13:  2.0850 -  2.0303 0.93   1240  128 0.1244 0.1924      4.8779      5.0954|
| 14:  2.0303 -  1.9809 0.31    401   52 0.1073 0.1964      4.7694      5.0689|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1430   158  0.93   9.96   0.96     0.93       8232.34|
|  2:  4.7272 -  3.7719  1375   153  0.95   8.77   1.01     0.99      10067.63|
|  3:  3.7719 -  3.3009  1342   151  0.93  12.53   1.02     1.02      11951.32|
|  4:  3.3009 -  3.0017  1351   142  0.91  15.04   1.01     0.99      11836.54|
|  5:  3.0017 -  2.7881  1309   155  0.88  18.18   1.00     0.97      10619.40|
|  6:  2.7881 -  2.6246  1334   144  0.87  19.20   0.97     0.94       9200.49|
|  7:  2.6246 -  2.4938  1309   150  0.88  17.99   0.98     0.94       7898.01|
|  8:  2.4938 -  2.3857  1324   142  0.89  17.64   0.99     0.94       6925.81|
|  9:  2.3857 -  2.2942  1312   145  0.88  18.11   0.99     0.95       6178.69|
| 10:  2.2942 -  2.2153  1295   143  0.88  18.29   0.98     0.94       5623.99|
| 11:  2.2153 -  2.1462  1313   156  0.88  18.45   0.97     0.92       5250.02|
| 12:  2.1462 -  2.0850  1295   140  0.88  18.41   0.99     0.98       4981.86|
| 13:  2.0850 -  2.0303  1240   128  0.88  18.32   0.97     0.95       4118.58|
| 14:  2.0303 -  1.9809   401    52  0.91  15.68   0.95     0.91       3139.71|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3139.71 max =        11951.32 mean =      7851.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.13|
|phase err.(test): min =        0.00 max =           89.21 mean =        15.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1724   ksol= 0.33   Bsol= 67.18   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-0.20,1.35,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252822                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1724   ksol= 0.33   Bsol= 67.18   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,-0.20,1.35,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252822                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7272 0.99   1430  158 0.1002 0.1365      5.4245      5.5933|
|  2:  4.7272 -  3.7719 0.99   1375  153 0.0900 0.1122      5.4834      5.6923|
|  3:  3.7719 -  3.3009 0.99   1342  151 0.1171 0.1612       5.551      5.8722|
|  4:  3.3009 -  3.0017 0.99   1351  142 0.1349 0.1816      5.5327      5.7193|
|  5:  3.0017 -  2.7881 0.99   1309  155 0.1519 0.1741      5.4481      5.5928|
|  6:  2.7881 -  2.6246 0.98   1334  144 0.1440 0.2356      5.3336      5.6431|
|  7:  2.6246 -  2.4938 0.99   1309  150 0.1460 0.1716      5.2946       5.416|
|  8:  2.4938 -  2.3857 0.98   1324  142 0.1328 0.1862      5.1971      5.4184|
|  9:  2.3857 -  2.2942 0.98   1312  145 0.1336 0.2161      5.1332       5.471|
| 10:  2.2942 -  2.2153 0.98   1295  143 0.1311 0.1765      5.0719      5.2427|
| 11:  2.2153 -  2.1462 0.99   1313  156 0.1330 0.2043      5.0348      5.3727|
| 12:  2.1462 -  2.0850 0.98   1295  140 0.1305 0.1757      4.9833       5.199|
| 13:  2.0850 -  2.0303 0.93   1240  128 0.1245 0.1926      4.8779      5.0954|
| 14:  2.0303 -  1.9809 0.31    401   52 0.1074 0.1963      4.7702      5.0689|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7272  1430   158  0.93   9.95   0.96     0.93       8206.72|
|  2:  4.7272 -  3.7719  1375   153  0.95   8.74   1.01     0.99      10032.24|
|  3:  3.7719 -  3.3009  1342   151  0.93  12.52   1.03     1.02      11924.20|
|  4:  3.3009 -  3.0017  1351   142  0.91  15.06   1.01     1.00      11848.06|
|  5:  3.0017 -  2.7881  1309   155  0.88  18.21   1.00     0.97      10651.62|
|  6:  2.7881 -  2.6246  1334   144  0.87  19.23   0.97     0.94       9221.60|
|  7:  2.6246 -  2.4938  1309   150  0.88  18.02   0.99     0.95       7916.58|
|  8:  2.4938 -  2.3857  1324   142  0.89  17.67   1.00     0.95       6939.39|
|  9:  2.3857 -  2.2942  1312   145  0.88  18.13   1.00     0.96       6186.44|
| 10:  2.2942 -  2.2153  1295   143  0.88  18.30   0.99     0.94       5624.35|
| 11:  2.2153 -  2.1462  1313   156  0.88  18.44   0.98     0.93       5244.04|
| 12:  2.1462 -  2.0850  1295   140  0.88  18.42   1.00     0.98       4982.98|
| 13:  2.0850 -  2.0303  1240   128  0.88  18.32   0.98     0.95       4118.59|
| 14:  2.0303 -  1.9809   401    52  0.91  15.69   0.96     0.91       3139.92|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3139.92 max =        11924.20 mean =      7852.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.13|
|phase err.(test): min =        0.00 max =           89.45 mean =        15.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.086)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.04    104.54  16.36    None  None   None       |
|    all(noH): 2823   0      2.04    104.54  16.36    None  None   None       |
|    Sol.    : 438    0      3.64    104.54  43.09    None  None   None       |
|    Mac.    : 2385   0      2.04    94.05   11.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.044 -  12.294: 1727   |   5:    53.294 -  63.544:   72        |
|      1:    12.294 -  22.544:  558   |   6:    63.544 -  73.794:   48        |
|      2:    22.544 -  32.794:  166   |   7:    73.794 -  84.043:   27        |
|      3:    32.794 -  43.044:  107   |   8:    84.043 -  94.293:   13        |
|      4:    43.044 -  53.294:  102   |   9:    94.293 - 104.543:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.439 - 5.443
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 339
   mapped sites are within: 0.731 - 5.443

peak=   10.160 closest distance to " CB  VAL A 230 " =    1.435
peak=    6.331 closest distance to " CG1 VAL A 296 " =    1.213
peak=    5.863 closest distance to " CD2 LEU A   5 " =    1.158
peak=    5.534 closest distance to " CD1AILE A 234 " =    1.065
peak=    5.458 closest distance to " O   HOH Z 210 " =    1.166
peak=    5.407 closest distance to " CB  GLN A 223 " =    1.535
peak=    5.386 closest distance to " CG  PRO A 280 " =    0.954
peak=    5.116 closest distance to " NH2 ARG A  56 " =    2.084
peak=    5.071 closest distance to " CG  PRO A  54 " =    1.434
peak=    5.000 closest distance to " CG2 VAL A 296 " =    1.048
peak=    4.997 closest distance to " CG  LEU A   5 " =    1.293
peak=    4.989 closest distance to " O   HOH Z 248 " =    1.302
peak=    4.842 closest distance to " CB  VAL A 296 " =    1.113
peak=    4.759 closest distance to " CG  LEU A 228 " =    1.338
peak=    4.715 closest distance to " O   HOH Z  76 " =    1.348
peak=    4.635 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.615 closest distance to " CA  TYR A  30 " =    0.993
peak=    4.611 closest distance to " NE2 GLN A  11 " =    1.010
peak=    4.592 closest distance to " CD2 LEU A 228 " =    1.258
peak=    4.573 closest distance to " CZ  PHE A 218 " =    1.168
peak=    4.559 closest distance to " O   HOH Z 128 " =    1.447
peak=    4.557 closest distance to " O   HOH Z 403 " =    1.689
peak=    4.491 closest distance to " CZ3 TRP A 266 " =    1.109
peak=    4.449 closest distance to " CB  PRO A  54 " =    0.985
peak=    4.436 closest distance to " CB  ASN A 142 " =    1.196
peak=    4.433 closest distance to " O   HOH Z 251 " =    1.837
peak=    4.383 closest distance to " O   HOH Z 402 " =    1.474
peak=    4.370 closest distance to " O   HOH Z 232 " =    2.251
peak=    4.353 closest distance to " O   HOH Z 142 " =    1.768
peak=    4.348 closest distance to " CD2 TRP A 179 " =    1.306
peak=    4.340 closest distance to " CG  PRO A 243 " =    1.162
peak=    4.280 closest distance to " O   HOH Z 126 " =    1.603
peak=    4.252 closest distance to " CB  GLU A 277 " =    3.796
peak=    4.251 closest distance to " O   PRO A 198 " =    1.561
peak=    4.247 closest distance to " O   HOH Z 214 " =    1.423
peak=    4.235 closest distance to " CG  PRO A 198 " =    1.278
peak=    4.217 closest distance to " O   HOH Z  91 " =    2.428
peak=    4.196 closest distance to " CB  ASN A 148 " =    1.428
peak=    4.184 closest distance to " O   HOH Z 411 " =    3.899
peak=    4.169 closest distance to " O   HOH Z 154 " =    1.664
peak=    4.150 closest distance to " O  BHOH Z  74 " =    1.225
peak=    4.139 closest distance to " O   HOH Z 188 " =    2.725
peak=    4.122 closest distance to " O   HOH Z 246 " =    1.266
peak=    4.112 closest distance to " O   HOH Z 369 " =    2.125
peak=    4.109 closest distance to " CB  ARG A  79 " =    1.377
peak=    4.098 closest distance to " CB  VAL A 230 " =    1.253
peak=    4.094 closest distance to " CB  ARG A 190 " =    1.753
peak=    4.085 closest distance to " CG  ARG A  66 " =    2.502
peak=    4.061 closest distance to " CE  LYS A  76 " =    0.920
peak=    4.056 closest distance to " O   HOH Z 261 " =    2.493
peak=    4.051 closest distance to " CB  TRP A 179 " =    1.450
peak=    4.043 closest distance to " NH2AARG A 145 " =    1.099
peak=    4.041 closest distance to " CA  ALA A  51 " =    1.014
peak=    4.036 closest distance to " O   HOH Z 313 " =    1.913
peak=    4.028 closest distance to " CB  PRO A  90 " =    1.146
peak=    4.017 closest distance to " CB  SER A  63 " =    1.142
peak=    4.009 closest distance to " O   HOH Z 346 " =    1.472
peak=    3.983 closest distance to " O   HOH Z 425 " =    1.513
peak=    3.968 closest distance to " CD  ARG A 269 " =    1.036
peak=    3.956 closest distance to " CB  GLN A 183 " =    1.225
peak=    3.948 closest distance to " CG AARG A 275 " =    1.250
peak=    3.931 closest distance to " O   HOH Z 162 " =    1.651
peak=    3.927 closest distance to " CA  ARG A  36 " =    1.005
peak=    3.920 closest distance to " CB  ASP A 124 " =    0.873
peak=    3.912 closest distance to " O   HOH Z 265 " =    1.955
peak=    3.905 closest distance to " O   HOH Z 359 " =    1.994
peak=    3.903 closest distance to " CA  ALA A 160 " =    0.948
peak=    3.901 closest distance to " O   HOH Z 238 " =    1.266
peak=    3.897 closest distance to " O   HOH Z 207 " =    1.166
peak=    3.893 closest distance to " CA  ARG A 195 " =    1.194
peak=    3.885 closest distance to " CZ  PHE A  38 " =    1.142
peak=    3.882 closest distance to " CG2AVAL A 121 " =    2.190
peak=    3.877 closest distance to " CB  TYR A 169 " =    0.796
peak=    3.871 closest distance to " O   HOH Z 214 " =    3.265
peak=    3.870 closest distance to " O   HOH Z 427 " =    2.934
peak=    3.867 closest distance to " O   HOH Z 394 " =    1.464
peak=    3.865 closest distance to " CB  ASN A  39 " =    0.879
peak=    3.849 closest distance to " CB  GLU A 152 " =    1.190
peak=    3.849 closest distance to " O   HOH Z 365 " =    2.686
peak=    3.846 closest distance to " O   HOH Z  49 " =    1.290
peak=    3.830 closest distance to " O   HOH Z 126 " =    1.923
peak=    3.821 closest distance to " CG  PHE A 204 " =    0.911
peak=    3.816 closest distance to " O   HOH Z 280 " =    2.887
peak=    3.816 closest distance to " ND2 ASN A 249 " =    0.926
peak=    3.813 closest distance to " O   HOH Z 193 " =    1.626
peak=    3.804 closest distance to " CG  PRO A 213 " =    1.229
peak=    3.793 closest distance to " CD1 ILE A 199 " =    1.208
peak=    3.789 closest distance to " CG2 ILE A 234 " =    1.004
peak=    3.781 closest distance to " CA  ALA A 295 " =    0.988
peak=    3.781 closest distance to " CB  VAL A 265 " =    1.218
peak=    3.777 closest distance to " O   HOH Z 287 " =    1.781
peak=    3.775 closest distance to " O   HOH Z 365 " =    2.447
peak=    3.772 closest distance to " O   HOH Z   4 " =    1.608
peak=    3.767 closest distance to " CG  GLN A  58 " =    1.055
peak=    3.767 closest distance to " O   HOH Z  43 " =    2.054
peak=    3.765 closest distance to " CB  TRP A 266 " =    1.052
peak=    3.758 closest distance to " O   ASP A 124 " =    1.247
peak=    3.758 closest distance to " CA  TYR A 116 " =    1.372
peak=    3.731 closest distance to " O   HOH Z 234 " =    3.710
peak=    3.725 closest distance to " CD  LYS A  76 " =    2.050
peak=    3.721 closest distance to " O   HOH Z 117 " =    1.049
peak=    3.719 closest distance to " OG  SER A 276 " =    1.564
peak=    3.715 closest distance to " N   ASN A  39 " =    1.271
peak=    3.714 closest distance to " O   HOH Z 199 " =    1.654
peak=    3.709 closest distance to " O   HOH Z 422 " =    2.595
peak=    3.680 closest distance to " O   HOH Z  63 " =    1.857
peak=    3.670 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.665 closest distance to " CG  ARG A 138 " =    1.369
peak=    3.663 closest distance to " CD  LYS A 166 " =    1.407
peak=    3.658 closest distance to " O   HOH Z 303 " =    2.228
peak=    3.657 closest distance to " O   HOH Z 316 " =    3.128
peak=    3.655 closest distance to " O   HOH Z 406 " =    1.553
peak=    3.639 closest distance to " CA  ILE A 106 " =    0.776
peak=    3.635 closest distance to " O   HOH Z 209 " =    2.253
peak=    3.621 closest distance to " CB  PRO A 198 " =    1.066
peak=    3.607 closest distance to " CB AVAL A  41 " =    1.180
peak=    3.606 closest distance to " CA  VAL A  41 " =    0.732
peak=    3.604 closest distance to " O   HOH Z 290 " =    1.126
peak=    3.604 closest distance to " CB  THR A  52 " =    0.868
peak=    3.597 closest distance to " CB  SER A  26 " =    1.820
peak=    3.596 closest distance to " CB  VAL A 202 " =    1.478
peak=    3.595 closest distance to " O   HOH Z 383 " =    1.947
peak=    3.586 closest distance to " O   HOH Z  80 " =    1.909
peak=    3.582 closest distance to " CD1 LEU A  96 " =    0.797
peak=    3.581 closest distance to " O   HOH Z 368 " =    3.420
peak=    3.569 closest distance to " O   HOH Z 337 " =    1.944
peak=    3.569 closest distance to " CB  SER A 273 " =    0.969
peak=    3.566 closest distance to " CB  ALA A 248 " =    1.401
peak=    3.556 closest distance to " O   HOH Z 107 " =    0.914
peak=    3.556 closest distance to " CG  MET A 185 " =    1.237
peak=    3.550 closest distance to " CG  LEU A 167 " =    1.124
peak=    3.549 closest distance to " CB  ALA A 114 " =    0.731
peak=    3.547 closest distance to " CA  SER A  87 " =    0.982
peak=    3.546 closest distance to " O   HOH Z 361 " =    2.542
peak=    3.546 closest distance to " OG BSER A 164 " =    2.277
peak=    3.543 closest distance to " O   HOH Z 124 " =    1.141
peak=    3.540 closest distance to " CG1 VAL A 153 " =    0.990
peak=    3.536 closest distance to " O   HOH Z 144 " =    1.697
peak=    3.535 closest distance to " O   HOH Z 258 " =    1.852
peak=    3.534 closest distance to " CE3 TRP A 150 " =    1.201
peak=    3.531 closest distance to " CB  SER A   3 " =    1.431
peak=    3.531 closest distance to " O   HOH Z  78 " =    1.670
peak=    3.525 closest distance to " CG1 ILE A  20 " =    1.255
peak=    3.516 closest distance to " CB  ASP A 107 " =    1.189
peak=    3.513 closest distance to " CB  LYS A 117 " =    1.226
peak=    3.513 closest distance to " CB  GLN A  89 " =    1.171
peak=    3.512 closest distance to " O   HOH Z 353 " =    2.753
peak=    3.510 closest distance to " O   HOH Z 189 " =    2.871
peak=    3.507 closest distance to " ND2 ASN A 187 " =    1.807
peak=    3.506 closest distance to " NZ  LYS A 117 " =    2.941
peak=    3.504 closest distance to " CB  GLU A 128 " =    1.138
peak=    3.501 closest distance to " O   HOH Z 372 " =    0.936
peak=    3.497 closest distance to " O   HOH Z 417 " =    3.110
peak=    3.494 closest distance to " O   THR A 182 " =    1.438
peak=    3.493 closest distance to " CB  THR A 235 " =    1.372
peak=    3.492 closest distance to " O   HOH Z 357 " =    2.155
peak=    3.486 closest distance to " CA  ALA A  21 " =    1.123
peak=    3.485 closest distance to " CE1 TYR A 186 " =    1.303
peak=    3.485 closest distance to " CE3 TRP A  85 " =    1.134
peak=    3.484 closest distance to " O   HOH Z 298 " =    1.833
peak=    3.479 closest distance to " CB  PRO A 243 " =    1.052
peak=    3.479 closest distance to " O   HOH Z 154 " =    2.290
peak=    3.478 closest distance to " CB  ASN A 215 " =    1.195
peak=    3.474 closest distance to " NZ  LYS A  48 " =    1.115
peak=    3.474 closest distance to " CB  GLU A  46 " =    0.942
peak=    3.466 closest distance to " O   HOH Z 203 " =    1.748
peak=    3.462 closest distance to " O   HOH Z 371 " =    2.719
peak=    3.462 closest distance to " CA  ASP A 162 " =    0.968
peak=    3.455 closest distance to " CA  ASN A 217 " =    1.142
peak=    3.452 closest distance to " CB  MET A  40 " =    0.828
peak=    3.449 closest distance to " O   HOH Z 258 " =    1.356
peak=    3.445 closest distance to " O   THR A 220 " =    1.308
peak=    3.444 closest distance to " CG2 VAL A 257 " =    0.773
peak=    3.442 closest distance to " CD  ARG A 139 " =    1.181
peak=    3.441 closest distance to " CB  ASN A 110 " =    1.117
peak=    3.440 closest distance to " CB  ASP A 298 " =    1.179
peak=    3.437 closest distance to " CB  SER A 210 " =    0.833
peak=    3.435 closest distance to " O  BHOH Z 338 " =    2.169
peak=    3.434 closest distance to " NH2 ARG A 156 " =    1.116
peak=    3.428 closest distance to " OG  SER A 245 " =    1.548
peak=    3.427 closest distance to " NE2 GLN A  77 " =    3.286
peak=    3.424 closest distance to " CD2 LEU A 297 " =    0.796
peak=    3.422 closest distance to " CA  MET A 105 " =    1.087
peak=    3.421 closest distance to " O   HOH Z 193 " =    1.771
peak=    3.419 closest distance to " O   HOH Z   9 " =    1.093
peak=    3.419 closest distance to " O   HOH Z  85 " =    1.102
peak=    3.419 closest distance to " NH1AARG A 145 " =    1.320
peak=    3.417 closest distance to " CA  VAL A 125 " =    1.152
peak=    3.416 closest distance to " CG  GLU A  37 " =    0.959
peak=    3.415 closest distance to " O   HOH Z 172 " =    3.730
peak=    3.407 closest distance to " O   HOH Z 423 " =    1.774
peak=    3.403 closest distance to " CD1 ILE A  33 " =    1.674
peak=    3.401 closest distance to " O   ALA A 165 " =    1.408
peak=    3.399 closest distance to " CD  LYS A 119 " =    1.846
peak=    3.397 closest distance to " CG AARG A 102 " =    1.185
peak=    3.394 closest distance to " CD  PRO A  54 " =    1.005
peak=    3.393 closest distance to " CB  ASP A 140 " =    1.227
peak=    3.383 closest distance to " O   CYS A 168 " =    1.219
peak=    3.380 closest distance to " NE2 HIS A 207 " =    1.051
peak=    3.377 closest distance to " O   ASN A  74 " =    1.359
peak=    3.375 closest distance to " O   HOH Z 394 " =    1.802
peak=    3.373 closest distance to " O   HOH Z 272 " =    1.841
peak=    3.372 closest distance to " O   HOH Z 430 " =    5.443
peak=    3.364 closest distance to " ND2BASN A 224 " =    0.885
peak=    3.354 closest distance to " O   HOH Z  97 " =    2.196
peak=    3.352 closest distance to " CB  PHE A 204 " =    1.061
peak=    3.348 closest distance to " O   HOH Z 174 " =    2.411
peak=    3.345 closest distance to " N   ALA A 256 " =    1.162
peak=    3.345 closest distance to " CA  ALA A 154 " =    1.063
peak=    3.342 closest distance to " O   HOH Z 327 " =    2.530
peak=    3.338 closest distance to " ND2 ASN A 249 " =    1.924
peak=    3.338 closest distance to " O   ASP A 200 " =    1.615
peak=    3.335 closest distance to " CB  SER A  62 " =    0.998
peak=    3.326 closest distance to " CB  ASN A 173 " =    1.056
peak=    3.324 closest distance to " CA  ASP A 191 " =    1.216
peak=    3.320 closest distance to " CG1 VAL A 257 " =    1.372
peak=    3.318 closest distance to " CA  ALA A 100 " =    0.902
peak=    3.317 closest distance to " O   HOH Z 368 " =    4.144
peak=    3.317 closest distance to " NH2 ARG A  56 " =    1.141
peak=    3.315 closest distance to " O   HOH Z 391 " =    2.958
peak=    3.314 closest distance to " O   GLN A  88 " =    1.677
peak=    3.314 closest distance to " CB  SER A 288 " =    1.477
peak=    3.308 closest distance to " CA  ALA A 291 " =    0.851
peak=    3.305 closest distance to " CB  THR A  31 " =    1.375
peak=    3.304 closest distance to " O   HOH Z 393 " =    3.206
peak=    3.301 closest distance to " O   HOH Z 130 " =    1.101
peak=    3.297 closest distance to " O   HOH Z 433 " =    1.480
peak=    3.294 closest distance to " CA  LYS A 117 " =    1.272
peak=    3.293 closest distance to " O   HOH Z 344 " =    2.900
peak=    3.291 closest distance to " CB  ASN A 285 " =    0.998
peak=    3.291 closest distance to " O   LEU A 228 " =    1.792
peak=    3.287 closest distance to " CB  ARG A 219 " =    1.244
peak=    3.285 closest distance to " OE2 GLU A  53 " =    1.887
peak=    3.284 closest distance to " O   HOH Z 345 " =    3.380
peak=    3.282 closest distance to " C   ALA A 299 " =    0.856
peak=    3.278 closest distance to " CG2 ILE A  20 " =    1.464
peak=    3.276 closest distance to " NE1 TRP A  92 " =    1.797
peak=    3.270 closest distance to " CA  GLU A 152 " =    0.850
peak=    3.268 closest distance to " O   HOH Z 421 " =    3.081
peak=    3.264 closest distance to " CG1 ILE A  49 " =    1.675
peak=    3.263 closest distance to " CA  ALA A 158 " =    1.451
peak=    3.259 closest distance to " CA  ASN A 127 " =    1.174
peak=    3.258 closest distance to " CA  ILE A 234 " =    0.988
peak=    3.258 closest distance to " O   HOH Z 343 " =    2.801
peak=    3.256 closest distance to " CB  ALA A 292 " =    0.950
peak=    3.256 closest distance to " OG BSER A 134 " =    2.824
peak=    3.246 closest distance to " O   HOH Z 299 " =    4.376
peak=    3.246 closest distance to " O   HOH Z 193 " =    1.632
peak=    3.244 closest distance to " O   PHE A 192 " =    1.337
peak=    3.243 closest distance to " O   HOH Z  83 " =    1.494
peak=    3.238 closest distance to " O   HOH Z 187 " =    2.242
peak=    3.238 closest distance to " O   HOH Z 258 " =    1.539
peak=    3.234 closest distance to " O   HOH Z 421 " =    3.045
peak=    3.223 closest distance to " O   HOH Z 146 " =    1.406
peak=    3.223 closest distance to " O   HOH Z 305 " =    3.480
peak=    3.223 closest distance to " OD1 ASP A 231 " =    1.956
peak=    3.222 closest distance to " CB  MET A  47 " =    0.926
peak=    3.205 closest distance to " CG2 THR A 220 " =    0.794
peak=    3.203 closest distance to " O   HOH Z 359 " =    1.982
peak=    3.202 closest distance to " O   HOH Z 368 " =    1.849
peak=    3.201 closest distance to " CB  SER A 216 " =    1.063
peak=    3.199 closest distance to " CD2 LEU A  83 " =    1.437
peak=    3.193 closest distance to " O   HOH Z 293 " =    2.069
peak=    3.190 closest distance to " OG1 THR A  82 " =    0.986
peak=    3.188 closest distance to " N   ASP A 162 " =    1.272
peak=    3.186 closest distance to " OG BSER A 212 " =    2.606
peak=    3.185 closest distance to " CG  GLN A  11 " =    1.652
peak=    3.180 closest distance to " O   HOH Z 141 " =    1.597
peak=    3.180 closest distance to " O   TYR A 116 " =    1.325
peak=    3.179 closest distance to " O   HOH Z 298 " =    2.390
peak=    3.178 closest distance to " CA  ASN A  74 " =    1.107
peak=    3.177 closest distance to " CA  LYS A 290 " =    1.140
peak=    3.176 closest distance to " CA  LEU A 282 " =    1.189
peak=    3.175 closest distance to " O   HOH Z  54 " =    1.597
peak=    3.173 closest distance to " O   HOH Z 236 " =    1.614
peak=    3.167 closest distance to " O   HOH Z 151 " =    1.613
peak=    3.163 closest distance to " CB  ALA A   9 " =    1.644
peak=    3.162 closest distance to " O   HOH Z  47 " =    1.749
peak=    3.160 closest distance to " NH1 ARG A  14 " =    1.171
peak=    3.157 closest distance to " O   HOH Z  40 " =    1.897
peak=    3.154 closest distance to " O   HOH Z 148 " =    3.389
peak=    3.149 closest distance to " CA  GLN A  94 " =    0.800
peak=    3.148 closest distance to " CG2 VAL A 126 " =    0.871
peak=    3.147 closest distance to " OE2 GLU A  53 " =    0.998
peak=    3.145 closest distance to " CD  ARG A 195 " =    1.068
peak=    3.145 closest distance to " O   HOH Z 438 " =    2.587
peak=    3.144 closest distance to " CG2 VAL A 197 " =    1.078
peak=    3.144 closest distance to " O   THR A 251 " =    1.099
peak=    3.144 closest distance to " O   HOH Z 426 " =    1.349
peak=    3.140 closest distance to " CA  ARG A 156 " =    1.113
peak=    3.138 closest distance to " O   HOH Z  94 " =    2.683
peak=    3.138 closest distance to " OD1 ASN A  69 " =    2.519
peak=    3.137 closest distance to " O   HOH Z   1 " =    2.323
peak=    3.135 closest distance to " CE  LYS A 119 " =    0.997
peak=    3.133 closest distance to " CG BARG A 102 " =    1.894
peak=    3.133 closest distance to " CG  MET A 185 " =    1.038
peak=    3.132 closest distance to " O   HOH Z 393 " =    3.986
peak=    3.131 closest distance to " CB  ARG A 145 " =    0.895
peak=    3.131 closest distance to " CG2 ILE A 120 " =    1.316
peak=    3.131 closest distance to " CB  ARG A 156 " =    1.240
peak=    3.130 closest distance to " CG2BVAL A 121 " =    0.734
peak=    3.128 closest distance to " CA  ASP A 253 " =    1.372
peak=    3.121 closest distance to " O   HOH Z 357 " =    2.539
peak=    3.121 closest distance to " O   HOH Z  21 " =    1.744
peak=    3.119 closest distance to " O   HOH Z  35 " =    4.441
peak=    3.114 closest distance to " O   HOH Z 250 " =    1.246
peak=    3.110 closest distance to " N   ARG A 156 " =    1.651
peak=    3.108 closest distance to " CB  LEU A 143 " =    1.162
peak=    3.108 closest distance to " O   GLU A   2 " =    1.505
peak=    3.106 closest distance to " NE2 GLN A  58 " =    4.662
peak=    3.102 closest distance to " N   PHE A 130 " =    1.374
peak=    3.101 closest distance to " O   HOH Z  40 " =    1.543
peak=    3.094 closest distance to " O   HOH Z 145 " =    2.435
peak=    3.093 closest distance to " O   HOH Z 371 " =    1.221
peak=    3.093 closest distance to " CB  TYR A 247 " =    1.011
peak=    3.089 closest distance to " CA  THR A 264 " =    0.815
peak=    3.083 closest distance to " N   ALA A 292 " =    1.013
peak=    3.079 closest distance to " O   MET A 105 " =    1.940
peak=    3.078 closest distance to " O   THR A 157 " =    1.166
peak=    3.077 closest distance to " CB  ASP A 272 " =    1.149
peak=    3.072 closest distance to " CA  ARG A 102 " =    1.150
peak=    3.072 closest distance to " O   HOH Z 227 " =    1.407
peak=    3.065 closest distance to " CG  LEU A 281 " =    1.035
peak=    3.064 closest distance to " CE3 TRP A 274 " =    1.238
peak=    3.059 closest distance to " O   HOH Z 117 " =    1.892
peak=    3.059 closest distance to " O   HOH Z 109 " =    2.500
peak=    3.046 closest distance to " CB  TRP A 179 " =    1.402
peak=    3.033 closest distance to " O   HOH Z 329 " =    4.141
peak=    3.025 closest distance to " O   HOH Z 361 " =    2.742
peak=    3.019 closest distance to " O   HOH Z 371 " =    2.623

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 224         
Filter by distance & map next to the model:
   mapped sites are within: 0.663 - 5.682
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 222 from: 224
   mapped sites are within: 0.753 - 5.682

peak=   -4.666 closest distance to " SG  CYS A 254 " =    3.223
peak=   -4.564 closest distance to " CG2 VAL A 230 " =    0.753
peak=   -4.435 closest distance to " O   PRO A 198 " =    1.281
peak=   -4.386 closest distance to " CG1 VAL A 296 " =    1.045
peak=   -4.276 closest distance to " CG  GLN A  58 " =    1.026
peak=   -4.260 closest distance to " CG2BVAL A  41 " =    2.567
peak=   -4.207 closest distance to " OG BSER A 134 " =    1.484
peak=   -4.201 closest distance to " CD  ARG A 156 " =    2.114
peak=   -4.151 closest distance to " CB  PRO A 243 " =    2.798
peak=   -4.128 closest distance to " O   HOH Z 196 " =    2.304
peak=   -4.090 closest distance to " CD2 LEU A 237 " =    2.705
peak=   -4.076 closest distance to " CD2 TYR A 293 " =    1.928
peak=   -4.073 closest distance to " O   PRO A 163 " =    2.142
peak=   -4.032 closest distance to " CG2 ILE A  49 " =    2.869
peak=   -4.030 closest distance to " C   HIS A 108 " =    1.147
peak=   -4.012 closest distance to " CE3 TRP A 150 " =    2.316
peak=   -4.007 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.983 closest distance to " O   HOH Z 214 " =    2.553
peak=   -3.979 closest distance to " CE2 TRP A  70 " =    2.195
peak=   -3.959 closest distance to " O   HOH Z 166 " =    1.744
peak=   -3.897 closest distance to " O   HOH Z 411 " =    5.596
peak=   -3.895 closest distance to " CE2 TYR A  30 " =    2.701
peak=   -3.892 closest distance to " O   HOH Z 211 " =    1.086
peak=   -3.885 closest distance to " O   HOH Z 285 " =    2.004
peak=   -3.879 closest distance to " O   SER A 271 " =    2.086
peak=   -3.852 closest distance to " CG2BVAL A  41 " =    1.796
peak=   -3.851 closest distance to " CG  PRO A 243 " =    1.609
peak=   -3.849 closest distance to " O   HOH Z 154 " =    1.444
peak=   -3.845 closest distance to " CG2 VAL A 189 " =    2.022
peak=   -3.780 closest distance to " O   HOH Z 131 " =    4.149
peak=   -3.777 closest distance to " O   HOH Z 119 " =    2.154
peak=   -3.776 closest distance to " CD1 PHE A  59 " =    2.142
peak=   -3.757 closest distance to " OXT GLY A 302 " =    2.990
peak=   -3.742 closest distance to " OE1 GLN A 223 " =    2.422
peak=   -3.723 closest distance to " CG  GLN A  11 " =    1.576
peak=   -3.722 closest distance to " NE2 GLN A  88 " =    1.090
peak=   -3.718 closest distance to " O   HOH Z 216 " =    1.151
peak=   -3.712 closest distance to " CG1 VAL A 112 " =    2.715
peak=   -3.707 closest distance to " O   HOH Z 133 " =    0.902
peak=   -3.701 closest distance to " O   HOH Z  73 " =    2.532
peak=   -3.693 closest distance to " O   HOH Z 231 " =    2.254
peak=   -3.686 closest distance to " O   HOH Z 128 " =    2.516
peak=   -3.679 closest distance to " O   HOH Z 106 " =    1.836
peak=   -3.678 closest distance to " ND2 ASN A  45 " =    1.266
peak=   -3.653 closest distance to " O   HOH Z 394 " =    1.752
peak=   -3.645 closest distance to " NE  ARG A  66 " =    4.354
peak=   -3.637 closest distance to " CG  GLU A 277 " =    1.286
peak=   -3.621 closest distance to " O   HOH Z 351 " =    1.750
peak=   -3.620 closest distance to " CD1 LEU A 101 " =    2.329
peak=   -3.620 closest distance to " O   SER A 210 " =    1.722
peak=   -3.606 closest distance to " CD  PRO A 243 " =    1.918
peak=   -3.605 closest distance to " O   HOH Z 102 " =    1.511
peak=   -3.596 closest distance to " O   HOH Z 359 " =    2.712
peak=   -3.594 closest distance to " O   HOH Z  68 " =    1.251
peak=   -3.591 closest distance to " CG  ARG A 269 " =    2.323
peak=   -3.591 closest distance to " CZ3 TRP A 274 " =    2.357
peak=   -3.584 closest distance to " O   HOH Z 423 " =    2.445
peak=   -3.576 closest distance to " CB  ALA A  51 " =    1.931
peak=   -3.548 closest distance to " O   HOH Z 348 " =    2.352
peak=   -3.543 closest distance to " CG2 ILE A  20 " =    2.924
peak=   -3.543 closest distance to " CB  HIS A  86 " =    1.170
peak=   -3.542 closest distance to " O   HOH Z 191 " =    5.682
peak=   -3.542 closest distance to " CG  GLN A 103 " =    2.439
peak=   -3.538 closest distance to " OG  SER A  97 " =    2.375
peak=   -3.537 closest distance to " CA  GLY A 241 " =    2.341
peak=   -3.533 closest distance to " O   HOH Z 295 " =    1.557
peak=   -3.529 closest distance to " O   HOH Z  13 " =    1.942
peak=   -3.524 closest distance to " O   HOH Z  64 " =    1.726
peak=   -3.522 closest distance to " CB  VAL A 230 " =    1.125
peak=   -3.517 closest distance to " O   HOH Z 198 " =    1.746
peak=   -3.517 closest distance to " N   THR A  52 " =    1.607
peak=   -3.512 closest distance to " CB  ALA A  10 " =    2.265
peak=   -3.508 closest distance to " O   HOH Z 275 " =    1.861
peak=   -3.506 closest distance to " CZ  PHE A  38 " =    2.399
peak=   -3.503 closest distance to " CB  ALA A 248 " =    2.137
peak=   -3.502 closest distance to " NH2 ARG A  79 " =    2.349
peak=   -3.501 closest distance to " CD  LYS A 289 " =    2.405
peak=   -3.489 closest distance to " O   HOH Z  19 " =    2.299
peak=   -3.483 closest distance to " O   HOH Z 149 " =    1.962
peak=   -3.480 closest distance to " O   HOH Z 340 " =    1.648
peak=   -3.476 closest distance to " O   GLY A  17 " =    1.192
peak=   -3.467 closest distance to " CA  GLY A 203 " =    2.387
peak=   -3.465 closest distance to " CE  LYS A  76 " =    2.628
peak=   -3.453 closest distance to " N   ALA A  43 " =    2.689
peak=   -3.448 closest distance to " CB  ALA A 248 " =    2.250
peak=   -3.448 closest distance to " O   HOH Z 431 " =    2.063
peak=   -3.440 closest distance to " O   TYR A 186 " =    1.754
peak=   -3.440 closest distance to " O   HOH Z 165 " =    1.991
peak=   -3.436 closest distance to " CD2 HIS A 207 " =    2.114
peak=   -3.434 closest distance to " CG1 VAL A 296 " =    0.953
peak=   -3.423 closest distance to " O   ALA A 227 " =    1.399
peak=   -3.412 closest distance to " O   HOH Z 136 " =    1.496
peak=   -3.410 closest distance to " O   HOH Z  10 " =    1.559
peak=   -3.399 closest distance to " O   HOH Z 390 " =    1.452
peak=   -3.397 closest distance to " O   HOH Z 377 " =    2.085
peak=   -3.393 closest distance to " OG1 THR A  82 " =    1.288
peak=   -3.391 closest distance to " O   HOH Z 128 " =    1.121
peak=   -3.390 closest distance to " CG  LEU A   5 " =    0.958
peak=   -3.389 closest distance to " CD1 ILE A 199 " =    2.495
peak=   -3.389 closest distance to " ND2 ASN A 187 " =    1.638
peak=   -3.386 closest distance to " CG  MET A 105 " =    0.977
peak=   -3.386 closest distance to " O   HOH Z  52 " =    1.885
peak=   -3.385 closest distance to " CB  ALA A  43 " =    2.656
peak=   -3.377 closest distance to " CG1 VAL A 112 " =    2.705
peak=   -3.372 closest distance to " CG2AVAL A  41 " =    2.854
peak=   -3.372 closest distance to " CA  VAL A 296 " =    1.031
peak=   -3.370 closest distance to " O   HOH Z 107 " =    1.081
peak=   -3.361 closest distance to " O   HOH Z  37 " =    1.922
peak=   -3.361 closest distance to " OE1 GLN A  88 " =    0.997
peak=   -3.360 closest distance to " O   HOH Z 110 " =    1.526
peak=   -3.354 closest distance to " O   HOH Z 174 " =    2.453
peak=   -3.352 closest distance to " O   GLY A 203 " =    2.411
peak=   -3.345 closest distance to " CG2 THR A 178 " =    2.454
peak=   -3.339 closest distance to " O   HOH Z 278 " =    1.170
peak=   -3.338 closest distance to " CB  PHE A 192 " =    2.096
peak=   -3.338 closest distance to " CG2 VAL A 202 " =    2.758
peak=   -3.333 closest distance to " O   TRP A  70 " =    1.585
peak=   -3.330 closest distance to " C   ASN A 285 " =    2.275
peak=   -3.329 closest distance to " OD1 ASN A 148 " =    1.345
peak=   -3.324 closest distance to " OG  SER A  62 " =    4.201
peak=   -3.320 closest distance to " CG  GLU A  53 " =    1.540
peak=   -3.318 closest distance to " CE BMET A  47 " =    1.434
peak=   -3.316 closest distance to " CG2 VAL A 296 " =    1.153
peak=   -3.312 closest distance to " O   ILE A 106 " =    1.770
peak=   -3.312 closest distance to " ND2BASN A 224 " =    1.932
peak=   -3.311 closest distance to " CE  LYS A  76 " =    0.846
peak=   -3.303 closest distance to " CG  ASP A 231 " =    0.971
peak=   -3.298 closest distance to " NH2 ARG A 159 " =    2.313
peak=   -3.292 closest distance to " CB  ALA A 161 " =    2.436
peak=   -3.290 closest distance to " O   HOH Z 250 " =    1.857
peak=   -3.287 closest distance to " O   HOH Z  38 " =    1.852
peak=   -3.286 closest distance to " O   HOH Z 177 " =    1.874
peak=   -3.284 closest distance to " CB  GLN A  55 " =    1.405
peak=   -3.283 closest distance to " CB  SER A 210 " =    1.078
peak=   -3.278 closest distance to " CA  ASN A 127 " =    1.090
peak=   -3.277 closest distance to " O   HOH Z 301 " =    2.533
peak=   -3.276 closest distance to " O   GLU A 152 " =    1.368
peak=   -3.276 closest distance to " CH2 TRP A 179 " =    1.235
peak=   -3.275 closest distance to " OG  SER A  63 " =    1.094
peak=   -3.274 closest distance to " N   ALA A 226 " =    1.972
peak=   -3.273 closest distance to " CE3 TRP A  70 " =    1.810
peak=   -3.272 closest distance to " O   HOH Z 252 " =    3.577
peak=   -3.272 closest distance to " O   SER A   3 " =    1.027
peak=   -3.271 closest distance to " CZ  TYR A 169 " =    1.851
peak=   -3.267 closest distance to " NE  ARG A  79 " =    1.208
peak=   -3.267 closest distance to " O   HOH Z 139 " =    5.343
peak=   -3.265 closest distance to " O   HOH Z 137 " =    1.760
peak=   -3.262 closest distance to " O   HOH Z 251 " =    4.880
peak=   -3.262 closest distance to " CB  ALA A   9 " =    2.428
peak=   -3.250 closest distance to " O   HOH Z 429 " =    1.888
peak=   -3.250 closest distance to " CB  ASN A  45 " =    2.161
peak=   -3.247 closest distance to " O   HOH Z 136 " =    2.714
peak=   -3.244 closest distance to " CG1 VAL A 189 " =    2.745
peak=   -3.243 closest distance to " O   HOH Z 275 " =    1.609
peak=   -3.243 closest distance to " CZ  ARG A 259 " =    1.009
peak=   -3.243 closest distance to " O   HOH Z 111 " =    1.577
peak=   -3.242 closest distance to " CZ  TYR A 172 " =    1.911
peak=   -3.240 closest distance to " CG1 VAL A  78 " =    2.451
peak=   -3.239 closest distance to " O   GLY A  75 " =    2.027
peak=   -3.235 closest distance to " O   HOH Z 421 " =    3.582
peak=   -3.232 closest distance to " O   HOH Z  11 " =    2.171
peak=   -3.232 closest distance to " CE1 TYR A 247 " =    2.663
peak=   -3.231 closest distance to " NE2 GLN A 194 " =    2.025
peak=   -3.230 closest distance to " O   HOH Z  43 " =    1.533
peak=   -3.230 closest distance to " O   SER A 276 " =    1.675
peak=   -3.227 closest distance to " CG  GLN A  58 " =    1.467
peak=   -3.226 closest distance to " CG  TRP A 266 " =    1.813
peak=   -3.225 closest distance to " NH1 ARG A  66 " =    3.113
peak=   -3.223 closest distance to " OD1 ASN A 173 " =    1.367
peak=   -3.221 closest distance to " C   ALA A 158 " =    1.280
peak=   -3.219 closest distance to " O   HOH Z 145 " =    2.735
peak=   -3.215 closest distance to " O   HOH Z 196 " =    1.939
peak=   -3.215 closest distance to " CB  ASN A  39 " =    2.474
peak=   -3.208 closest distance to " CG1 VAL A 125 " =    1.884
peak=   -3.208 closest distance to " CD  GLU A 236 " =    1.162
peak=   -3.206 closest distance to " O   HOH Z  30 " =    1.593
peak=   -3.204 closest distance to " ND2 ASN A  69 " =    1.995
peak=   -3.203 closest distance to " O   GLY A 196 " =    1.102
peak=   -3.197 closest distance to " CA  GLY A 133 " =    2.346
peak=   -3.196 closest distance to " O   HOH Z 290 " =    1.087
peak=   -3.185 closest distance to " O   HOH Z 116 " =    1.663
peak=   -3.185 closest distance to " O   PHE A 218 " =    1.429
peak=   -3.184 closest distance to " N   SER A 276 " =    1.414
peak=   -3.181 closest distance to " O   HOH Z 244 " =    1.968
peak=   -3.177 closest distance to " OD1 ASN A  39 " =    1.241
peak=   -3.173 closest distance to " O   HOH Z 140 " =    1.124
peak=   -3.173 closest distance to " O   HOH Z 357 " =    2.168
peak=   -3.171 closest distance to " CD1 ILE A 239 " =    2.170
peak=   -3.171 closest distance to " CA  ALA A 299 " =    2.260
peak=   -3.171 closest distance to " ND2 ASN A  45 " =    2.045
peak=   -3.170 closest distance to " CE1 PHE A 192 " =    1.951
peak=   -3.170 closest distance to " O   HOH Z  96 " =    1.463
peak=   -3.169 closest distance to " CB  TRP A  85 " =    2.576
peak=   -3.167 closest distance to " CH2 TRP A 150 " =    1.173
peak=   -3.165 closest distance to " O   GLY A  80 " =    2.661
peak=   -3.149 closest distance to " CD2 PHE A 225 " =    1.051
peak=   -3.147 closest distance to " ND2 ASN A 249 " =    2.334
peak=   -3.139 closest distance to " O   HOH Z 171 " =    2.325
peak=   -3.136 closest distance to " O   HOH Z 174 " =    3.636
peak=   -3.132 closest distance to " O   HOH Z 407 " =    2.726
peak=   -3.129 closest distance to " CA  GLY A 241 " =    3.186
peak=   -3.128 closest distance to " O   HOH Z 426 " =    1.675
peak=   -3.127 closest distance to " O   HOH Z 231 " =    2.072
peak=   -3.125 closest distance to " CG  LYS A 166 " =    2.073
peak=   -3.123 closest distance to " CB  PRO A 163 " =    2.509
peak=   -3.119 closest distance to " O   HOH Z 260 " =    1.847
peak=   -3.109 closest distance to " OD2 ASP A  50 " =    2.247
peak=   -3.105 closest distance to " CD  GLN A 223 " =    1.691
peak=   -3.105 closest distance to " N   ALA A 295 " =    0.982
peak=   -3.094 closest distance to " OE1 GLN A 183 " =    1.575
peak=   -3.077 closest distance to " CA  ASP A  65 " =    1.349
peak=   -3.076 closest distance to " OG  SER A  28 " =    2.073
peak=   -3.073 closest distance to " SG  CYS A 260 " =    1.936
peak=   -3.066 closest distance to " CA  SER A  62 " =    2.565
peak=   -3.057 closest distance to " CA  HIS A 207 " =    1.268
peak=   -3.053 closest distance to " O   HOH Z  60 " =    1.906
peak=   -3.037 closest distance to " O   HOH Z 351 " =    1.451
peak=   -3.034 closest distance to " O   HOH Z 162 " =    3.018
peak=   -3.030 closest distance to " O   ALA A 180 " =    1.306
peak=   -3.027 closest distance to " O   HOH Z   2 " =    1.621
peak=   -3.025 closest distance to " O   HOH Z 326 " =    5.105
peak=   -3.003 closest distance to " CB  PRO A 213 " =    2.196

================= 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    :  0.4890 0.4735   6.290465e+00   6.276495e+00
   1_bss:  0.4794 0.4656   6.283877e+00   6.269349e+00
   1_xyz:  0.3993 0.4245   6.177767e+00   6.211900e+00
   1_adp:  0.3560 0.4077   6.102520e+00   6.181554e+00
   1_occ:  0.3557 0.4083   6.102160e+00   6.182823e+00
   2_bss:  0.3523 0.4025   6.102911e+00   6.182203e+00
   2_xyz:  0.2747 0.3288   5.900277e+00   6.041343e+00
   2_adp:  0.2530 0.3094   5.843946e+00   6.003392e+00
   2_occ:  0.2527 0.3093   5.843323e+00   6.003539e+00
   3_bss:  0.2515 0.3101   5.845040e+00   6.005038e+00
   3_xyz:  0.1826 0.2351   5.558728e+00   5.758486e+00
   3_adp:  0.1645 0.2139   5.465906e+00   5.670334e+00
   3_occ:  0.1642 0.2141   5.465975e+00   5.671126e+00
   4_bss:  0.1633 0.2122   5.463725e+00   5.666948e+00
   4_xyz:  0.1366 0.1796   5.309162e+00   5.518832e+00
   4_adp:  0.1295 0.1768   5.276576e+00   5.500837e+00
   4_occ:  0.1294 0.1767   5.276542e+00   5.500992e+00
   5_bss:  0.1294 0.1772   5.276303e+00   5.501458e+00
   5_xyz:  0.1265 0.1731   5.258200e+00   5.486255e+00
   5_adp:  0.1255 0.1725   5.252943e+00   5.482325e+00
   5_occ:  0.1254 0.1725   5.252731e+00   5.482096e+00
   5_bss:  0.1253 0.1724   5.252822e+00   5.482196e+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:  0.316   6.770   6.706   8.657  12.047   0.000   0.000   0.000
   1_xyz:  0.316   6.770   6.706   8.657  12.047   0.000   0.000   0.000
   1_adp:  0.316   6.770   6.706   8.657  12.047   0.000   0.000   0.000
   1_occ:  0.316   6.770   6.706   8.657  12.047   0.000   0.000   0.000
   2_bss:  0.324  43.642   2.539   4.431   7.578   0.000   0.000   0.000
   2_xyz:  0.324  43.642   2.539   4.431   7.578   0.000   0.000   0.000
   2_adp:  0.324  43.642   2.539   4.431   7.578   0.000   0.000   0.000
   2_occ:  0.324  43.642   2.539   4.431   7.578   0.000   0.000   0.000
   3_bss:  0.309  56.798   1.376   2.968   5.135   0.000   0.000   0.000
   3_xyz:  0.309  56.798   1.376   2.968   5.135   0.000   0.000   0.000
   3_adp:  0.309  56.798   1.376   2.968   5.135   0.000   0.000   0.000
   3_occ:  0.309  56.798   1.376   2.968   5.135   0.000   0.000   0.000
   4_bss:  0.320  56.798   0.665   1.838   3.610   0.000   0.000   0.000
   4_xyz:  0.320  56.798   0.665   1.838   3.610   0.000   0.000   0.000
   4_adp:  0.320  56.798   0.665   1.838   3.610   0.000   0.000   0.000
   4_occ:  0.320  56.798   0.665   1.838   3.610   0.000   0.000   0.000
   5_bss:  0.332  70.761   0.705   1.694   3.311   0.000   0.000   0.000
   5_xyz:  0.332  70.761   0.705   1.694   3.311   0.000   0.000   0.000
   5_adp:  0.332  70.761   0.705   1.694   3.311   0.000   0.000   0.000
   5_occ:  0.332  70.761   0.705   1.694   3.311   0.000   0.000   0.000
   5_bss:  0.326  67.184  -1.144  -0.205   1.349  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.550 0.4385  0.5064    69664.958
   1_bss:  56.020 0.4444  0.6709    68299.195
   1_xyz:  48.580 0.5370  0.7923    52275.312
   1_adp:  44.908 0.5832  0.9098    47139.046
   1_occ:  45.010 0.5820  0.9068    47306.118
   2_bss:  44.617 0.5870  0.7923    47041.841
   2_xyz:  34.899 0.7020  0.9281    29652.614
   2_adp:  32.484 0.7300  0.9552    26695.124
   2_occ:  32.473 0.7301  0.9552    26689.331
   3_bss:  32.423 0.7309  0.9012    26799.908
   3_xyz:  23.362 0.8279  0.9818    14305.860
   3_adp:  20.687 0.8553  0.9940    11953.163
   3_occ:  20.723 0.8549  0.9937    11965.128
   4_bss:  20.554 0.8564  0.9564    11769.736
   4_xyz:  17.011 0.8894  0.9716     8523.263
   4_adp:  16.602 0.8930  0.9652     8239.222
   4_occ:  16.601 0.8930  0.9651     8241.879
   5_bss:  16.601 0.8931  0.9610     8252.252
   5_xyz:  16.174 0.8971  0.9630     7912.366
   5_adp:  16.074 0.8981  0.9570     7853.671
   5_occ:  16.071 0.8981  0.9569     7851.372
   5_bss:  16.077 0.8981  0.9616     7851.988
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4229e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4229e+01
   1_xyz:   1.740  0.014  0.108 18.269  0.007  4.111   1.4820e-01
   1_adp:   1.740  0.014  0.108 18.269  0.007  4.111   1.4820e-01
   1_occ:   1.740  0.014  0.108 18.269  0.007  4.111   1.4820e-01
   2_bss:   1.740  0.014  0.108 18.269  0.007  4.111   1.4820e-01
   2_xyz:   1.226  0.009  0.080 16.138  0.004  4.112   8.4207e-02
   2_adp:   1.226  0.009  0.080 16.138  0.004  4.112   8.4207e-02
   2_occ:   1.226  0.009  0.080 16.138  0.004  4.112   8.4207e-02
   3_bss:   1.226  0.009  0.080 16.138  0.004  4.112   8.4207e-02
   3_xyz:   1.197  0.009  0.086 15.993  0.004  4.136   8.0883e-02
   3_adp:   1.197  0.009  0.086 15.993  0.004  4.136   8.0883e-02
   3_occ:   1.197  0.009  0.086 15.993  0.004  4.136   8.0883e-02
   4_bss:   1.197  0.009  0.086 15.993  0.004  4.136   8.0883e-02
   4_xyz:   1.062  0.008  0.080 15.564  0.004  4.118   6.8008e-02
   4_adp:   1.062  0.008  0.080 15.564  0.004  4.118   6.8008e-02
   4_occ:   1.062  0.008  0.080 15.564  0.004  4.118   6.8008e-02
   5_bss:   1.062  0.008  0.080 15.564  0.004  4.118   6.8008e-02
   5_xyz:   0.960  0.007  0.075 15.175  0.003  4.121   5.6811e-02
   5_adp:   0.960  0.007  0.075 15.175  0.003  4.121   5.6811e-02
   5_occ:   0.960  0.007  0.075 15.175  0.003  4.121   5.6811e-02
   5_bss:   0.960  0.007  0.075 15.175  0.003  4.121   5.6811e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.157   7.0287e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.157   7.0287e+00
   1_xyz:  14.805  0.173  0.470 86.271  0.060  2.149   1.0849e-01
   1_adp:  14.805  0.173  0.470 86.271  0.060  2.149   1.0849e-01
   1_occ:  14.805  0.173  0.470 86.271  0.060  2.149   1.0849e-01
   2_bss:  14.805  0.173  0.470 86.271  0.060  2.149   1.0849e-01
   2_xyz:   7.770  0.086  0.260 86.782  0.027  2.115   7.1820e-02
   2_adp:   7.770  0.086  0.260 86.782  0.027  2.115   7.1820e-02
   2_occ:   7.770  0.086  0.260 86.782  0.027  2.115   7.1820e-02
   3_bss:   7.770  0.086  0.260 86.782  0.027  2.115   7.1820e-02
   3_xyz:   9.333  0.060  0.314 84.500  0.039  2.211   5.5612e-02
   3_adp:   9.333  0.060  0.314 84.500  0.039  2.211   5.5612e-02
   3_occ:   9.333  0.060  0.314 84.500  0.039  2.211   5.5612e-02
   4_bss:   9.333  0.060  0.314 84.500  0.039  2.211   5.5612e-02
   4_xyz:   7.074  0.046  0.336 89.197  0.034  2.293   4.4608e-02
   4_adp:   7.074  0.046  0.336 89.197  0.034  2.293   4.4608e-02
   4_occ:   7.074  0.046  0.336 89.197  0.034  2.293   4.4608e-02
   5_bss:   7.074  0.046  0.336 89.197  0.034  2.293   4.4608e-02
   5_xyz:   6.555  0.041  0.332 81.591  0.034  2.381   3.1005e-02
   5_adp:   6.555  0.041  0.332 81.591  0.034  2.381   3.1005e-02
   5_occ:   6.555  0.041  0.332 81.591  0.034  2.381   3.1005e-02
   5_bss:   6.555  0.041  0.332 81.591  0.034  2.381   3.1005e-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:  82.22   0.00  13.90  65.26   0.00  11.65  82.22   0.00  26.20
   1_occ:  82.22   0.00  13.90  65.26   0.00  11.65  82.22   0.00  26.20
   2_bss:  82.22   0.00  13.90  65.26   0.00  11.65  82.22   0.00  26.20
   2_xyz:  82.22   0.00  13.90  65.26   0.00  11.65  82.22   0.00  26.20
   2_adp:  79.27   0.00  13.82  71.90   0.00  10.43  79.27   0.00  32.27
   2_occ:  79.27   0.00  13.82  71.90   0.00  10.43  79.27   0.00  32.27
   3_bss:  79.27   0.00  13.82  71.90   0.00  10.43  79.27   0.00  32.27
   3_xyz:  79.27   0.00  13.82  71.90   0.00  10.43  79.27   0.00  32.27
   3_adp: 108.29   0.00  13.61 108.29   0.00   9.50  78.23   1.96  36.02
   3_occ: 108.29   0.00  13.61 108.29   0.00   9.50  78.23   1.96  36.02
   4_bss: 108.29   0.00  13.61 108.29   0.00   9.50  78.23   1.96  36.02
   4_xyz: 108.29   0.00  13.61 108.29   0.00   9.50  78.23   1.96  36.02
   4_adp: 101.87   0.00  14.55  90.00   0.00   9.56 101.87   1.50  41.71
   4_occ: 101.87   0.00  14.55  90.00   0.00   9.56 101.87   1.50  41.71
   5_bss: 101.87   0.00  14.55  90.00   0.00   9.56 101.87   1.50  41.71
   5_xyz: 101.87   0.00  14.55  90.00   0.00   9.56 101.87   1.50  41.71
   5_adp: 102.50   0.00  14.31  92.00   0.00   9.40 102.50   1.60  41.04
   5_occ: 102.50   0.00  14.31  92.00   0.00   9.40 102.50   1.60  41.04
   5_bss: 104.54   2.04  16.36  94.05   2.04  11.45 104.54   3.64  43.09
------------------------------------------------------------------------
 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:    1.294    0.026    0.415
   1_adp:    1.294    0.026    0.415
   1_occ:    1.294    0.026    0.415
   2_bss:    1.294    0.026    0.415
   2_xyz:    1.994    0.037    0.580
   2_adp:    1.994    0.037    0.580
   2_occ:    1.994    0.037    0.580
   3_bss:    1.994    0.037    0.580
   3_xyz:    1.823    0.024    0.693
   3_adp:    1.823    0.024    0.693
   3_occ:    1.823    0.024    0.693
   4_bss:    1.823    0.024    0.693
   4_xyz:    1.995    0.032    0.741
   4_adp:    1.995    0.032    0.741
   4_occ:    1.995    0.032    0.741
   5_bss:    1.995    0.032    0.741
   5_xyz:    2.135    0.014    0.753
   5_adp:    2.135    0.014    0.753
   5_occ:    2.135    0.014    0.753
   5_bss:    2.135    0.014    0.753
------------------------------------------------------------------------

CPU time actual refinement: 279.33


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_450/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_450/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_450/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_450/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_450/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 279.19 
  Macro-tasks:
    bulk solvent and scale       = 34.87  
    individual site refinement   = 118.44 
    weights calculation          = 26.25  
    collect and process          = 5.39   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 185.05 
  Micro-tasks:
    mask                            = 1.99   
    f_calc                          = 84.97  
    alpha_beta                      = 7.07   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 95.22  
    fmodel                         = 5.97   
    r_factors                      = 0.16   
    phase_errors                   = 8.76   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 205.36 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.887 micro seconds
Total CPU time: 4.85 minutes
from_scatterers_fft:    651 calls, 84.64 s
gradients_fft:          596 calls, 83.35 s

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

# Date 2008-01-16 Time 01:37:02 PST -0800 (1200476222.11 s)
Start R-work = 0.4890, R-free = 0.4735 (no bulk solvent and anisotropic scale)
Final R-work = 0.1422, R-free = 0.1870 (no bulk solvent and anisotropic scale)

Start R-work = 0.4794, R-free = 0.4656
Final R-work = 0.1253, R-free = 0.1724