# Date 2008-01-16 Time 01:32:55 PST -0800 (1200475975.39 s)
#phil __OFF__

Command line arguments: "../461.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10437
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 461

-------------------------------------------------------------------------------
  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, 47.6339, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98087
Completeness in resolution range: 0.931125
Completeness with d_max=infinity: 0.928301

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, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98087
Completeness in resolution range: 0.931125
Completeness with d_max=infinity: 0.928301

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2385 [2214/2242]  1991   223  10.1%
  bin  2:  4.2385 -  3.3769 [2110/2133]  1896   214  10.1%
  bin  3:  3.3769 -  2.9537 [2088/2110]  1885   203   9.7%
  bin  4:  2.9537 -  2.6854 [2087/2106]  1877   210  10.1%
  bin  5:  2.6854 -  2.4938 [2052/2081]  1837   215  10.5%
  bin  6:  2.4938 -  2.3474 [2048/2090]  1847   201   9.8%
  bin  7:  2.3474 -  2.2302 [2042/2078]  1849   193   9.5%
  bin  8:  2.2302 -  2.1334 [2041/2079]  1826   215  10.5%
  bin  9:  2.1334 -  2.0515 [2024/2055]  1829   195   9.6%
  bin 10:  2.0515 -  1.9809 [ 883/2064]   793    90  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_461/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.41 -     2.11: 12
        2.11 -     2.81: 770
        2.81 -     3.51: 4397
        3.51 -     4.20: 9182
        4.20 -     4.90: 13543
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.413 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.588 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.714 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  50 " - " O   HOH Z  95 "  1.797 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27899 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_461/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_461/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 47.63395 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= 0.5037   r_free= 0.4914   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.302219                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7273 0.99   1437  158 0.4076 0.4000      6.6311      6.6266|
|  2:  4.7273 -  3.7719 0.99   1386  154 0.4380 0.4967      6.8302      6.9673|
|  3:  3.7719 -  3.3009 0.99   1347  151 0.4786 0.4399      6.7095      6.6768|
|  4:  3.3009 -  3.0018 0.99   1349  144 0.5004 0.4559       6.541       6.509|
|  5:  3.0018 -  2.7881 0.99   1326  154 0.5322 0.4984      6.3779      6.4042|
|  6:  2.7881 -  2.6246 0.98   1333  146 0.5307 0.5458      6.2928      6.2074|
|  7:  2.6246 -  2.4938 0.99   1308  158 0.5281 0.4815      6.2457      6.1537|
|  8:  2.4938 -  2.3857 0.99   1341  136 0.5477 0.4680      6.1937      6.1384|
|  9:  2.3857 -  2.2942 0.98   1320  145 0.5431 0.5876      6.1333      6.2063|
| 10:  2.2942 -  2.2153 0.98   1298  144 0.5606 0.5020      6.1021      6.1027|
| 11:  2.2153 -  2.1462 0.98   1303  155 0.5329 0.5699      6.0226      6.0352|
| 12:  2.1462 -  2.0850 0.99   1311  144 0.5465 0.5198      5.9577      5.9434|
| 13:  2.0850 -  2.0303 0.91   1231  121 0.5523 0.5373       5.886      5.8485|
| 14:  2.0303 -  1.9809 0.26    340   49 0.5266 0.4507      5.9121      5.7468|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7273  1437   158  0.67  36.46   0.79     0.68      77939.46|
|  2:  4.7273 -  3.7719  1386   154  0.64  39.96   0.85     0.70     128200.02|
|  3:  3.7719 -  3.3009  1347   151  0.54  48.75   0.78     0.65     133035.47|
|  4:  3.3009 -  3.0018  1349   144  0.44  56.48   0.78     0.54     113496.66|
|  5:  3.0018 -  2.7881  1326   154  0.38  61.62   0.71     0.44      86533.52|
|  6:  2.7881 -  2.6246  1333   146  0.34  64.66   0.70     0.40      77319.89|
|  7:  2.6246 -  2.4938  1308   158  0.37  62.26   0.72     0.42      65575.57|
|  8:  2.4938 -  2.3857  1341   136  0.39  60.48   0.70     0.46      55812.33|
|  9:  2.3857 -  2.2942  1320   145  0.37  62.04   0.69     0.44      53357.13|
| 10:  2.2942 -  2.2153  1298   144  0.30  67.54   0.71     0.36      51136.85|
| 11:  2.2153 -  2.1462  1303   155  0.23  72.73   0.74     0.30      53129.60|
| 12:  2.1462 -  2.0850  1311   144  0.22  73.47   0.71     0.29      47694.84|
| 13:  2.0850 -  2.0303  1231   121  0.23  73.04   0.71     0.30      41745.44|
| 14:  2.0303 -  1.9809   340    49  0.28  69.26   0.76     0.29      31443.93|
|alpha:            min =        0.29 max =            0.70 mean =         0.46|
|beta:             min =    31443.93 max =       133035.47 mean =     75499.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.99 mean =        59.79|
|phase err.(test): min =        0.00 max =           89.98 mean =        60.07|
|-----------------------------------------------------------------------------|

============================== 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 = 18.630338             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.308   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.751987              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.536   (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 |  1.190 -  1.561:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.561 -  1.932:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.932 -  2.303:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.303 -  2.674:      679 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.674 -  3.045:     1480 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.045 -  3.416:     2586 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.416 -  3.787:     3860 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.787 -  4.158:     5012 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.158 -  4.529:     6503 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.529 -  4.900:     7638 |
|-----------------------------------------------------------------------------|
|-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 |       54.297 |
| 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  1.190 |       1.977 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    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 = 12.139)------------------------------------------|
|    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= 0.5085   r_free= 0.4955   ksol= 0.00   Bsol= 0.00   scale= 0.740    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.303289                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4951   r_free= 0.4864   ksol= 0.30   Bsol= 0.00   scale= 0.972    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.27,9.56,11.42,0.00,0.00,0.00); trace/3= 9.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.296951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.967676             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.314   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.524058              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.679   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4951      final r-factor (work) = 0.4257          |
| start r-factor (free) = 0.4864      final r-factor (free) = 0.4483          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.5884 = 15.97 * 0.50 * 6.2991 + 1.00 * 54.2972                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.9181 = 15.97 * 0.50 * 6.2331 + 1.00 * 0.1536                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4257      final r-factor (work) = 0.3822          |
| start r-factor (free) = 0.4483      final r-factor (free) = 0.4395          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5141 = 1.52 * 1.00 * 6.2331 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4226 = 1.52 * 1.00 * 6.1683 + 1.00 * 0.0218                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.21   15.59    None  None   None       |
|    all(noH): 2823   0      0.00    93.21   15.59    None  None   None       |
|    Sol.    : 438    0      0.00    93.21   26.72    None  None   None       |
|    Mac.    : 2385   0      0.00    80.74   13.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.321: 1152   |   5:    46.604 -  55.924:   57        |
|      1:     9.321 -  18.642:  765   |   6:    55.924 -  65.245:   29        |
|      2:    18.642 -  27.962:  459   |   7:    65.245 -  74.566:   11        |
|      3:    27.962 -  37.283:  232   |   8:    74.566 -  83.887:    8        |
|      4:    37.283 -  46.604:  108   |   9:    83.887 -  93.207:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3822 r_free = 0.4395             target_work(ml) = 6.155         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3816 r_free = 0.4393             target_work(ml) = 6.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3816   r_free= 0.4393   ksol= 0.30   Bsol= 0.00   scale= 1.106    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.27,9.56,11.42,0.00,0.00,0.00); trace/3= 9.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.154752                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3795   r_free= 0.4336   ksol= 0.31   Bsol= 32.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,5.66,7.33,0.00,0.00,0.00); trace/3= 5.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.156278                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.332227              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.873  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.604888              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.092  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3795      final r-factor (work) = 0.3115          |
| start r-factor (free) = 0.4336      final r-factor (free) = 0.3694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.7529 = 7.33 * 0.50 * 6.1644 + 1.00 * 0.1536                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3517 = 7.33 * 0.50 * 6.0706 + 1.00 * 0.0960                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3115      final r-factor (work) = 0.2936          |
| start r-factor (free) = 0.3694      final r-factor (free) = 0.3541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7130 = 0.60 * 1.00 * 6.0706 + 1.00 * 0.0410                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6740 = 0.60 * 1.00 * 5.9792 + 1.00 * 0.0572                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.03   14.85    None  None   None       |
|    all(noH): 2823   0      0.00    94.03   14.85    None  None   None       |
|    Sol.    : 438    0      0.00    94.03   30.80    None  None   None       |
|    Mac.    : 2385   0      0.00    74.36   11.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.403: 1232   |   5:    47.013 -  56.416:   46        |
|      1:     9.403 -  18.805:  800   |   6:    56.416 -  65.819:   23        |
|      2:    18.805 -  28.208:  408   |   7:    65.819 -  75.222:    7        |
|      3:    28.208 -  37.611:  196   |   8:    75.222 -  84.624:    7        |
|      4:    37.611 -  47.013:  103   |   9:    84.624 -  94.027:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2936 r_free = 0.3541             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2934 r_free = 0.3541             target_work(ml) = 5.964         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2934   r_free= 0.3541   ksol= 0.31   Bsol= 32.00   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,5.66,7.33,0.00,0.00,0.00); trace/3= 5.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.964212                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2918   r_free= 0.3538   ksol= 0.30   Bsol= 52.33   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.00,3.19,4.70,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.965666                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.420721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.897   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.702285              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.042   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2918      final r-factor (work) = 0.2300          |
| start r-factor (free) = 0.3538      final r-factor (free) = 0.2815          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3166 = 4.42 * 0.50 * 5.9812 + 1.00 * 0.0960                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0516 = 4.42 * 0.50 * 5.8716 + 1.00 * 0.0733                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2300      final r-factor (work) = 0.2081          |
| start r-factor (free) = 0.2815      final r-factor (free) = 0.2703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.8884 = 2.70 * 1.00 * 5.8716 + 1.00 * 0.0217                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.4455 = 2.70 * 1.00 * 5.7078 + 1.00 * 0.0212                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.57  16.47    None  None   None       |
|    all(noH): 2823   0      0.00    106.57  16.47    None  None   None       |
|    Sol.    : 438    0      0.42    106.57  43.09    None  None   None       |
|    Mac.    : 2385   0      0.00    100.92  11.58    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 -  10.657: 1500   |   5:    53.285 -  63.942:   82        |
|      1:    10.657 -  21.314:  647   |   6:    63.942 -  74.598:   58        |
|      2:    21.314 -  31.971:  263   |   7:    74.598 -  85.255:   31        |
|      3:    31.971 -  42.628:  126   |   8:    85.255 -  95.912:   12        |
|      4:    42.628 -  53.285:   99   |   9:    95.912 - 106.569:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2081 r_free = 0.2703             target_work(ml) = 5.690         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2079 r_free = 0.2703             target_work(ml) = 5.689         |
| 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= 0.2079   r_free= 0.2703   ksol= 0.30   Bsol= 52.33   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.00,3.19,4.70,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.689476                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2077   r_free= 0.2701   ksol= 0.33   Bsol= 75.36   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.40,2.09,3.53,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.688504                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.579557              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.836  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.210148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.871  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2077      final r-factor (work) = 0.1731          |
| start r-factor (free) = 0.2701      final r-factor (free) = 0.2292          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4376 = 2.58 * 0.50 * 5.7098 + 1.00 * 0.0733                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3013 = 2.58 * 0.50 * 5.6154 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1731      final r-factor (work) = 0.1625          |
| start r-factor (free) = 0.2292      final r-factor (free) = 0.2165          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8165 = 1.21 * 1.00 * 5.6154 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6794 = 1.21 * 1.00 * 5.5047 + 1.00 * 0.0178                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.59  16.03    None  None   None       |
|    all(noH): 2823   0      0.00    110.59  16.03    None  None   None       |
|    Sol.    : 438    0      1.75    110.59  44.99    None  None   None       |
|    Mac.    : 2385   0      0.00    103.09  10.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.059: 1630   |   5:    55.295 -  66.354:   85        |
|      1:    11.059 -  22.118:  634   |   6:    66.354 -  77.413:   45        |
|      2:    22.118 -  33.177:  168   |   7:    77.413 -  88.472:   31        |
|      3:    33.177 -  44.236:  121   |   8:    88.472 -  99.531:   11        |
|      4:    44.236 -  55.295:   93   |   9:    99.531 - 110.590:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1625 r_free = 0.2165             target_work(ml) = 5.476         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1624 r_free = 0.2166             target_work(ml) = 5.477         |
| 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= 0.1624   r_free= 0.2166   ksol= 0.33   Bsol= 75.36   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.40,2.09,3.53,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.476543                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1626   r_free= 0.2169   ksol= 0.34   Bsol= 82.40   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.31,1.68,3.02,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.477028                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.332469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.491  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.621393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.683  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1626      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.2169      final r-factor (free) = 0.1894          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2320 = 3.33 * 0.50 * 5.5054 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0891 = 3.33 * 0.50 * 5.4106 + 1.00 * 0.0737                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1380      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1806          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3799 = 0.62 * 1.00 * 5.4106 + 1.00 * 0.0178                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3236 = 0.62 * 1.00 * 5.3208 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.43  15.43    None  None   None       |
|    all(noH): 2823   0      0.00    110.43  15.43    None  None   None       |
|    Sol.    : 438    0      2.12    110.43  43.88    None  None   None       |
|    Mac.    : 2385   0      0.00    98.25   10.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.043: 1694   |   5:    55.214 -  66.257:   75        |
|      1:    11.043 -  22.086:  610   |   6:    66.257 -  77.300:   48        |
|      2:    22.086 -  33.128:  152   |   7:    77.300 -  88.342:   19        |
|      3:    33.128 -  44.171:  103   |   8:    88.342 -  99.385:   14        |
|      4:    44.171 -  55.214:  104   |   9:    99.385 - 110.428:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1329 r_free = 0.1806             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1328 r_free = 0.1805             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1805   ksol= 0.34   Bsol= 82.40   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.31,1.68,3.02,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.297067                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7273 0.99   1437  158 0.1006 0.1367      5.4362      5.6229|
|  2:  4.7273 -  3.7719 0.99   1386  154 0.0932 0.1140      5.5169      5.7234|
|  3:  3.7719 -  3.3009 0.99   1347  151 0.1253 0.1696      5.6158      5.9516|
|  4:  3.3009 -  3.0018 0.99   1349  144 0.1453 0.1953      5.5877      5.7876|
|  5:  3.0018 -  2.7881 0.99   1326  154 0.1658 0.1819      5.5121      5.6292|
|  6:  2.7881 -  2.6246 0.98   1333  146 0.1499 0.2475      5.3774      5.6855|
|  7:  2.6246 -  2.4938 0.99   1308  158 0.1540 0.1794      5.3361      5.4577|
|  8:  2.4938 -  2.3857 0.99   1341  136 0.1477 0.2121      5.2691      5.5038|
|  9:  2.3857 -  2.2942 0.98   1320  145 0.1458 0.2211      5.1821      5.4678|
| 10:  2.2942 -  2.2153 0.98   1298  144 0.1404 0.1889      5.1224      5.2821|
| 11:  2.2153 -  2.1462 0.98   1303  155 0.1356 0.2151      5.0455      5.3976|
| 12:  2.1462 -  2.0850 0.99   1311  144 0.1367 0.1814      4.9974       5.212|
| 13:  2.0850 -  2.0303 0.91   1231  121 0.1318 0.1954      4.9102      5.1312|
| 14:  2.0303 -  1.9809 0.26    340   49 0.1217 0.1792      4.8371      5.0433|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7273  1437   158  0.93  10.21   0.96     0.93       8467.91|
|  2:  4.7273 -  3.7719  1386   154  0.94   9.45   1.01     0.99      10863.28|
|  3:  3.7719 -  3.3009  1347   151  0.92  13.62   1.03     1.03      13562.49|
|  4:  3.3009 -  3.0018  1349   144  0.90  16.50   1.01     1.00      13440.37|
|  5:  3.0018 -  2.7881  1326   154  0.87  19.73   1.01     0.98      12168.86|
|  6:  2.7881 -  2.6246  1333   146  0.86  20.36   0.98     0.95      10225.47|
|  7:  2.6246 -  2.4938  1308   158  0.87  19.25   0.99     0.95       8707.38|
|  8:  2.4938 -  2.3857  1341   136  0.87  19.96   1.00     0.96       8162.95|
|  9:  2.3857 -  2.2942  1320   145  0.87  19.45   1.00     0.96       6764.30|
| 10:  2.2942 -  2.2153  1298   144  0.87  19.21   1.00     0.95       6061.00|
| 11:  2.2153 -  2.1462  1303   155  0.88  18.71   0.99     0.94       5378.26|
| 12:  2.1462 -  2.0850  1311   144  0.88  18.95   1.00     1.00       5026.57|
| 13:  2.0850 -  2.0303  1231   121  0.88  19.03   0.99     0.96       4309.15|
| 14:  2.0303 -  1.9809   340    49  0.89  17.14   0.96     0.90       3469.48|
|alpha:            min =        0.90 max =            1.03 mean =         0.97|
|beta:             min =     3469.48 max =        13562.49 mean =      8655.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           90.00 mean =        17.17|
|phase err.(test): min =        0.00 max =           89.70 mean =        16.30|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1808   ksol= 0.34   Bsol= 77.39   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.12,1.34,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.298809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1808   ksol= 0.34   Bsol= 77.39   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.12,1.34,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.298809                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7273 0.99   1437  158 0.1021 0.1392      5.4488      5.6327|
|  2:  4.7273 -  3.7719 0.99   1386  154 0.0940 0.1134      5.5239      5.7232|
|  3:  3.7719 -  3.3009 0.99   1347  151 0.1254 0.1692       5.616      5.9478|
|  4:  3.3009 -  3.0018 0.99   1349  144 0.1458 0.1953      5.5886      5.7882|
|  5:  3.0018 -  2.7881 0.99   1326  154 0.1658 0.1816      5.5129      5.6304|
|  6:  2.7881 -  2.6246 0.98   1333  146 0.1499 0.2474      5.3775      5.6856|
|  7:  2.6246 -  2.4938 0.99   1308  158 0.1542 0.1794      5.3365       5.457|
|  8:  2.4938 -  2.3857 0.99   1341  136 0.1477 0.2120      5.2693      5.5042|
|  9:  2.3857 -  2.2942 0.98   1320  145 0.1457 0.2214      5.1819      5.4689|
| 10:  2.2942 -  2.2153 0.98   1298  144 0.1403 0.1891      5.1223      5.2815|
| 11:  2.2153 -  2.1462 0.98   1303  155 0.1357 0.2149      5.0452      5.3973|
| 12:  2.1462 -  2.0850 0.99   1311  144 0.1367 0.1817      4.9976      5.2131|
| 13:  2.0850 -  2.0303 0.91   1231  121 0.1319 0.1945      4.9097      5.1286|
| 14:  2.0303 -  1.9809 0.26    340   49 0.1215 0.1791      4.8381      5.0432|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7273  1437   158  0.93  10.58   0.96     0.93       8801.28|
|  2:  4.7273 -  3.7719  1386   154  0.94   9.54   1.01     0.99      10993.28|
|  3:  3.7719 -  3.3009  1347   151  0.92  13.60   1.03     1.03      13524.27|
|  4:  3.3009 -  3.0018  1349   144  0.90  16.49   1.01     1.00      13400.44|
|  5:  3.0018 -  2.7881  1326   154  0.87  19.73   1.01     0.98      12179.33|
|  6:  2.7881 -  2.6246  1333   146  0.86  20.35   0.98     0.95      10229.05|
|  7:  2.6246 -  2.4938  1308   158  0.87  19.26   0.99     0.94       8713.98|
|  8:  2.4938 -  2.3857  1341   136  0.87  19.97   1.00     0.95       8164.60|
|  9:  2.3857 -  2.2942  1320   145  0.87  19.46   1.00     0.95       6772.59|
| 10:  2.2942 -  2.2153  1298   144  0.87  19.21   1.00     0.95       6062.99|
| 11:  2.2153 -  2.1462  1303   155  0.88  18.71   0.99     0.94       5376.29|
| 12:  2.1462 -  2.0850  1311   144  0.88  18.94   1.00     0.99       5026.45|
| 13:  2.0850 -  2.0303  1231   121  0.88  19.00   0.98     0.96       4298.35|
| 14:  2.0303 -  1.9809   340    49  0.89  17.12   0.96     0.90       3454.42|
|alpha:            min =        0.90 max =            1.03 mean =         0.96|
|beta:             min =     3454.42 max =        13524.27 mean =      8688.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.20|
|phase err.(test): min =        0.00 max =           89.69 mean =        16.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    112.04  17.04    None  None   None       |
|    all(noH): 2823   0      1.61    112.04  17.04    None  None   None       |
|    Sol.    : 438    0      3.73    112.04  45.49    None  None   None       |
|    Mac.    : 2385   0      1.61    99.86   11.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.610 -  12.652: 1694   |   5:    56.823 -  67.866:   75        |
|      1:    12.652 -  23.695:  610   |   6:    67.866 -  78.909:   48        |
|      2:    23.695 -  34.738:  152   |   7:    78.909 -  89.952:   19        |
|      3:    34.738 -  45.781:  103   |   8:    89.952 - 100.995:   14        |
|      4:    45.781 -  56.823:  104   |   9:   100.995 - 112.037:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.674 - 5.017
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 323
   mapped sites are within: 0.738 - 5.017

peak=    8.874 closest distance to " CB  VAL A 230 " =    1.393
peak=    7.309 closest distance to " CG1 VAL A 296 " =    1.296
peak=    6.258 closest distance to " CD1AILE A 234 " =    1.253
peak=    6.045 closest distance to " CG  ARG A 138 " =    1.217
peak=    5.748 closest distance to " O   HOH Z 210 " =    1.472
peak=    5.507 closest distance to " O   HOH Z 248 " =    1.478
peak=    5.397 closest distance to " CD2 LEU A   5 " =    1.201
peak=    5.266 closest distance to " CD2 LEU A 228 " =    1.243
peak=    5.051 closest distance to " O   HOH Z 403 " =    2.085
peak=    4.950 closest distance to " O   HOH Z 255 " =    0.949
peak=    4.895 closest distance to " O   HOH Z 404 " =    1.268
peak=    4.889 closest distance to " O   HOH Z 107 " =    1.100
peak=    4.845 closest distance to " NH1 ARG A 138 " =    0.978
peak=    4.836 closest distance to " O   HOH Z 128 " =    1.776
peak=    4.809 closest distance to " O   HOH Z 127 " =    0.988
peak=    4.808 closest distance to " CZ3 TRP A 266 " =    1.092
peak=    4.807 closest distance to " O   HOH Z  69 " =    1.038
peak=    4.697 closest distance to " O   HOH Z  65 " =    0.860
peak=    4.664 closest distance to " O   HOH Z 425 " =    1.673
peak=    4.664 closest distance to " O   HOH Z 431 " =    1.387
peak=    4.656 closest distance to " NE2 GLN A  11 " =    1.192
peak=    4.644 closest distance to " CG  PRO A  54 " =    1.417
peak=    4.614 closest distance to " CB  GLN A 223 " =    1.466
peak=    4.594 closest distance to " O   HOH Z 251 " =    1.888
peak=    4.580 closest distance to " O   HOH Z 203 " =    0.826
peak=    4.579 closest distance to " CA  TYR A  30 " =    1.001
peak=    4.555 closest distance to " O   HOH Z 214 " =    1.635
peak=    4.549 closest distance to " CB  ARG A 275 " =    0.919
peak=    4.542 closest distance to " CD2 TRP A 179 " =    1.316
peak=    4.512 closest distance to " CG  PRO A 280 " =    0.944
peak=    4.471 closest distance to " O   HOH Z 246 " =    1.309
peak=    4.466 closest distance to " CG  LEU A   5 " =    1.314
peak=    4.461 closest distance to " O   HOH Z 124 " =    1.276
peak=    4.458 closest distance to " O   HOH Z 394 " =    1.641
peak=    4.418 closest distance to " CB  SER A  63 " =    1.230
peak=    4.399 closest distance to " O   HOH Z 402 " =    1.527
peak=    4.397 closest distance to " O   HOH Z 232 " =    2.266
peak=    4.397 closest distance to " O   HOH Z 154 " =    1.764
peak=    4.394 closest distance to " O   SER A  87 " =    2.247
peak=    4.355 closest distance to " O   HOH Z  76 " =    1.391
peak=    4.351 closest distance to " NH2 ARG A  56 " =    2.102
peak=    4.313 closest distance to " O   HOH Z 372 " =    1.099
peak=    4.307 closest distance to " O   HOH Z  67 " =    1.074
peak=    4.290 closest distance to " O   HOH Z 331 " =    1.110
peak=    4.277 closest distance to " CB  SER A  26 " =    1.762
peak=    4.269 closest distance to " CA  VAL A 230 " =    1.287
peak=    4.258 closest distance to " O   PRO A 198 " =    1.588
peak=    4.254 closest distance to " O   HOH Z 258 " =    1.309
peak=    4.251 closest distance to " NH2 ARG A  56 " =    1.178
peak=    4.239 closest distance to " CG  PRO A 243 " =    1.118
peak=    4.232 closest distance to " CG2 ILE A 234 " =    1.176
peak=    4.226 closest distance to " CB  GLN A 183 " =    1.232
peak=    4.221 closest distance to " NH2AARG A 145 " =    1.052
peak=    4.221 closest distance to " O   HOH Z 130 " =    1.071
peak=    4.208 closest distance to " O   HOH Z 411 " =    3.771
peak=    4.205 closest distance to " CZ  PHE A 218 " =    1.167
peak=    4.191 closest distance to " O   HOH Z 126 " =    1.632
peak=    4.158 closest distance to " O   HOH Z  49 " =    1.660
peak=    4.138 closest distance to " CG1 ILE A 120 " =    1.000
peak=    4.092 closest distance to " CB  ASN A 148 " =    1.436
peak=    4.075 closest distance to " O   HOH Z 316 " =    3.141
peak=    4.075 closest distance to " O   HOH Z 433 " =    1.590
peak=    4.072 closest distance to " O   HOH Z 130 " =    2.478
peak=    4.057 closest distance to " O   HOH Z 207 " =    1.410
peak=    4.047 closest distance to " CB  TRP A 179 " =    1.362
peak=    4.026 closest distance to " O   HOH Z 117 " =    1.279
peak=    4.016 closest distance to " O   HOH Z 133 " =    1.472
peak=    4.007 closest distance to " O   HOH Z 261 " =    2.532
peak=    4.004 closest distance to " CG AARG A 275 " =    1.371
peak=    3.992 closest distance to " O   HOH Z 188 " =    1.253
peak=    3.958 closest distance to " O   HOH Z 406 " =    1.600
peak=    3.955 closest distance to " O   HOH Z 369 " =    1.994
peak=    3.946 closest distance to " O   HOH Z 365 " =    2.664
peak=    3.946 closest distance to " CB  GLU A 277 " =    3.773
peak=    3.942 closest distance to " CE3 TRP A 274 " =    1.321
peak=    3.936 closest distance to " CD  ARG A 159 " =    0.808
peak=    3.933 closest distance to " CA  ARG A 195 " =    1.209
peak=    3.917 closest distance to " CG  GLN A  58 " =    1.059
peak=    3.905 closest distance to " CD  PRO A  54 " =    1.061
peak=    3.885 closest distance to " O   HOH Z 263 " =    1.174
peak=    3.875 closest distance to " O   HOH Z 222 " =    1.058
peak=    3.875 closest distance to " NE2 GLN A  77 " =    3.197
peak=    3.869 closest distance to " CB  ARG A 138 " =    1.128
peak=    3.865 closest distance to " CA  ALA A  51 " =    1.120
peak=    3.863 closest distance to " O   HOH Z 422 " =    2.521
peak=    3.857 closest distance to " O   HOH Z 151 " =    1.817
peak=    3.857 closest distance to " O   HOH Z 287 " =    1.589
peak=    3.855 closest distance to " O  BHOH Z  74 " =    1.083
peak=    3.854 closest distance to " NH2 ARG A 156 " =    1.136
peak=    3.851 closest distance to " OE1 GLU A   2 " =    1.331
peak=    3.851 closest distance to " O   HOH Z 132 " =    3.112
peak=    3.845 closest distance to " CB  ASN A 142 " =    1.157
peak=    3.844 closest distance to " O   HOH Z 142 " =    1.691
peak=    3.842 closest distance to " O   HOH Z 199 " =    1.539
peak=    3.840 closest distance to " O   HOH Z  40 " =    1.845
peak=    3.832 closest distance to " CB BVAL A  41 " =    1.270
peak=    3.824 closest distance to " N   SER A 164 " =    0.902
peak=    3.820 closest distance to " O   HOH Z 193 " =    1.864
peak=    3.812 closest distance to " CA  ARG A  36 " =    1.019
peak=    3.811 closest distance to " O   HOH Z   4 " =    1.675
peak=    3.787 closest distance to " CB  GLN A  58 " =    1.082
peak=    3.785 closest distance to " CB  SER A  62 " =    1.073
peak=    3.759 closest distance to " CA  ALA A 100 " =    0.959
peak=    3.755 closest distance to " CB  ASN A  39 " =    0.800
peak=    3.751 closest distance to " O   HOH Z  80 " =    2.167
peak=    3.747 closest distance to " CG  LEU A 228 " =    1.388
peak=    3.737 closest distance to " CA  ALA A 295 " =    0.942
peak=    3.736 closest distance to " CA  ASP A 162 " =    1.018
peak=    3.731 closest distance to " O   HOH Z 137 " =    1.812
peak=    3.728 closest distance to " O   HOH Z 365 " =    2.322
peak=    3.724 closest distance to " CB  MET A  40 " =    0.967
peak=    3.722 closest distance to " O   HOH Z 188 " =    2.642
peak=    3.717 closest distance to " O   HOH Z 343 " =    2.880
peak=    3.712 closest distance to " O   HOH Z 357 " =    2.088
peak=    3.710 closest distance to " CA  VAL A 125 " =    1.201
peak=    3.707 closest distance to " O   HOH Z   9 " =    1.123
peak=    3.705 closest distance to " CB  ASP A 107 " =    1.255
peak=    3.698 closest distance to " O   ASP A 200 " =    1.621
peak=    3.696 closest distance to " CD  LYS A 119 " =    1.995
peak=    3.679 closest distance to " CB  THR A 235 " =    1.281
peak=    3.679 closest distance to " O   HOH Z 162 " =    1.745
peak=    3.669 closest distance to " O   HOH Z  63 " =    1.874
peak=    3.668 closest distance to " CB  PRO A  90 " =    1.061
peak=    3.665 closest distance to " O   HOH Z  88 " =    3.566
peak=    3.661 closest distance to " CB  GLN A  55 " =    0.907
peak=    3.660 closest distance to " CG2 VAL A 197 " =    1.193
peak=    3.654 closest distance to " CD  LYS A 166 " =    1.486
peak=    3.635 closest distance to " O   HOH Z 146 " =    1.559
peak=    3.629 closest distance to " O   THR A 251 " =    1.143
peak=    3.628 closest distance to " CB  GLN A  89 " =    1.271
peak=    3.627 closest distance to " CB  ARG A  79 " =    1.282
peak=    3.620 closest distance to " CB  VAL A 265 " =    1.219
peak=    3.619 closest distance to " CG  PHE A 204 " =    0.936
peak=    3.619 closest distance to " N   THR A  52 " =    1.162
peak=    3.610 closest distance to " O   HOH Z 154 " =    2.182
peak=    3.604 closest distance to " O   HOH Z 234 " =    3.671
peak=    3.597 closest distance to " O   HOH Z 284 " =    2.872
peak=    3.596 closest distance to " CA  TYR A 116 " =    1.427
peak=    3.587 closest distance to " CB  THR A  52 " =    0.978
peak=    3.584 closest distance to " O   HOH Z 426 " =    1.197
peak=    3.584 closest distance to " CB  TRP A 150 " =    1.392
peak=    3.583 closest distance to " O   HOH Z 141 " =    1.544
peak=    3.580 closest distance to " CA  ALA A 160 " =    0.975
peak=    3.579 closest distance to " ND2BASN A 224 " =    0.738
peak=    3.567 closest distance to " CG  MET A 185 " =    1.147
peak=    3.563 closest distance to " O   HOH Z 142 " =    1.906
peak=    3.563 closest distance to " CB  ASP A 124 " =    0.888
peak=    3.561 closest distance to " CB  PRO A  54 " =    0.892
peak=    3.558 closest distance to " O   HOH Z  19 " =    1.870
peak=    3.556 closest distance to " CD  LYS A  76 " =    1.859
peak=    3.550 closest distance to " CG2 VAL A 296 " =    1.022
peak=    3.547 closest distance to " CB  SER A 288 " =    1.629
peak=    3.547 closest distance to " CA  ILE A 106 " =    0.772
peak=    3.545 closest distance to " O   HOH Z 213 " =    1.728
peak=    3.539 closest distance to " ND1 HIS A 115 " =    3.324
peak=    3.536 closest distance to " CB  ARG A 190 " =    1.770
peak=    3.532 closest distance to " CB  PRO A 243 " =    1.273
peak=    3.531 closest distance to " OG  SER A 245 " =    1.525
peak=    3.527 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.520 closest distance to " O   HOH Z 359 " =    1.985
peak=    3.518 closest distance to " O   HOH Z 116 " =    1.210
peak=    3.510 closest distance to " CB  ASN A 187 " =    1.498
peak=    3.507 closest distance to " CE1 TYR A 186 " =    1.235
peak=    3.507 closest distance to " O   HOH Z 238 " =    1.447
peak=    3.507 closest distance to " CA  CYS A 260 " =    1.239
peak=    3.507 closest distance to " CG2AVAL A 121 " =    1.958
peak=    3.505 closest distance to " O   HOH Z  54 " =    0.922
peak=    3.502 closest distance to " O   HOH Z  85 " =    1.205
peak=    3.502 closest distance to " CA  LYS A 117 " =    1.321
peak=    3.498 closest distance to " O   HOH Z 189 " =    2.897
peak=    3.494 closest distance to " CG  LEU A 167 " =    1.059
peak=    3.491 closest distance to " CA  GLU A 152 " =    0.830
peak=    3.490 closest distance to " CD  GLN A  73 " =    1.090
peak=    3.487 closest distance to " O   HOH Z 277 " =    1.299
peak=    3.478 closest distance to " CB  VAL A 202 " =    1.356
peak=    3.477 closest distance to " ND2 ASN A 249 " =    2.143
peak=    3.477 closest distance to " O   HOH Z 113 " =    2.110
peak=    3.477 closest distance to " O   HOH Z  29 " =    1.250
peak=    3.476 closest distance to " O   HOH Z 265 " =    2.063
peak=    3.472 closest distance to " O   ALA A 165 " =    1.237
peak=    3.471 closest distance to " O   HOH Z 174 " =    2.356
peak=    3.469 closest distance to " O   GLU A   2 " =    1.609
peak=    3.462 closest distance to " CB  GLU A  46 " =    1.013
peak=    3.455 closest distance to " O   HOH Z 258 " =    1.453
peak=    3.454 closest distance to " CB  ASN A 285 " =    0.954
peak=    3.453 closest distance to " O   HOH Z 420 " =    5.017
peak=    3.453 closest distance to " CA  ASP A 140 " =    1.361
peak=    3.450 closest distance to " O   GLY A  91 " =    1.128
peak=    3.448 closest distance to " CB  PRO A 198 " =    1.162
peak=    3.446 closest distance to " OG BSER A 258 " =    2.814
peak=    3.444 closest distance to " NH2AARG A 275 " =    2.878
peak=    3.442 closest distance to " CA  ASN A 217 " =    1.294
peak=    3.431 closest distance to " O  BHOH Z 338 " =    2.191
peak=    3.425 closest distance to " CA  ASP A 191 " =    1.218
peak=    3.419 closest distance to " O   HOH Z   1 " =    2.365
peak=    3.417 closest distance to " O   HOH Z 437 " =    1.631
peak=    3.417 closest distance to " O   HOH Z 393 " =    3.429
peak=    3.408 closest distance to " CE3 TRP A  85 " =    1.079
peak=    3.406 closest distance to " O   HOH Z 279 " =    1.075
peak=    3.404 closest distance to " O   HOH Z 146 " =    1.175
peak=    3.403 closest distance to " O   HOH Z 435 " =    3.003
peak=    3.403 closest distance to " CB  GLU A 152 " =    1.211
peak=    3.400 closest distance to " CA  ARG A 156 " =    1.054
peak=    3.400 closest distance to " O   HOH Z 126 " =    1.817
peak=    3.397 closest distance to " CE1 HIS A 115 " =    1.007
peak=    3.397 closest distance to " NE1 TRP A  92 " =    1.772
peak=    3.396 closest distance to " O   HOH Z  83 " =    1.616
peak=    3.389 closest distance to " OG  SER A 135 " =    1.387
peak=    3.385 closest distance to " O   HOH Z 371 " =    2.394
peak=    3.383 closest distance to " O   HOH Z  67 " =    1.653
peak=    3.383 closest distance to " O   HOH Z 272 " =    1.831
peak=    3.374 closest distance to " O   HOH Z 298 " =    2.152
peak=    3.374 closest distance to " CD1 LEU A  96 " =    1.055
peak=    3.373 closest distance to " CG1 ILE A  33 " =    1.260
peak=    3.361 closest distance to " OD1 ASN A 301 " =    1.099
peak=    3.358 closest distance to " CB  TYR A 169 " =    0.977
peak=    3.353 closest distance to " CB  ASN A  45 " =    1.068
peak=    3.351 closest distance to " NZ  LYS A 117 " =    1.275
peak=    3.350 closest distance to " CB  PHE A 204 " =    1.037
peak=    3.347 closest distance to " O   HOH Z 147 " =    1.570
peak=    3.345 closest distance to " CG2 THR A 221 " =    1.147
peak=    3.344 closest distance to " CD  ARG A 195 " =    1.164
peak=    3.340 closest distance to " CA  GLN A  58 " =    0.823
peak=    3.336 closest distance to " O   HOH Z  47 " =    2.559
peak=    3.336 closest distance to " O   HOH Z   3 " =    1.880
peak=    3.336 closest distance to " O   HOH Z 303 " =    2.232
peak=    3.334 closest distance to " OE1 GLN A  88 " =    0.837
peak=    3.330 closest distance to " O   HOH Z 328 " =    1.495
peak=    3.329 closest distance to " CZ  PHE A  38 " =    1.078
peak=    3.325 closest distance to " CB  VAL A 296 " =    1.118
peak=    3.323 closest distance to " O   HOH Z  85 " =    1.804
peak=    3.323 closest distance to " O   HOH Z 361 " =    2.644
peak=    3.321 closest distance to " NH1AARG A 102 " =    1.015
peak=    3.319 closest distance to " CD1 ILE A 199 " =    1.104
peak=    3.318 closest distance to " O   HOH Z 193 " =    1.550
peak=    3.318 closest distance to " NH1AARG A 145 " =    1.218
peak=    3.315 closest distance to " O   HOH Z 172 " =    3.508
peak=    3.312 closest distance to " O   HOH Z 368 " =    4.050
peak=    3.312 closest distance to " O   HOH Z 285 " =    2.228
peak=    3.309 closest distance to " CD1 ILE A  33 " =    1.781
peak=    3.308 closest distance to " O   THR A 220 " =    1.242
peak=    3.291 closest distance to " CG2 THR A  31 " =    0.944
peak=    3.291 closest distance to " N   ASP A 132 " =    0.984
peak=    3.288 closest distance to " O   THR A 182 " =    1.513
peak=    3.287 closest distance to " O   HOH Z 298 " =    4.463
peak=    3.287 closest distance to " N   SER A 271 " =    1.048
peak=    3.286 closest distance to " O   HOH Z 313 " =    1.642
peak=    3.284 closest distance to " CA  ALA A  21 " =    1.153
peak=    3.283 closest distance to " CB  SER A 273 " =    0.939
peak=    3.283 closest distance to " CB  GLU A 128 " =    1.154
peak=    3.282 closest distance to " O   HOH Z  30 " =    1.109
peak=    3.276 closest distance to " CG1 ILE A  20 " =    1.193
peak=    3.274 closest distance to " CE1 HIS A 108 " =    1.192
peak=    3.264 closest distance to " CG  LYS A 119 " =    0.896
peak=    3.262 closest distance to " O   ALA A 158 " =    1.245
peak=    3.261 closest distance to " O   HOH Z 423 " =    3.045
peak=    3.261 closest distance to " CD  ARG A 139 " =    1.150
peak=    3.260 closest distance to " OG BSER A 164 " =    2.126
peak=    3.257 closest distance to " CZ  ARG A  14 " =    1.324
peak=    3.255 closest distance to " CB  SER A  95 " =    0.815
peak=    3.254 closest distance to " CA  MET A 105 " =    1.140
peak=    3.253 closest distance to " O   ASP A 124 " =    1.442
peak=    3.250 closest distance to " O   HOH Z 139 " =    1.657
peak=    3.247 closest distance to " CB  GLN A  88 " =    1.237
peak=    3.242 closest distance to " O   HOH Z 128 " =    2.431
peak=    3.228 closest distance to " O   HOH Z 250 " =    1.249
peak=    3.228 closest distance to " O   HOH Z 134 " =    1.275
peak=    3.227 closest distance to " O   HOH Z 134 " =    2.337
peak=    3.222 closest distance to " O   HOH Z 368 " =    3.303
peak=    3.217 closest distance to " CB  ALA A 248 " =    1.471
peak=    3.216 closest distance to " CA  ASP A 149 " =    1.072
peak=    3.208 closest distance to " CB  MET A 105 " =    0.942
peak=    3.204 closest distance to " CD1 LEU A   5 " =    1.508
peak=    3.201 closest distance to " CA  ALA A 291 " =    0.887
peak=    3.201 closest distance to " CB  ARG A 219 " =    1.367
peak=    3.198 closest distance to " ND2 ASN A 187 " =    1.605
peak=    3.197 closest distance to " CB  ASN A  74 " =    1.457
peak=    3.196 closest distance to " O   HOH Z 171 " =    3.620
peak=    3.195 closest distance to " CG  GLN A  11 " =    1.525
peak=    3.193 closest distance to " CB  SER A  99 " =    1.415
peak=    3.192 closest distance to " N   TYR A 247 " =    1.259
peak=    3.191 closest distance to " NH2 ARG A 269 " =    1.099
peak=    3.189 closest distance to " O   HOH Z 427 " =    2.872
peak=    3.180 closest distance to " N   ASN A  39 " =    1.354
peak=    3.172 closest distance to " O   HOH Z 116 " =    1.813
peak=    3.170 closest distance to " O   HOH Z 421 " =    1.944
peak=    3.169 closest distance to " CB  ASN A 215 " =    1.232
peak=    3.165 closest distance to " CB  SER A 141 " =    1.074
peak=    3.163 closest distance to " CB  LEU A   5 " =    1.377
peak=    3.163 closest distance to " N   VAL A 126 " =    1.478
peak=    3.163 closest distance to " N   ALA A 292 " =    1.074
peak=    3.156 closest distance to " O   LEU A 228 " =    1.753
peak=    3.154 closest distance to " NZ  LYS A 117 " =    2.864
peak=    3.149 closest distance to " N   ALA A 256 " =    1.046
peak=    3.147 closest distance to " OG1 THR A 221 " =    1.184
peak=    3.145 closest distance to " CA  ASP A 124 " =    0.820
peak=    3.139 closest distance to " O   HOH Z 189 " =    1.387
peak=    3.139 closest distance to " CG  LYS A 289 " =    1.446
peak=    3.139 closest distance to " O   HOH Z 158 " =    2.761
peak=    3.137 closest distance to " O   HOH Z 340 " =    1.097
peak=    3.132 closest distance to " CB  ALA A   1 " =    4.947
peak=    3.126 closest distance to " OG BSER A 212 " =    2.514
peak=    3.122 closest distance to " O   HOH Z 394 " =    3.796
peak=    3.116 closest distance to " CZ3 TRP A  85 " =    0.821
peak=    3.109 closest distance to " O   HOH Z 140 " =    1.565
peak=    3.107 closest distance to " CG2AVAL A  72 " =    1.706
peak=    3.107 closest distance to " CD2 LEU A 297 " =    0.803
peak=    3.107 closest distance to " O   HOH Z 329 " =    4.171
peak=    3.102 closest distance to " CE1 TYR A  30 " =    1.205
peak=    3.100 closest distance to " O   HOH Z 183 " =    1.991
peak=    3.097 closest distance to " CG2 ILE A  20 " =    1.538
peak=    3.094 closest distance to " O   HOH Z 336 " =    1.695
peak=    3.089 closest distance to " O   PHE A 192 " =    1.367
peak=    3.088 closest distance to " CA  GLY A 133 " =    3.734
peak=    3.085 closest distance to " O   HOH Z  63 " =    1.945
peak=    3.078 closest distance to " CA  SER A  12 " =    1.404
peak=    3.057 closest distance to " CB  LYS A 117 " =    1.200
peak=    3.027 closest distance to " CD1 LEU A  96 " =    1.666
peak=    2.960 closest distance to " CD2 LEU A 228 " =    1.285

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.486 - 5.989
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.773 - 5.989

peak=   -4.962 closest distance to " CG2 VAL A 230 " =    0.773
peak=   -4.757 closest distance to " OG BSER A 134 " =    1.448
peak=   -4.727 closest distance to " O   HOH Z 203 " =    1.062
peak=   -4.500 closest distance to " O   PRO A 198 " =    1.290
peak=   -4.451 closest distance to " CD1 PHE A  59 " =    2.064
peak=   -4.403 closest distance to " CG1 VAL A 296 " =    1.007
peak=   -4.367 closest distance to " CG  GLN A  58 " =    0.904
peak=   -4.340 closest distance to " O   HOH Z 411 " =    5.625
peak=   -4.245 closest distance to " CZ2 TRP A  92 " =    2.844
peak=   -4.201 closest distance to " CD2 LEU A 237 " =    2.679
peak=   -4.153 closest distance to " O   HOH Z 166 " =    1.439
peak=   -4.079 closest distance to " CG2 VAL A 189 " =    2.044
peak=   -4.041 closest distance to " CE2 TYR A  30 " =    2.684
peak=   -4.017 closest distance to " O   HOH Z  13 " =    1.742
peak=   -4.000 closest distance to " CG2BVAL A  41 " =    2.674
peak=   -4.000 closest distance to " CE3 TRP A 150 " =    2.366
peak=   -3.983 closest distance to " O   HOH Z 214 " =    2.673
peak=   -3.955 closest distance to " CG  PRO A 243 " =    1.695
peak=   -3.903 closest distance to " CB  ALA A 291 " =    2.502
peak=   -3.898 closest distance to " SG  CYS A 254 " =    3.243
peak=   -3.893 closest distance to " CB  VAL A 230 " =    1.093
peak=   -3.886 closest distance to " NE  ARG A 138 " =    1.322
peak=   -3.873 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.864 closest distance to " O   HOH Z 216 " =    1.035
peak=   -3.853 closest distance to " O   HOH Z 154 " =    1.280
peak=   -3.844 closest distance to " O   HOH Z 119 " =    2.168
peak=   -3.824 closest distance to " CD2 TYR A 293 " =    1.936
peak=   -3.824 closest distance to " O   SER A 271 " =    2.179
peak=   -3.815 closest distance to " CD  ARG A 156 " =    2.141
peak=   -3.815 closest distance to " O   HOH Z  19 " =    2.494
peak=   -3.796 closest distance to " O   HOH Z  10 " =    1.524
peak=   -3.733 closest distance to " O   HOH Z 345 " =    2.932
peak=   -3.730 closest distance to " CG  GLN A 103 " =    2.349
peak=   -3.725 closest distance to " O   HOH Z 340 " =    1.615
peak=   -3.705 closest distance to " O   HOH Z 221 " =    1.063
peak=   -3.699 closest distance to " O   HOH Z 388 " =    2.181
peak=   -3.699 closest distance to " O   HOH Z  68 " =    1.446
peak=   -3.692 closest distance to " O   HOH Z 351 " =    1.814
peak=   -3.672 closest distance to " CA  GLN A  58 " =    1.019
peak=   -3.654 closest distance to " CZ  TYR A 169 " =    1.947
peak=   -3.651 closest distance to " CD1 LEU A 101 " =    2.400
peak=   -3.644 closest distance to " CG  MET A 105 " =    1.020
peak=   -3.639 closest distance to " O   GLY A  17 " =    1.110
peak=   -3.635 closest distance to " O   HOH Z 384 " =    1.846
peak=   -3.635 closest distance to " O   GLY A  80 " =    2.710
peak=   -3.630 closest distance to " O   HOH Z 131 " =    4.199
peak=   -3.628 closest distance to " ND2BASN A 224 " =    2.061
peak=   -3.618 closest distance to " CG2 ILE A  20 " =    2.780
peak=   -3.617 closest distance to " O   PRO A 163 " =    2.080
peak=   -3.610 closest distance to " O   HOH Z 285 " =    1.941
peak=   -3.609 closest distance to " O   HOH Z  52 " =    1.870
peak=   -3.609 closest distance to " CG1 VAL A 112 " =    2.454
peak=   -3.601 closest distance to " O   HOH Z 359 " =    2.665
peak=   -3.598 closest distance to " O   HOH Z 275 " =    1.807
peak=   -3.590 closest distance to " CE  LYS A  76 " =    0.806
peak=   -3.588 closest distance to " O   HOH Z 211 " =    1.098
peak=   -3.574 closest distance to " CB  ALA A 248 " =    2.370
peak=   -3.560 closest distance to " NE2 GLN A  11 " =    1.555
peak=   -3.559 closest distance to " NH2 ARG A 156 " =    1.148
peak=   -3.558 closest distance to " CG2 THR A 178 " =    2.486
peak=   -3.554 closest distance to " O   ASP A 253 " =    2.063
peak=   -3.551 closest distance to " O   HOH Z 136 " =    1.278
peak=   -3.541 closest distance to " CG  ARG A 269 " =    2.286
peak=   -3.534 closest distance to " O   HOH Z 423 " =    2.782
peak=   -3.527 closest distance to " CG  TRP A 266 " =    1.818
peak=   -3.515 closest distance to " O   HOH Z 283 " =    2.686
peak=   -3.511 closest distance to " O   HOH Z  30 " =    1.656
peak=   -3.510 closest distance to " N   ILE A 120 " =    1.038
peak=   -3.507 closest distance to " O   HOH Z 377 " =    2.097
peak=   -3.500 closest distance to " CG2 VAL A 202 " =    2.742
peak=   -3.486 closest distance to " OG  SER A  97 " =    2.191
peak=   -3.485 closest distance to " CZ  ARG A 259 " =    0.950
peak=   -3.481 closest distance to " O   HOH Z  64 " =    2.063
peak=   -3.477 closest distance to " CB  ALA A  43 " =    2.649
peak=   -3.474 closest distance to " CB  ASP A 286 " =    1.889
peak=   -3.464 closest distance to " CG  ARG A 259 " =    2.536
peak=   -3.459 closest distance to " CE1 PHE A 218 " =    1.415
peak=   -3.455 closest distance to " O   HOH Z 275 " =    1.583
peak=   -3.454 closest distance to " CG2 THR A 182 " =    2.300
peak=   -3.454 closest distance to " NE2 GLN A 194 " =    2.106
peak=   -3.451 closest distance to " C   ASN A 285 " =    2.241
peak=   -3.450 closest distance to " NE  ARG A  66 " =    4.513
peak=   -3.441 closest distance to " O   HOH Z 150 " =    1.681
peak=   -3.439 closest distance to " CD  PRO A 243 " =    1.765
peak=   -3.436 closest distance to " O   GLN A  77 " =    1.795
peak=   -3.432 closest distance to " CD2 HIS A 207 " =    2.261
peak=   -3.431 closest distance to " O   SER A 210 " =    1.758
peak=   -3.431 closest distance to " O   HOH Z 165 " =    1.928
peak=   -3.429 closest distance to " ND2 ASN A  60 " =    1.273
peak=   -3.428 closest distance to " CG1 VAL A  78 " =    2.399
peak=   -3.428 closest distance to " CA  GLY A 241 " =    2.285
peak=   -3.426 closest distance to " CZ2 TRP A 123 " =    2.580
peak=   -3.415 closest distance to " O   HOH Z 213 " =    1.332
peak=   -3.410 closest distance to " C   HIS A 108 " =    1.244
peak=   -3.410 closest distance to " O   HOH Z 250 " =    1.714
peak=   -3.409 closest distance to " O   HOH Z 111 " =    1.558
peak=   -3.404 closest distance to " OG ASER A 212 " =    1.705
peak=   -3.402 closest distance to " O   SER A 273 " =    1.120
peak=   -3.402 closest distance to " NH1 ARG A 195 " =    1.047
peak=   -3.399 closest distance to " O   GLY A 203 " =    2.520
peak=   -3.395 closest distance to " CE3 TRP A  70 " =    1.706
peak=   -3.385 closest distance to " CH2 TRP A 179 " =    1.236
peak=   -3.371 closest distance to " CG  ASP A 286 " =    1.437
peak=   -3.366 closest distance to " CG  GLN A 223 " =    2.474
peak=   -3.366 closest distance to " O   HOH Z  43 " =    1.654
peak=   -3.366 closest distance to " O   TRP A  92 " =    2.189
peak=   -3.363 closest distance to " O   HOH Z  60 " =    1.984
peak=   -3.359 closest distance to " O   GLY A 262 " =    2.406
peak=   -3.356 closest distance to " O   HOH Z 329 " =    0.860
peak=   -3.347 closest distance to " CG  ARG A 138 " =    0.916
peak=   -3.345 closest distance to " O   HOH Z 102 " =    1.638
peak=   -3.341 closest distance to " C   ALA A 165 " =    1.841
peak=   -3.335 closest distance to " CB  PRO A 243 " =    2.880
peak=   -3.333 closest distance to " CD  LYS A 289 " =    2.349
peak=   -3.322 closest distance to " OXT GLY A 302 " =    3.024
peak=   -3.322 closest distance to " CA  ASP A  65 " =    1.336
peak=   -3.319 closest distance to " O   HOH Z 251 " =    4.458
peak=   -3.318 closest distance to " O   HOH Z 411 " =    1.434
peak=   -3.309 closest distance to " CD2 TYR A  15 " =    2.301
peak=   -3.307 closest distance to " OG  SER A 141 " =    1.831
peak=   -3.305 closest distance to " OE1 GLN A  88 " =    1.196
peak=   -3.304 closest distance to " CG  GLN A  58 " =    1.289
peak=   -3.294 closest distance to " CG  GLN A  88 " =    1.004
peak=   -3.287 closest distance to " ND2 ASN A  45 " =    1.232
peak=   -3.286 closest distance to " O   HOH Z 205 " =    0.864
peak=   -3.284 closest distance to " O   HOH Z 231 " =    2.395
peak=   -3.282 closest distance to " O   HOH Z 191 " =    5.588
peak=   -3.282 closest distance to " CD2 TYR A 172 " =    2.025
peak=   -3.281 closest distance to " O   HOH Z   9 " =    1.941
peak=   -3.281 closest distance to " SD  MET A 105 " =    2.606
peak=   -3.276 closest distance to " CD1 ILE A 109 " =    2.717
peak=   -3.268 closest distance to " O   HOH Z 290 " =    1.029
peak=   -3.267 closest distance to " CG  LEU A 281 " =    2.187
peak=   -3.266 closest distance to " CB  ASN A  45 " =    2.165
peak=   -3.266 closest distance to " O   HOH Z 106 " =    1.946
peak=   -3.264 closest distance to " O   HOH Z 422 " =    1.454
peak=   -3.261 closest distance to " O   HOH Z 103 " =    2.261
peak=   -3.260 closest distance to " O   HOH Z 124 " =    1.842
peak=   -3.259 closest distance to " CD2 HIS A 115 " =    0.866
peak=   -3.257 closest distance to " NZ  LYS A 119 " =    1.212
peak=   -3.256 closest distance to " O   TYR A 186 " =    1.810
peak=   -3.256 closest distance to " O   SER A 276 " =    1.579
peak=   -3.245 closest distance to " CD1 TRP A 179 " =    1.075
peak=   -3.242 closest distance to " O   PHE A 218 " =    1.410
peak=   -3.242 closest distance to " O   HOH Z 278 " =    1.106
peak=   -3.238 closest distance to " CB  ALA A  10 " =    2.160
peak=   -3.234 closest distance to " O   HOH Z 107 " =    0.922
peak=   -3.230 closest distance to " CG  LEU A   5 " =    1.020
peak=   -3.229 closest distance to " O   ALA A 180 " =    1.402
peak=   -3.228 closest distance to " CB  SER A  62 " =    5.989
peak=   -3.227 closest distance to " CG1 VAL A 257 " =    2.442
peak=   -3.226 closest distance to " O   HOH Z 196 " =    1.872
peak=   -3.225 closest distance to " C   VAL A 265 " =    1.009
peak=   -3.217 closest distance to " CE2 TRP A  70 " =    2.335
peak=   -3.215 closest distance to " OE2 GLU A 152 " =    1.514
peak=   -3.213 closest distance to " N   ALA A 295 " =    1.035
peak=   -3.213 closest distance to " CB  HIS A  86 " =    1.242
peak=   -3.211 closest distance to " CD1 ILE A 239 " =    2.132
peak=   -3.206 closest distance to " CD  ARG A 139 " =    1.140
peak=   -3.203 closest distance to " CZ  TYR A 172 " =    1.847
peak=   -3.203 closest distance to " OD2 ASP A 298 " =    0.999
peak=   -3.199 closest distance to " O   TYR A  15 " =    1.771
peak=   -3.198 closest distance to " ND2 ASN A  39 " =    1.341
peak=   -3.197 closest distance to " CA  PRO A 280 " =    0.941
peak=   -3.196 closest distance to " O   HOH Z 216 " =    3.809
peak=   -3.194 closest distance to " O   HOH Z 145 " =    2.807
peak=   -3.193 closest distance to " CB  ALA A   9 " =    2.320
peak=   -3.188 closest distance to " O   HOH Z 372 " =    2.493
peak=   -3.188 closest distance to " CZ  PHE A  38 " =    2.485
peak=   -3.188 closest distance to " O   HOH Z 149 " =    1.941
peak=   -3.180 closest distance to " OD1 ASN A 148 " =    1.327
peak=   -3.178 closest distance to " O   HOH Z 183 " =    1.714
peak=   -3.176 closest distance to " O   GLN A 240 " =    2.724
peak=   -3.173 closest distance to " O   LEU A 143 " =    1.501
peak=   -3.171 closest distance to " OG  SER A  63 " =    1.041
peak=   -3.169 closest distance to " OG  SER A  22 " =    1.862
peak=   -3.164 closest distance to " CD2 LEU A 167 " =    2.207
peak=   -3.160 closest distance to " O   HOH Z 166 " =    1.580
peak=   -3.157 closest distance to " O   ILE A 263 " =    2.208
peak=   -3.152 closest distance to " CB  SER A 210 " =    1.290
peak=   -3.150 closest distance to " O   HOH Z 295 " =    1.463
peak=   -3.148 closest distance to " O   HOH Z 429 " =    1.440
peak=   -3.143 closest distance to " NH2 ARG A 159 " =    2.446
peak=   -3.141 closest distance to " CD2 LEU A  96 " =    1.985
peak=   -3.140 closest distance to " O   HOH Z  78 " =    2.032
peak=   -3.129 closest distance to " O   VAL A  67 " =    2.648
peak=   -3.126 closest distance to " CD1 ILE A 151 " =    2.037
peak=   -3.125 closest distance to " N   SER A 134 " =    1.184
peak=   -3.121 closest distance to " O   HOH Z  29 " =    1.125
peak=   -3.120 closest distance to " O   HOH Z  54 " =    1.683
peak=   -3.114 closest distance to " CG  GLN A  55 " =    1.097
peak=   -3.110 closest distance to " O   HOH Z 192 " =    2.104
peak=   -3.104 closest distance to " CE  MET A 105 " =    2.254
peak=   -3.099 closest distance to " O   HOH Z 313 " =    1.277
peak=   -3.099 closest distance to " OE2 GLU A 277 " =    2.585
peak=   -3.094 closest distance to " O   ASN A  45 " =    1.957
peak=   -3.093 closest distance to " N   PHE A  59 " =    1.939
peak=   -3.080 closest distance to " CB  GLN A  55 " =    1.617
peak=   -3.076 closest distance to " N   ALA A 226 " =    1.988
peak=   -3.074 closest distance to " O   HOH Z 174 " =    2.060
peak=   -3.069 closest distance to " O   HOH Z 109 " =    0.962
peak=   -3.063 closest distance to " O   HOH Z  90 " =    3.731
peak=   -3.057 closest distance to " CB  ALA A 161 " =    2.476
peak=   -3.045 closest distance to " O   HOH Z 348 " =    2.293
peak=   -3.044 closest distance to " O   HOH Z  69 " =    1.749

================= 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    :  0.5037 0.4914   6.302219e+00   6.291148e+00
   1_bss:  0.4951 0.4864   6.296951e+00   6.287839e+00
   1_xyz:  0.4257 0.4483   6.216166e+00   6.242990e+00
   1_adp:  0.3822 0.4395   6.155129e+00   6.225975e+00
   1_occ:  0.3816 0.4393   6.154752e+00   6.226867e+00
   2_bss:  0.3795 0.4336   6.156278e+00   6.226545e+00
   2_xyz:  0.3115 0.3694   6.000546e+00   6.129436e+00
   2_adp:  0.2936 0.3541   5.964581e+00   6.100062e+00
   2_occ:  0.2934 0.3541   5.964212e+00   6.100148e+00
   3_bss:  0.2918 0.3538   5.965666e+00   6.100754e+00
   3_xyz:  0.2300 0.2815   5.753730e+00   5.921199e+00
   3_adp:  0.2081 0.2703   5.689854e+00   5.886379e+00
   3_occ:  0.2079 0.2703   5.689476e+00   5.886498e+00
   4_bss:  0.2077 0.2701   5.688504e+00   5.885313e+00
   4_xyz:  0.1731 0.2292   5.530721e+00   5.746306e+00
   4_adp:  0.1625 0.2165   5.476371e+00   5.690812e+00
   4_occ:  0.1624 0.2166   5.476543e+00   5.691465e+00
   5_bss:  0.1626 0.2169   5.477028e+00   5.691243e+00
   5_xyz:  0.1380 0.1894   5.334335e+00   5.564316e+00
   5_adp:  0.1329 0.1806   5.297369e+00   5.522360e+00
   5_occ:  0.1328 0.1805   5.297067e+00   5.522376e+00
   5_bss:  0.1331 0.1808   5.298809e+00   5.522912e+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:  0.302   0.000   6.267   9.560  11.417   0.000   0.000   0.000
   1_xyz:  0.302   0.000   6.267   9.560  11.417   0.000   0.000   0.000
   1_adp:  0.302   0.000   6.267   9.560  11.417   0.000   0.000   0.000
   1_occ:  0.302   0.000   6.267   9.560  11.417   0.000   0.000   0.000
   2_bss:  0.309  32.002   2.711   5.656   7.326   0.000   0.000   0.000
   2_xyz:  0.309  32.002   2.711   5.656   7.326   0.000   0.000   0.000
   2_adp:  0.309  32.002   2.711   5.656   7.326   0.000   0.000   0.000
   2_occ:  0.309  32.002   2.711   5.656   7.326   0.000   0.000   0.000
   3_bss:  0.296  52.326   0.995   3.190   4.696   0.000   0.000   0.000
   3_xyz:  0.296  52.326   0.995   3.190   4.696   0.000   0.000   0.000
   3_adp:  0.296  52.326   0.995   3.190   4.696   0.000   0.000   0.000
   3_occ:  0.296  52.326   0.995   3.190   4.696   0.000   0.000   0.000
   4_bss:  0.328  75.361   0.404   2.091   3.527   0.000   0.000   0.000
   4_xyz:  0.328  75.361   0.404   2.091   3.527   0.000   0.000   0.000
   4_adp:  0.328  75.361   0.404   2.091   3.527   0.000   0.000   0.000
   4_occ:  0.328  75.361   0.404   2.091   3.527   0.000   0.000   0.000
   5_bss:  0.338  82.404   0.314   1.678   3.016   0.000   0.000   0.000
   5_xyz:  0.338  82.404   0.314   1.678   3.016   0.000   0.000   0.000
   5_adp:  0.338  82.404   0.314   1.678   3.016   0.000   0.000   0.000
   5_occ:  0.338  82.404   0.314   1.678   3.016   0.000   0.000   0.000
   5_bss:  0.336  77.392  -1.222  -0.115   1.337   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.822 0.3964  0.4618    75497.035
   1_bss:  60.023 0.3927  0.5913    75147.307
   1_xyz:  52.395 0.4891  0.7249    59337.923
   1_adp:  49.624 0.5245  0.8412    55902.837
   1_occ:  49.733 0.5231  0.8375    56051.028
   2_bss:  49.351 0.5282  0.7485    55972.440
   2_xyz:  40.691 0.6336  0.8887    38967.772
   2_adp:  38.440 0.6611  0.9214    36033.984
   2_occ:  38.429 0.6613  0.9216    36025.670
   3_bss:  38.271 0.6632  0.8542    35983.964
   3_xyz:  29.229 0.7659  0.9505    21538.713
   3_adp:  27.514 0.7846  0.9555    19510.791
   3_occ:  27.498 0.7848  0.9556    19512.303
   4_bss:  27.396 0.7859  0.9259    19393.849
   4_xyz:  22.882 0.8327  0.9616    13852.394
   4_adp:  21.199 0.8500  0.9655    12441.864
   4_occ:  21.218 0.8498  0.9653    12449.200
   5_bss:  21.190 0.8501  0.9545    12440.937
   5_xyz:  18.155 0.8786  0.9700     9397.393
   5_adp:  17.083 0.8888  0.9671     8653.388
   5_occ:  17.084 0.8888  0.9670     8655.590
   5_bss:  17.115 0.8886  0.9649     8688.235
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4297e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4297e+01
   1_xyz:   1.772  0.014  0.109 18.398  0.007  4.111   1.5364e-01
   1_adp:   1.772  0.014  0.109 18.398  0.007  4.111   1.5364e-01
   1_occ:   1.772  0.014  0.109 18.398  0.007  4.111   1.5364e-01
   2_bss:   1.772  0.014  0.109 18.398  0.007  4.111   1.5364e-01
   2_xyz:   1.275  0.010  0.082 16.103  0.005  4.110   9.6034e-02
   2_adp:   1.275  0.010  0.082 16.103  0.005  4.110   9.6034e-02
   2_occ:   1.275  0.010  0.082 16.103  0.005  4.110   9.6034e-02
   3_bss:   1.275  0.010  0.082 16.103  0.005  4.110   9.6034e-02
   3_xyz:   1.122  0.008  0.077 15.796  0.004  4.130   7.3290e-02
   3_adp:   1.122  0.008  0.077 15.796  0.004  4.130   7.3290e-02
   3_occ:   1.122  0.008  0.077 15.796  0.004  4.130   7.3290e-02
   4_bss:   1.122  0.008  0.077 15.796  0.004  4.130   7.3290e-02
   4_xyz:   0.964  0.007  0.069 15.150  0.004  4.116   5.8715e-02
   4_adp:   0.964  0.007  0.069 15.150  0.004  4.116   5.8715e-02
   4_occ:   0.964  0.007  0.069 15.150  0.004  4.116   5.8715e-02
   5_bss:   0.964  0.007  0.069 15.150  0.004  4.116   5.8715e-02
   5_xyz:   1.138  0.009  0.083 15.473  0.004  4.128   7.3740e-02
   5_adp:   1.138  0.009  0.083 15.473  0.004  4.128   7.3740e-02
   5_occ:   1.138  0.009  0.083 15.473  0.004  4.128   7.3740e-02
   5_bss:   1.138  0.009  0.083 15.473  0.004  4.128   7.3740e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.190   7.0375e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.190   7.0375e+00
   1_xyz:  15.248  0.175  0.479 86.617  0.054  2.140   1.0944e-01
   1_adp:  15.248  0.175  0.479 86.617  0.054  2.140   1.0944e-01
   1_occ:  15.248  0.175  0.479 86.617  0.054  2.140   1.0944e-01
   2_bss:  15.248  0.175  0.479 86.617  0.054  2.140   1.0944e-01
   2_xyz:   9.331  0.089  0.297 85.101  0.045  2.100   1.6416e-01
   2_adp:   9.331  0.089  0.297 85.101  0.045  2.100   1.6416e-01
   2_occ:   9.331  0.089  0.297 85.101  0.045  2.100   1.6416e-01
   3_bss:   9.331  0.089  0.297 85.101  0.045  2.100   1.6416e-01
   3_xyz:   6.448  0.082  0.284 87.976  0.036  2.244   6.5326e-02
   3_adp:   6.448  0.082  0.284 87.976  0.036  2.244   6.5326e-02
   3_occ:   6.448  0.082  0.284 87.976  0.036  2.244   6.5326e-02
   4_bss:   6.448  0.082  0.284 87.976  0.036  2.244   6.5326e-02
   4_xyz:   6.057  0.053  0.228 81.254  0.037  2.266   4.6412e-02
   4_adp:   6.057  0.053  0.228 81.254  0.037  2.266   4.6412e-02
   4_occ:   6.057  0.053  0.228 81.254  0.037  2.266   4.6412e-02
   5_bss:   6.057  0.053  0.228 81.254  0.037  2.266   4.6412e-02
   5_xyz:   8.821  0.053  0.342 82.821  0.039  2.243   4.9604e-02
   5_adp:   8.821  0.053  0.342 82.821  0.039  2.243   4.9604e-02
   5_occ:   8.821  0.053  0.342 82.821  0.039  2.243   4.9604e-02
   5_bss:   8.821  0.053  0.342 82.821  0.039  2.243   4.9604e-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:  93.21   0.00  15.59  80.74   0.00  13.54  93.21   0.00  26.72
   1_occ:  93.21   0.00  15.59  80.74   0.00  13.54  93.21   0.00  26.72
   2_bss:  93.21   0.00  15.59  80.74   0.00  13.54  93.21   0.00  26.72
   2_xyz:  93.21   0.00  15.59  80.74   0.00  13.54  93.21   0.00  26.72
   2_adp:  94.03   0.00  14.85  74.36   0.00  11.92  94.03   0.00  30.80
   2_occ:  94.03   0.00  14.85  74.36   0.00  11.92  94.03   0.00  30.80
   3_bss:  94.03   0.00  14.85  74.36   0.00  11.92  94.03   0.00  30.80
   3_xyz:  94.03   0.00  14.85  74.36   0.00  11.92  94.03   0.00  30.80
   3_adp: 106.57   0.00  16.47 100.92   0.00  11.58 106.57   0.42  43.09
   3_occ: 106.57   0.00  16.47 100.92   0.00  11.58 106.57   0.42  43.09
   4_bss: 106.57   0.00  16.47 100.92   0.00  11.58 106.57   0.42  43.09
   4_xyz: 106.57   0.00  16.47 100.92   0.00  11.58 106.57   0.42  43.09
   4_adp: 110.59   0.00  16.03 103.09   0.00  10.71 110.59   1.75  44.99
   4_occ: 110.59   0.00  16.03 103.09   0.00  10.71 110.59   1.75  44.99
   5_bss: 110.59   0.00  16.03 103.09   0.00  10.71 110.59   1.75  44.99
   5_xyz: 110.59   0.00  16.03 103.09   0.00  10.71 110.59   1.75  44.99
   5_adp: 110.43   0.00  15.43  98.25   0.00  10.20 110.43   2.12  43.88
   5_occ: 110.43   0.00  15.43  98.25   0.00  10.20 110.43   2.12  43.88
   5_bss: 112.04   1.61  17.04  99.86   1.61  11.81 112.04   3.73  45.49
------------------------------------------------------------------------
 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:    1.291    0.017    0.414
   1_adp:    1.291    0.017    0.414
   1_occ:    1.291    0.017    0.414
   2_bss:    1.291    0.017    0.414
   2_xyz:    2.028    0.027    0.582
   2_adp:    2.028    0.027    0.582
   2_occ:    2.028    0.027    0.582
   3_bss:    2.028    0.027    0.582
   3_xyz:    1.866    0.071    0.680
   3_adp:    1.866    0.071    0.680
   3_occ:    1.866    0.071    0.680
   4_bss:    1.866    0.071    0.680
   4_xyz:    2.170    0.086    0.763
   4_adp:    2.170    0.086    0.763
   4_occ:    2.170    0.086    0.763
   5_bss:    2.170    0.086    0.763
   5_xyz:    2.207    0.044    0.809
   5_adp:    2.207    0.044    0.809
   5_occ:    2.207    0.044    0.809
   5_bss:    2.207    0.044    0.809
------------------------------------------------------------------------

CPU time actual refinement: 363.27


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_461/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_461/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_461/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_461/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_461/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 363.12 
  Macro-tasks:
    bulk solvent and scale       = 53.29  
    individual site refinement   = 150.42 
    weights calculation          = 31.73  
    collect and process          = 6.41   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 241.97 
  Micro-tasks:
    mask                            = 3.01   
    f_calc                          = 110.90 
    alpha_beta                      = 8.26   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 121.75 
    fmodel                         = 8.68   
    r_factors                      = 0.27   
    phase_errors                   = 10.19  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 264.42 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.008 micro seconds
Total CPU time: 6.28 minutes
from_scatterers_fft:    659 calls, 110.52 s
gradients_fft:          603 calls, 108.03 s

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

# Date 2008-01-16 Time 01:39:12 PST -0800 (1200476352.67 s)
Start R-work = 0.5037, R-free = 0.4914 (no bulk solvent and anisotropic scale)
Final R-work = 0.1496, R-free = 0.1959 (no bulk solvent and anisotropic scale)

Start R-work = 0.4951, R-free = 0.4864
Final R-work = 0.1331, R-free = 0.1808