# Date 2008-10-14 Time 09:44:24 PDT -0700 (1224002664.21 s)
#phil __OFF__

Command line arguments: "1bov.mtz" "1bov.pdb" "main.ncs=true" "--overwrite" "ncs.excessive_distance_limit=None" "ordered_solvent=true"

HOST = chevy.lbl.gov
HOSTTYPE = x86_64-linux
USER = afonine
PID = 3925

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: 1.4
  Release tag: 1
  cctbx tag: 2008_10_09_1338
  Platform: intel-linux-2.6-x86_64 linux
  User: afonine
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Nathaniel Echols,
  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.main.ncs = true

  refinement.ncs.excessive_distance_limit = None

  refinement.main.ordered_solvent = true

Working crystal symmetry after inspecting all inputs:
  Unit cell: (59.6, 102.4, 56.1, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

  Monomer Library directory:
    "/net/chevy/raid1/afonine/PROJ/phenix/phenix-1.4-1/ext_ref_files/mon_lib"
  Total number of atoms: 2890
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 540
          Classifications: {'peptide': 69}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "B"
      Number of atoms: 540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 540
          Classifications: {'peptide': 69}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "C"
      Number of atoms: 540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 540
          Classifications: {'peptide': 69}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "D"
      Number of atoms: 540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 540
          Classifications: {'peptide': 69}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "E"
      Number of atoms: 551
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 69, 540
          Classifications: {'peptide': 69}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
      Conformer: "B"
        Number of residues, atoms: 69, 540
          Classifications: {'peptide': 69}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
          bond proxies already assigned to first conformer: 535
    Chain: " "
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 179
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3, 'water': 176}
          Link IDs: {None: 178}
  Time building chain proxies: 1.54, per 1000 atoms: 0.53

  Number of scatterers: 2890
  At special positions: 0
  Unit cell: (59.6, 102.4, 56.1, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      3     29.99
     S      15     16.00
     O     716      8.00
     N     451      7.00
     C    1705      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

F-obs:
  1bov.mtz:Fobs,SIGFobs

R-free flags:
  1bov.mtz:RFREE

Miller array info: 1bov.mtz:Fobs,SIGFobs
Observation type: xray.amplitude
Type of data: double, size=19617
Type of sigmas: double, size=19617
Number of Miller indices: 19617
Anomalous flag: False
Unit cell: (59.6, 102.4, 56.1, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2213
Resolution range: 24.6343 2.0525
Completeness in resolution range: 0.887888
Completeness with d_max=infinity: 0.887085

Number of F-obs in resolution range:                   19617
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  24.6343
                             d_min =   2.0525

Miller array info: 1bov.mtz:RFREE
Observation type: None
Type of data: int, size=19617
Type of sigmas: None
Number of Miller indices: 19617
Anomalous flag: False
Unit cell: (59.6, 102.4, 56.1, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2213
Resolution range: 24.6343 2.0525
Completeness in resolution range: 0.887888
Completeness with d_max=infinity: 0.887085

Test (R-free flags) flag value: 0

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 24.6361 -  4.4143 [2359/2362]  2228   131   5.6%
  bin  2:  4.4143 -  3.5070 [2237/2239]  2151    86   3.8%
  bin  3:  3.5070 -  3.0646 [2229/2231]  2109   120   5.4%
  bin  4:  3.0646 -  2.7849 [2176/2204]  2028   148   6.8%
  bin  5:  2.7849 -  2.5855 [2105/2184]  2023    82   3.9%
  bin  6:  2.5855 -  2.4332 [2069/2189]  1960   109   5.3%
  bin  7:  2.4332 -  2.3114 [2003/2195]  1906    97   4.8%
  bin  8:  2.3114 -  2.2109 [1904/2164]  1784   120   6.3%
  bin  9:  2.2109 -  2.1258 [1778/2171]  1666   112   6.3%
  bin 10:  2.1258 -  2.0525 [ 757/2155]   757     0   0.0%
                                overall 18612  1005   5.1%

No array of experimental phases found.


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

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

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

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  57 " distance=2.48
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  57 " distance=2.38
    Simple disulfide: pdb=" SG  CYS C   4 " - pdb=" SG  CYS C  57 " distance=2.18
    Simple disulfide: pdb=" SG  CYS D   4 " - pdb=" SG  CYS D  57 " distance=1.87
    Simple disulfide: pdb=" SG  CYS E   4 " - pdb=" SG  CYS E  57 " distance=1.82
  Time building geometry restraints manager: 0.10 seconds
  Histogram of bond lengths:
        0.60 -     0.98: 104
        0.98 -     1.35: 851
        1.35 -     1.73: 1316
        1.73 -     2.10: 481
        2.10 -     2.48: 12
  Bond restraints sorted by residual:
                 atom i - atom j                ideal  model  delta   weight residual
  pdb=" NE1BTRP E  34 " - pdb=" CE2BTRP E  34 " 1.370  1.874 -0.504 8.26e+03 2.10e+03
  pdb=" CG  HIS A  58 " - pdb=" ND1 HIS A  58 " 1.378  1.854 -0.476 8.26e+03 1.87e+03
  pdb=" C   MET C  48 " - pdb=" N   THR C  49 " 1.329  1.921 -0.592 5.10e+03 1.79e+03
  pdb=" CG  HIS D  58 " - pdb=" ND1 HIS D  58 " 1.378  0.923  0.455 8.26e+03 1.71e+03
  pdb=" C   MET D  48 " - pdb=" N   THR D  49 " 1.329  0.758  0.571 5.10e+03 1.66e+03
  ... (remaining 2759 not shown)
  Histogram of nonbonded interaction distances:
        1.46 -     2.15: 23
        2.15 -     2.83: 1161
        2.83 -     3.52: 4450
        3.52 -     4.21: 8347
        4.21 -     4.90: 12952
  Nonbonded interactions sorted by model distance:
                 atom i - atom j                 model   vdw sym.op. j
  pdb=" ND2 ASN A  59 " - pdb=" CH2 TRP B  34 "  1.457 3.420 x-1/2,-y+1/2,-z-1
  pdb=" NH2 ARG D  69 " - pdb=" O   HOH   154 "  1.808 3.120
  pdb=" OH  TYR E  11 " - pdb=" OE2 GLU E  28 "  1.858 3.040
  pdb=" CD1 LEU A  39 " - pdb=" CD2 LEU B  41 "  1.867 3.880
  pdb=" OH  TYR C  11 " - pdb=" OE2 GLU C  28 "  1.894 3.040
  ... (remaining 26928 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.04 -    17.08: 531
       17.08 -    34.12: 306
       34.12 -    51.16: 90
       51.16 -    68.20: 33
       68.20 -    85.24: 9
  Dihedral angle restraints sorted by residual:
  pdb=" CA  THR E  31 "
  pdb=" C   THR E  31 "
  pdb=" N   ASN E  32 "
  pdb=" CA  ASN E  32 "
      ideal   model   delta periodicty    weight residual
     180.00  131.87   48.13     1       4.00e-02 9.27e+01
  pdb=" CA  LYS E  23 "
  pdb=" C   LYS E  23 "
  pdb=" N   VAL E  24 "
  pdb=" CA  VAL E  24 "
      ideal   model   delta periodicty    weight residual
     180.00 -133.28  -46.72     1       4.00e-02 8.73e+01
  pdb=" CA  ASN A  59 "
  pdb=" C   ASN A  59 "
  pdb=" N   GLY A  60 "
  pdb=" CA  GLY A  60 "
      ideal   model   delta periodicty    weight residual
     180.00 -134.62  -45.38     1       4.00e-02 8.24e+01
  ... (remaining 966 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 5
  Type Number    sf(0)   Gaussians
   Zn      3     29.90       2
   S      15     15.96       2
   O     716      7.97       2
   N     451      6.97       2
   C    1705      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

Refinement flags and selection counts:
  individual_sites       =  True (2890 atoms)
  rigid_body             = False (0 atoms in 0 groups)
  individual_adp         =  True (iso = 2890 aniso = 0)
  group_adp              = False (0 atoms in 0 groups)
  tls                    = False (0 atoms in 0 groups)
  occupancies            =  True (24 atoms)
  group_anomalous        = False

n_use            =  2890
n_use_u_iso      =  2890
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 =  2890

==================== Process input NCS or/and find new NCS ====================

NCS groups found in parameter file: 0

Automatic NCS search:

Updated/new NCS groups: 
refinement.ncs.restraint_group {
  reference = chain 'A' and (resseq 1:69 )
  selection = chain 'B' and (resseq 1:69 )
  selection = chain 'C' and (resseq 1:69 )
  selection = chain 'D' and (resseq 1:69 )
  selection = chain 'E' and (resseq 1:69 )
}


                  ----------Building NCS restraints----------                  

NCS restraint group 1:
  NCS operator 1:
    Reference selection: "chain A and (resseq 1:69 )"
        Other selection: "chain B and (resseq 1:69 )"
    Number of atom pairs: 540
    Rotation={{0.66613, -0.506769, -0.547226},
              {0.74356, 0.393951, 0.540298},
              {-0.058226, -0.766804, 0.639235}}
    Translation={{6.46034}, {5.99494}, {18.0577}}
    Histogram of differences:
      0.075446 - 0.498478: 326
      0.498478 - 0.921510: 192
      0.921510 - 1.344541: 9
      1.344541 - 1.767573: 4
      1.767573 - 2.190605: 7
      2.190605 - 2.613637: 2
    RMS difference with respect to the reference: 0.572732
  NCS operator 2:
    Reference selection: "chain A and (resseq 1:69 )"
        Other selection: "chain C and (resseq 1:69 )"
    Number of atom pairs: 540
    Rotation={{0.0973515, -0.15397, -0.983268},
              {0.695168, -0.696489, 0.177891},
              {-0.712225, -0.700854, 0.0392311}}
    Translation={{3.60527}, {27.4174}, {18.5758}}
    Histogram of differences:
      0.072123 - 0.600318: 430
      0.600318 - 1.128513: 101
      1.128513 - 1.656708: 4
      1.656708 - 2.184903: 4
      2.184903 - 2.713099: 0
      2.713099 - 3.241294: 1
    RMS difference with respect to the reference: 0.534985
  NCS operator 3:
    Reference selection: "chain A and (resseq 1:69 )"
        Other selection: "chain D and (resseq 1:69 )"
    Number of atom pairs: 540
    Rotation={{0.0844828, 0.632076, -0.770287},
              {-0.0746571, -0.766863, -0.637454},
              {-0.993624, 0.111361, -0.0175977}}
    Translation={{-10.3547}, {31.3616}, {3.27874}}
    Histogram of differences:
      0.050733 - 0.458156: 310
      0.458156 - 0.865580: 204
      0.865580 - 1.273003: 11
      1.273003 - 1.680427: 6
      1.680427 - 2.087850: 4
      2.087850 - 2.495274: 5
    RMS difference with respect to the reference: 0.562878
  NCS operator 4:
    Reference selection: "chain A and (resseq 1:69 )"
        Other selection: "chain E and (resseq 1:69 )"
    Number of atom pairs: 529
    Rotation={{0.623869, 0.77143, -0.125234},
              {-0.536111, 0.305834, -0.786798},
              {-0.568659, 0.557998, 0.604372}}
    Translation={{-13.0762}, {13.8452}, {-7.00003}}
    Histogram of differences:
      0.050199 - 0.438608: 285
      0.438608 - 0.827017: 222
      0.827017 - 1.215426: 6
      1.215426 - 1.603834: 6
      1.603834 - 1.992243: 1
      1.992243 - 2.380652: 9
    RMS difference with respect to the reference: 0.558952


=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/ncs/1bov_refine_001.eff

Writing geometry restraints to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/ncs/1bov_refine_001.geo

CPU time processing inputs: 5.32


============================ 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 = 59.59999847 102.4000015 56.09999847 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/ncs/1bov.pdb"
    }
    xray_data {
      file_name = "1bov.mtz"
      labels = "Fobs,SIGFobs"
      r_free_flags {
        file_name = "1bov.mtz"
        label = "RFREE"
        test_flag_value = 0
      }
    }
  }
  output {
    prefix = "1bov_refine"
    serial = 1
  }
  main {
    ordered_solvent = True
    ncs = True
  }
  ncs {
    excessive_distance_limit = None
    restraint_group {
      reference = "chain A and (resseq 1:69 )"
      selection = "chain B and (resseq 1:69 )"
      selection = "chain C and (resseq 1:69 )"
      selection = "chain D and (resseq 1:69 )"
      selection = "chain E and (resseq 1:69 )"
    }
  }
}
#phil __OFF__


=============================== refinement start ==============================


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


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

|--(resolution: 2.05 - 24.63 A; n_refl. = 19617)------------------------------|
|                                                                             |
| r_work= 0.3422   r_free= 0.4513   ksol= 0.00   Bsol= 0.00   scale= 4.615    |
|                                                                             |
| 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:   0.44 A                  |
| x-ray target function (ml) for work reflections: 7.570033                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 24.6361 -  3.9217 1.00   3164  165 0.3172 0.5116       8.474      8.5133|
|  2:  3.9217 -  3.1148 1.00   2999  172 0.2901 0.2968      7.9805      7.9973|
|  3:  3.1148 -  2.7216 0.99   2955  148 0.3357 0.3839      7.5044      7.5766|
|  4:  2.7216 -  2.4730 0.95   2789  191 0.3685 0.3959       7.296      7.2706|
|  5:  2.4730 -  2.2959 0.92   2759   97 0.3754 0.4333      7.1805      7.2809|
|  6:  2.2959 -  2.1606 0.86   2560  120 0.3825 0.3578      7.0773      7.1005|
|  7:  2.1606 -  2.0525 0.48   1386  112 0.3788 0.3942      6.9952      7.1479|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 24.6361 -  3.9217  3164   165  0.25  70.40   4.28     1.28    5910633.67|
|  2:  3.9217 -  3.1148  2999   172  0.49  52.06   5.37     3.69    2576428.11|
|  3:  3.1148 -  2.7216  2955   148  0.65  39.56   5.16     4.65     764366.37|
|  4:  2.7216 -  2.4730  2789   191  0.60  43.73   5.12     4.34     519180.29|
|  5:  2.4730 -  2.2959  2759    97  0.58  45.93   5.53     4.20     415515.77|
|  6:  2.2959 -  2.1606  2560   120  0.54  49.53   5.76     4.20     371623.73|
|  7:  2.1606 -  2.0525  1386   112  0.50  52.14   6.05     4.15     342772.30|
|alpha:            min =        1.28 max =            4.65 mean =         3.71|
|beta:             min =   342772.30 max =      5910633.67 mean =   1757333.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.99 mean =        50.69|
|phase err.(test): min =        0.00 max =           89.90 mean =        49.16|
|-----------------------------------------------------------------------------|

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

Distribution of F-obs values before outliers rejection:
    53.000 - 1071.100   : 10912
  1071.100 - 2089.200   : 5770
  2089.200 - 3107.300   : 1773
  3107.300 - 4125.400   : 735
  4125.400 - 5143.500   : 282
  5143.500 - 6161.600   : 96
  6161.600 - 7179.700   : 35
  7179.700 - 8197.800   : 8
  8197.800 - 9215.900   : 2
  9215.900 - 10234.000  : 4

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 1
beamstop_shadow_outliers = 0
total                    = 1

Distribution of F-obs values after outliers rejection:
    53.000 - 1071.100   : 10912
  1071.100 - 2089.200   : 5770
  2089.200 - 3107.300   : 1773
  3107.300 - 4125.400   : 735
  4125.400 - 5143.500   : 282
  5143.500 - 6161.600   : 95
  6161.600 - 7179.700   : 35
  7179.700 - 8197.800   : 8
  8197.800 - 9215.900   : 2
  9215.900 - 10234.000  : 4

        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.077:   635 |   0.002 -   5.582:   985 |  1.457 -  1.801:        1 |
| 0.077 - 0.154:   619 |   5.582 -  11.161:   920 |  1.801 -  2.146:       22 |
| 0.154 - 0.231:   461 |  11.161 -  16.740:   716 |  2.146 -  2.490:      242 |
| 0.231 - 0.308:   395 |  16.740 -  22.319:   540 |  2.490 -  2.834:      919 |
| 0.308 - 0.385:   292 |  22.319 -  27.898:   313 |  2.834 -  3.179:     1768 |
| 0.385 - 0.462:   194 |  27.898 -  33.477:   170 |  3.179 -  3.523:     2682 |
| 0.462 - 0.538:   112 |  33.477 -  39.056:    68 |  3.523 -  3.867:     3730 |
| 0.538 - 0.615:    44 |  39.056 -  44.635:    25 |  3.867 -  4.211:     4617 |
| 0.615 - 0.692:    11 |  44.635 -  50.214:     3 |  4.211 -  4.556:     5732 |
| 0.692 - 0.769:     1 |  50.214 -  55.793:     2 |  4.556 -  4.900:     7220 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2764 |   0.249    0.769  0.000 |     165.923 |              |
|     angle |     3742 |  15.591   55.793  0.002 |      78.048 |              |
| chirality |      436 |   1.194    5.428  0.002 |      35.621 |       23.220 |
| planarity |      477 |   0.090    0.211  0.000 |      94.930 |              |
|  dihedral |      969 |  23.952   85.244  0.037 |       6.178 |              |
| nonbonded |     2764 |   4.104    4.900  1.457 |       0.974 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 21.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2890   0      25.00   25.00   25.00    None  None   None       |
|    all(noH): 2890   0      25.00   25.00   25.00    None  None   None       |
|    Sol.    : 176    0      25.00   25.00   25.00    None  None   None       |
|    Mac.    : 2714   0      25.00   25.00   25.00    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:    25.000 -  25.000: 2890   |   5:    25.000 -  25.000:    0        |
|      1:    25.000 -  25.000:    0   |   6:    25.000 -  25.000:    0        |
|      2:    25.000 -  25.000:    0   |   7:    25.000 -  25.000:    0        |
|      3:    25.000 -  25.000:    0   |   8:    25.000 -  25.000:    0        |
|      4:    25.000 -  25.000:    0   |   9:    25.000 -  25.000:    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 = 21.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2890   0      14.00   34.00   24.04    None  None   None       |
|    all(noH): 2890   0      14.00   34.00   24.04    None  None   None       |
|    Sol.    : 176    0      14.00   34.00   23.88    None  None   None       |
|    Mac.    : 2714   0      14.01   33.99   24.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    14.001 -  16.001:  285   |   5:    24.000 -  25.999:  281        |
|      1:    16.001 -  18.000:  276   |   6:    25.999 -  27.999:  299        |
|      2:    18.000 -  20.000:  303   |   7:    27.999 -  29.999:  286        |
|      3:    20.000 -  22.000:  276   |   8:    29.999 -  31.999:  268        |
|      4:    22.000 -  24.000:  306   |   9:    31.999 -  33.998:  310        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.3441   r_free= 0.4453   ksol= 0.00   Bsol= 0.00   scale= 4.475    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 7.586508                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.3051   r_free= 0.3229   ksol= 0.31   Bsol= 20.00   scale= 5.443   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.06,-0.26,9.42,-0.00,0.00,0.00); trace/3= 3.41                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 7.432308                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.518023             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.910   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.355948              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 74.165   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3051      final r-factor (work) = 0.2738          |
| start r-factor (free) = 0.3229      final r-factor (free) = 0.3063          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.4262 = 17.52 * 0.50 * 7.5700 + 1.00 * 25.1202                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 65.1232 = 17.52 * 0.50 * 7.3707 + 1.00 * 0.5628                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2738      final r-factor (work) = 0.2213          |
| start r-factor (free) = 0.3063      final r-factor (free) = 0.2560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6393 = 0.36 * 1.00 * 7.3707 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5856 = 0.36 * 1.00 * 7.2456 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 21.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2890   0      8.30    79.66   23.48    None  None   None       |
|    all(noH): 2890   0      8.30    79.66   23.48    None  None   None       |
|    Sol.    : 176    0      11.94   56.81   31.92    None  None   None       |
|    Mac.    : 2714   0      8.30    79.66   22.94    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:     8.300 -  15.437:  477   |   5:    43.982 -  51.118:   70        |
|      1:    15.437 -  22.573: 1208   |   6:    51.118 -  58.255:   35        |
|      2:    22.573 -  29.709:  637   |   7:    58.255 -  65.391:   20        |
|      3:    29.709 -  36.846:  278   |   8:    65.391 -  72.527:    2        |
|      4:    36.846 -  43.982:  158   |   9:    72.527 -  79.664:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2213 r_free = 0.2560             target_work(ml) = 7.166         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2213 r_free = 0.2560             target_work(ml) = 7.166         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.2213   r_free= 0.2560   ksol= 0.31   Bsol= 20.00   scale= 5.417   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.06,-0.26,9.42,-0.00,0.00,0.00); trace/3= 3.41                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 7.165738                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.2190   r_free= 0.2538   ksol= 0.31   Bsol= 33.42   scale= 5.339   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.04,-0.73,8.27,-0.00,0.00,0.00); trace/3= 2.50                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 7.161477                   |
|-----------------------------------------------------------------------------|

================== ordered solvent: location/analysis/update ==================

Start model:
  number           = 176    
  b_iso_min        = 11.94   (limit = 1.00)
  b_iso_max        = 56.81   (limit = 80.00)
  b_iso_mean       = 31.92               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.01    (limit = 1.80)
  dist_sol_mol_max = 4.92    (limit = 6.00)
Filtered:
  number           = 150    
  b_iso_min        = 11.94   (limit = 1.00)
  b_iso_max        = 50.80   (limit = 80.00)
  b_iso_mean       = 30.98               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.01    (limit = 1.80)
  dist_sol_mol_max = 4.53    (limit = 6.00)
Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 230         
Filter by distance & map next to the model:
   mapped sites are within: 0.287 - 5.088
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 81 from: 230
   mapped sites are within: 1.811 - 5.088
Just added new:
  number           = 231    
  b_iso_min        = 11.94   (limit = 1.00)
  b_iso_max        = 50.80   (limit = 80.00)
  b_iso_mean       = 28.16               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.81    (limit = 1.80)
  dist_sol_mol_max = 5.64    (limit = 6.00)
Filtered:
  number           = 181    
  b_iso_min        = 11.94   (limit = 1.00)
  b_iso_max        = 50.80   (limit = 80.00)
  b_iso_mean       = 29.60               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.86    (limit = 1.80)
  dist_sol_mol_max = 4.53    (limit = 6.00)
Number of peaks found at 2mFobs-DFmodel map (map cutoff=1.00 sigma)= 1860        
Filter by distance & map next to the model:
   mapped sites are within: 0.010 - 0.499
   number of sites selected in [dist_min= 0.01, dist_max= 0.50]: 964 from: 1860
   mapped sites are within: 0.024 - 0.499
ADP refinement (water only), start r_work=0.2189 r_free=0.2438
ADP refinement (water only), final r_work=0.2170 r_free=0.2450
2Fo-Fc map selection:
  number           = 160    
  b_iso_min        = 10.91   (limit = 1.00)
  b_iso_max        = 63.96   (limit = 80.00)
  b_iso_mean       = 32.75               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.61    (limit = 1.80)
  dist_sol_mol_max = 4.58    (limit = 6.00)
Before filtering:
  number           = 160    
  b_iso_min        = 10.91   (limit = 1.00)
  b_iso_max        = 63.96   (limit = 80.00)
  b_iso_mean       = 32.75               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.61    (limit = 1.80)
  dist_sol_mol_max = 4.58    (limit = 6.00)
Final:
  number           = 149    
  b_iso_min        = 10.91   (limit = 1.00)
  b_iso_max        = 59.54   (limit = 80.00)
  b_iso_mean       = 32.11               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.86    (limit = 1.80)
  dist_sol_mol_max = 4.58    (limit = 6.00)

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.437338              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.299  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.263157              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 148.551  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2192      final r-factor (work) = 0.2132          |
| start r-factor (free) = 0.2454      final r-factor (free) = 0.2491          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.7396 = 8.44 * 0.50 * 7.1519 + 1.00 * 0.5680                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.3064 = 8.44 * 0.50 * 7.1369 + 1.00 * 0.1981                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2132      final r-factor (work) = 0.2083          |
| start r-factor (free) = 0.2491      final r-factor (free) = 0.2455          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8848 = 0.26 * 1.00 * 7.1369 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8838 = 0.26 * 1.00 * 7.1285 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2863   0      7.63    84.46   23.70    None  None   None       |
|    all(noH): 2863   0      7.63    84.46   23.70    None  None   None       |
|    Sol.    : 149    0      11.92   48.19   31.02    None  None   None       |
|    Mac.    : 2714   0      7.63    84.46   23.30    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:     7.630 -  15.312:  482   |   5:    46.044 -  53.726:   68        |
|      1:    15.312 -  22.995: 1227   |   6:    53.726 -  61.409:   37        |
|      2:    22.995 -  30.678:  607   |   7:    61.409 -  69.092:   12        |
|      3:    30.678 -  38.361:  293   |   8:    69.092 -  76.775:    1        |
|      4:    38.361 -  46.044:  131   |   9:    76.775 -  84.457:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2083 r_free = 0.2455             target_work(ml) = 7.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2083 r_free = 0.2455             target_work(ml) = 7.123         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.2083   r_free= 0.2455   ksol= 0.31   Bsol= 33.42   scale= 5.397   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.04,-0.73,8.27,-0.00,0.00,0.00); trace/3= 2.50                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 7.123138                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.2083   r_free= 0.2446   ksol= 0.32   Bsol= 33.42   scale= 5.407   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.04,-0.73,8.27,-0.00,0.00,0.00); trace/3= 2.50                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 7.119218                   |
|-----------------------------------------------------------------------------|

================== ordered solvent: location/analysis/update ==================

Start model:
  number           = 149    
  b_iso_min        = 11.92   (limit = 1.00)
  b_iso_max        = 48.19   (limit = 80.00)
  b_iso_mean       = 31.02               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.19    (limit = 1.80)
  dist_sol_mol_max = 4.43    (limit = 6.00)
Filtered:
  number           = 147    
  b_iso_min        = 11.92   (limit = 1.00)
  b_iso_max        = 48.19   (limit = 80.00)
  b_iso_mean       = 30.94               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.19    (limit = 1.80)
  dist_sol_mol_max = 4.43    (limit = 6.00)
Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.372 - 5.182
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 66 from: 216
   mapped sites are within: 1.806 - 5.182
Just added new:
  number           = 213    
  b_iso_min        = 11.92   (limit = 1.00)
  b_iso_max        = 48.19   (limit = 80.00)
  b_iso_mean       = 28.58               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.81    (limit = 1.80)
  dist_sol_mol_max = 5.66    (limit = 6.00)
Filtered:
  number           = 180    
  b_iso_min        = 11.92   (limit = 1.00)
  b_iso_max        = 48.19   (limit = 80.00)
  b_iso_mean       = 29.54               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.83    (limit = 1.80)
  dist_sol_mol_max = 4.43    (limit = 6.00)
Number of peaks found at 2mFobs-DFmodel map (map cutoff=1.00 sigma)= 1814        
Filter by distance & map next to the model:
   mapped sites are within: 0.026 - 0.500
   number of sites selected in [dist_min= 0.01, dist_max= 0.50]: 993 from: 1814
   mapped sites are within: 0.026 - 0.500
ADP refinement (water only), start r_work=0.2087 r_free=0.2414
ADP refinement (water only), final r_work=0.2061 r_free=0.2397
2Fo-Fc map selection:
  number           = 169    
  b_iso_min        = 11.85   (limit = 1.00)
  b_iso_max        = 58.27   (limit = 80.00)
  b_iso_mean       = 34.18               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.38    (limit = 1.80)
  dist_sol_mol_max = 4.54    (limit = 6.00)
Before filtering:
  number           = 169    
  b_iso_min        = 11.85   (limit = 1.00)
  b_iso_max        = 58.27   (limit = 80.00)
  b_iso_mean       = 34.18               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.38    (limit = 1.80)
  dist_sol_mol_max = 4.54    (limit = 6.00)
Final:
  number           = 163    
  b_iso_min        = 11.85   (limit = 1.00)
  b_iso_max        = 54.90   (limit = 80.00)
  b_iso_mean       = 33.87               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.83    (limit = 1.80)
  dist_sol_mol_max = 4.54    (limit = 6.00)

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.489020              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.249  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxu = 0.233670              wxu_scale = 1.000            wu = 1.000         |
| angle between Xray and ADP gradient vectors: 159.722  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2068      final r-factor (work) = 0.2031          |
| start r-factor (free) = 0.2404      final r-factor (free) = 0.2412          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7195 = 5.49 * 0.50 * 7.1108 + 1.00 * 0.2039                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6221 = 5.49 * 0.50 * 7.1036 + 1.00 * 0.1262                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2031      final r-factor (work) = 0.2009          |
| start r-factor (free) = 0.2412      final r-factor (free) = 0.2380          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6680 = 0.23 * 1.00 * 7.1036 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6663 = 0.23 * 1.00 * 7.0991 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2877   0      7.79    84.90   23.68    None  None   None       |
|    all(noH): 2877   0      7.79    84.90   23.68    None  None   None       |
|    Sol.    : 163    0      10.88   56.20   32.13    None  None   None       |
|    Mac.    : 2714   0      7.79    84.90   23.17    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:     7.792 -  15.503:  491   |   5:    46.347 -  54.058:   70        |
|      1:    15.503 -  23.214: 1251   |   6:    54.058 -  61.769:   37        |
|      2:    23.214 -  30.925:  624   |   7:    61.769 -  69.480:   10        |
|      3:    30.925 -  38.636:  281   |   8:    69.480 -  77.191:    0        |
|      4:    38.636 -  46.347:  108   |   9:    77.191 -  84.902:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


============================= Occupancy refinement ============================

|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2009 r_free = 0.2380             target_work(ml) = 7.096         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2009 r_free = 0.2380             target_work(ml) = 7.096         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

======================= ordered solvent: final clean up =======================

Start model:
  number           = 163    
  b_iso_min        = 10.88   (limit = 1.00)
  b_iso_max        = 56.20   (limit = 80.00)
  b_iso_mean       = 32.13               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.25    (limit = 1.80)
  dist_sol_mol_max = 4.49    (limit = 6.00)
Filtered:
  number           = 161    
  b_iso_min        = 10.88   (limit = 1.00)
  b_iso_max        = 56.20   (limit = 80.00)
  b_iso_mean       = 32.07               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.25    (limit = 1.80)
  dist_sol_mol_max = 4.49    (limit = 6.00)
Before filtering:
  number           = 161    
  b_iso_min        = 10.88   (limit = 1.00)
  b_iso_max        = 56.20   (limit = 80.00)
  b_iso_mean       = 32.07               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.25    (limit = 1.80)
  dist_sol_mol_max = 4.49    (limit = 6.00)
Final:
  number           = 161    
  b_iso_min        = 10.88   (limit = 1.00)
  b_iso_max        = 56.20   (limit = 80.00)
  b_iso_mean       = 32.07               
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.25    (limit = 1.80)
  dist_sol_mol_max = 4.49    (limit = 6.00)

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

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.2009   r_free= 0.2370   ksol= 0.32   Bsol= 33.42   scale= 5.419   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.04,-0.73,8.27,-0.00,0.00,0.00); trace/3= 2.50                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 7.093956                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 24.6361 -  3.9217 1.00   3164  165 0.1617 0.1818      7.5936      7.7704|
|  2:  3.9217 -  3.1148 1.00   2999  172 0.1931 0.2202      7.4268      7.5422|
|  3:  3.1148 -  2.7216 0.99   2954  148 0.2215 0.2672      7.1569      7.3151|
|  4:  2.7216 -  2.4730 0.95   2789  191 0.2307 0.2821      6.9253      6.9971|
|  5:  2.4730 -  2.2959 0.92   2759   97 0.2252 0.2753      6.8075      6.9597|
|  6:  2.2959 -  2.1606 0.86   2560  120 0.2386 0.2834      6.7229      6.8668|
|  7:  2.1606 -  2.0525 0.48   1386  112 0.2597 0.3190      6.6938      6.8835|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 24.6361 -  3.9217  3164   165  0.87  17.88   5.37     5.06     657475.34|
|  2:  3.9217 -  3.1148  2999   172  0.85  21.11   5.56     5.41     505101.36|
|  3:  3.1148 -  2.7216  2954   148  0.81  25.69   5.45     5.28     343792.13|
|  4:  2.7216 -  2.4730  2789   191  0.80  27.19   5.24     4.75     215854.61|
|  5:  2.4730 -  2.2959  2759    97  0.80  27.36   5.37     4.99     182448.09|
|  6:  2.2959 -  2.1606  2560   120  0.78  29.68   5.47     5.04     163913.53|
|  7:  2.1606 -  2.0525  1386   112  0.75  31.63   5.54     4.86     153235.93|
|alpha:            min =        4.75 max =            5.41 mean =         5.08|
|beta:             min =   153235.93 max =       657475.34 mean =    341089.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.82|
|phase err.(work): min =        0.00 max =           89.97 mean =        25.09|
|phase err.(test): min =        0.00 max =           88.90 mean =        24.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.2009   r_free= 0.2370   ksol= 0.32   Bsol= 35.92   scale= 5.419   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-3.23,5.77,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 7.093956                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 24.63 A; n_refl. = 19616)------------------------------|
|                                                                             |
| r_work= 0.2009   r_free= 0.2370   ksol= 0.32   Bsol= 35.92   scale= 5.419   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-3.23,5.77,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 7.093956                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 24.6361 -  3.9217 1.00   3164  165 0.1617 0.1818      7.5936      7.7704|
|  2:  3.9217 -  3.1148 1.00   2999  172 0.1931 0.2202      7.4268      7.5422|
|  3:  3.1148 -  2.7216 0.99   2954  148 0.2215 0.2672      7.1569      7.3151|
|  4:  2.7216 -  2.4730 0.95   2789  191 0.2307 0.2821      6.9253      6.9971|
|  5:  2.4730 -  2.2959 0.92   2759   97 0.2252 0.2753      6.8075      6.9597|
|  6:  2.2959 -  2.1606 0.86   2560  120 0.2386 0.2834      6.7229      6.8668|
|  7:  2.1606 -  2.0525 0.48   1386  112 0.2597 0.3190      6.6938      6.8835|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 24.6361 -  3.9217  3164   165  0.87  17.88   5.37     5.06     657475.34|
|  2:  3.9217 -  3.1148  2999   172  0.85  21.11   5.56     5.41     505101.36|
|  3:  3.1148 -  2.7216  2954   148  0.81  25.69   5.45     5.28     343792.13|
|  4:  2.7216 -  2.4730  2789   191  0.80  27.19   5.24     4.75     215854.61|
|  5:  2.4730 -  2.2959  2759    97  0.80  27.36   5.37     4.99     182448.09|
|  6:  2.2959 -  2.1606  2560   120  0.78  29.68   5.47     5.04     163913.53|
|  7:  2.1606 -  2.0525  1386   112  0.75  31.63   5.54     4.86     153235.93|
|alpha:            min =        4.75 max =            5.41 mean =         5.08|
|beta:             min =   153235.93 max =       657475.34 mean =    341089.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.82|
|phase err.(work): min =        0.00 max =           89.97 mean =        25.09|
|phase err.(test): min =        0.00 max =           88.90 mean =        24.53|
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2875   0      10.29   87.40   26.17    None  None   None       |
|    all(noH): 2875   0      10.29   87.40   26.17    None  None   None       |
|    Sol.    : 161    0      13.38   58.70   34.57    None  None   None       |
|    Mac.    : 2714   0      10.29   87.40   25.67    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:    10.290 -  18.001:  491   |   5:    48.845 -  56.556:   70        |
|      1:    18.001 -  25.712: 1251   |   6:    56.556 -  64.267:   37        |
|      2:    25.712 -  33.423:  624   |   7:    64.267 -  71.978:   10        |
|      3:    33.423 -  41.134:  280   |   8:    71.978 -  79.689:    0        |
|      4:    41.134 -  48.845:  107   |   9:    79.689 -  87.400:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.50 sigma)= 96          
Filter by distance & map next to the model:
   mapped sites are within: 0.666 - 3.570
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 95 from: 96
   mapped sites are within: 0.748 - 3.570

peak=    3.921 closest distance to pdb=" N   THR A   1 " =    1.153
peak=    5.250 closest distance to pdb=" CG  GLU A  10 " =    2.189
peak=    4.956 closest distance to pdb=" CB  VAL A  22 " =    1.399
peak=    4.534 closest distance to pdb=" CG  LEU A  29 " =    1.741
peak=    6.235 closest distance to pdb=" CZ  ARG A  33 " =    2.001
peak=    4.130 closest distance to pdb=" CA  TRP A  34 " =    1.081
peak=    4.714 closest distance to pdb=" CA  TRP A  34 " =    1.546
peak=    5.458 closest distance to pdb=" CB  TRP A  34 " =    1.528
peak=    4.885 closest distance to pdb=" CB  TRP A  34 " =    1.989
peak=    4.174 closest distance to pdb=" CB  TRP A  34 " =    1.074
peak=    4.686 closest distance to pdb=" CE3 TRP A  34 " =    1.975
peak=    6.665 closest distance to pdb=" CG  LEU A  36 " =    1.250
peak=    4.494 closest distance to pdb=" CB  SER A  38 " =    1.002
peak=    3.583 closest distance to pdb=" O   ASN A  55 " =    1.212
peak=    8.667 closest distance to pdb=" CG  ASN A  55 " =    1.959
peak=    4.349 closest distance to pdb=" CE1 HIS A  58 " =    0.800
peak=    3.798 closest distance to pdb=" CE1 HIS A  58 " =    0.828
peak=    4.451 closest distance to pdb=" CG1 ILE A  67 " =    1.310
peak=    3.866 closest distance to pdb=" OXT ARG A  69 " =    3.570
peak=    4.896 closest distance to pdb=" N   THR B   1 " =    1.321
peak=    4.076 closest distance to pdb=" CG  PRO B   2 " =    1.485
peak=    3.708 closest distance to pdb=" CD  PRO B   2 " =    0.850
peak=    4.766 closest distance to pdb=" CG  GLU B  10 " =    2.115
peak=    3.790 closest distance to pdb=" C   LYS B  13 " =    1.291
peak=    3.692 closest distance to pdb=" CD  LYS B  13 " =    2.073
peak=    3.886 closest distance to pdb=" CD  LYS B  13 " =    1.686
peak=    7.159 closest distance to pdb=" CB  TYR B  14 " =    2.060
peak=    4.161 closest distance to pdb=" CE2 TYR B  14 " =    2.260
peak=    3.800 closest distance to pdb=" CE2 TYR B  14 " =    2.177
peak=    3.620 closest distance to pdb=" CE2 TYR B  14 " =    1.769
peak=    4.336 closest distance to pdb=" C   ASN B  15 " =    1.462
peak=    3.662 closest distance to pdb=" CG  ASN B  15 " =    1.538
peak=    4.822 closest distance to pdb=" C   ASP B  16 " =    1.685
peak=    4.333 closest distance to pdb=" N   ASP B  17 " =    1.606
peak=    5.028 closest distance to pdb=" CB  ASP B  17 " =    1.182
peak=    3.727 closest distance to pdb=" N   THR B  19 " =    1.483
peak=    3.769 closest distance to pdb=" N   THR B  19 " =    1.364
peak=    4.926 closest distance to pdb=" CB  VAL B  22 " =    1.398
peak=    3.891 closest distance to pdb=" CG  LEU B  29 " =    1.554
peak=    3.836 closest distance to pdb=" CA  TRP B  34 " =    1.181
peak=    4.674 closest distance to pdb=" CB  TRP B  34 " =    2.579
peak=    3.935 closest distance to pdb=" OD1 ASN B  35 " =    1.310
peak=    5.409 closest distance to pdb=" N   SER B  38 " =    1.233
peak=    3.557 closest distance to pdb=" CB  LEU B  39 " =    1.062
peak=    3.975 closest distance to pdb=" CD2 LEU B  39 " =    0.932
peak=    6.903 closest distance to pdb=" CB  LEU B  41 " =    1.736
peak=    6.394 closest distance to pdb=" CB  LEU B  41 " =    1.815
peak=    3.929 closest distance to pdb=" CB  ILE B  45 " =    1.459
peak=    8.643 closest distance to pdb=" CG2 ILE B  45 " =    1.861
peak=    8.889 closest distance to pdb=" CG  ASN B  55 " =    2.076
peak=    5.453 closest distance to pdb=" OE2 GLU B  65 " =    1.221
peak=    3.757 closest distance to pdb=" NE  ARG B  69 " =    1.270
peak=    3.625 closest distance to pdb=" NH1 ARG B  69 " =    1.899
peak=    5.503 closest distance to pdb=" N   THR C   1 " =    1.368
peak=    3.715 closest distance to pdb=" CA  PRO C   2 " =    1.207
peak=    3.905 closest distance to pdb=" CA  LYS C   8 " =    0.975
peak=    4.367 closest distance to pdb=" CD2 TYR C  14 " =    1.153
peak=    3.816 closest distance to pdb=" CB  VAL C  22 " =    1.334
peak=    4.488 closest distance to pdb=" CA  ASP C  26 " =    3.455
peak=    3.705 closest distance to pdb=" NH2 ARG C  33 " =    1.055
peak=    4.055 closest distance to pdb=" CD1 LEU C  39 " =    0.975
peak=    3.988 closest distance to pdb=" CD1 LEU C  41 " =    1.234
peak=    3.682 closest distance to pdb=" CG2 THR C  46 " =    0.886
peak=    8.489 closest distance to pdb=" CG  ASN C  55 " =    1.410
peak=    5.189 closest distance to pdb=" ND2 ASN C  55 " =    0.865
peak=    3.955 closest distance to pdb=" O   ASN C  59 " =    3.082
peak=    4.684 closest distance to pdb=" CG  ARG C  69 " =    2.736
peak=    4.154 closest distance to pdb=" CD  ARG C  69 " =    2.352
peak=    4.106 closest distance to pdb=" NH2 ARG C  69 " =    1.807
peak=    3.693 closest distance to pdb=" CB  GLU D  10 " =    1.152
peak=    4.551 closest distance to pdb=" CB  VAL D  22 " =    1.383
peak=    3.647 closest distance to pdb=" CE  LYS D  27 " =    2.127
peak=    4.350 closest distance to pdb=" CG  LEU D  29 " =    1.149
peak=    4.581 closest distance to pdb=" CZ3 TRP D  34 " =    1.278
peak=    3.684 closest distance to pdb=" CD2 LEU D  39 " =    1.097
peak=    3.667 closest distance to pdb=" CG  LEU D  41 " =    0.748
peak=    5.141 closest distance to pdb=" O   ASN D  55 " =    1.328
peak=    8.229 closest distance to pdb=" CB  ASN D  55 " =    1.618
peak=    4.317 closest distance to pdb=" CA  HIS D  58 " =    1.199
peak=    3.585 closest distance to pdb=" CD  GLU D  65 " =    1.189
peak=    3.695 closest distance to pdb=" CD  ARG D  69 " =    2.316
peak=    3.728 closest distance to pdb=" CG  ASP E   3 " =    1.449
peak=    4.243 closest distance to pdb=" CD2 TYR E  14 " =    0.999
peak=    4.134 closest distance to pdb=" CE1 TYR E  14 " =    1.058
peak=    5.305 closest distance to pdb=" CG  LEU E  29 " =    1.498
peak=    3.648 closest distance to pdb=" CB ATRP E  34 " =    1.782
peak=    3.829 closest distance to pdb=" CD1ATRP E  34 " =    2.719
peak=    4.950 closest distance to pdb=" CE3ATRP E  34 " =    1.473
peak=    3.824 closest distance to pdb=" CG  LEU E  41 " =    0.913
peak=    3.583 closest distance to pdb=" CB  SER E  42 " =    0.859
peak=    3.995 closest distance to pdb=" CA  THR E  46 " =    1.304
peak=    3.766 closest distance to pdb=" CB  ASN E  55 " =    1.674
peak=    3.624 closest distance to pdb=" CG  ASN E  59 " =    1.290
peak=    3.673 closest distance to pdb=" O   HOH S  56 " =    2.072
peak=    3.752 closest distance to pdb=" O   HOH S  96 " =    2.534

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.50 sigma)= 79          
Filter by distance & map next to the model:
   mapped sites are within: 0.082 - 5.000
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 63 from: 79
   mapped sites are within: 0.731 - 5.000

peak=   -3.929 closest distance to pdb=" CB  ASP A  18 " =    2.176
peak=   -3.590 closest distance to pdb=" CG2 VAL A  22 " =    1.493
peak=   -3.872 closest distance to pdb=" CG2 VAL A  22 " =    1.054
peak=   -3.670 closest distance to pdb=" CB  VAL A  24 " =    2.793
peak=   -3.711 closest distance to pdb=" O   ASN A  35 " =    0.970
peak=   -5.080 closest distance to pdb=" ND2 ASN A  35 " =    1.082
peak=   -3.685 closest distance to pdb=" C   ALA A  56 " =    1.213
peak=   -3.700 closest distance to pdb=" OD1 ASN A  59 " =    1.396
peak=   -3.854 closest distance to pdb=" CG  GLU A  65 " =    0.923
peak=   -3.956 closest distance to pdb=" CG  PRO B   2 " =    0.981
peak=   -3.918 closest distance to pdb=" CB  LYS B   8 " =    2.287
peak=   -3.684 closest distance to pdb=" N   VAL B   9 " =    1.388
peak=   -3.745 closest distance to pdb=" OE2 GLU B  10 " =    2.368
peak=   -4.723 closest distance to pdb=" N   TYR B  14 " =    0.837
peak=   -6.929 closest distance to pdb=" CD2 TYR B  14 " =    0.816
peak=   -3.995 closest distance to pdb=" CG1 VAL B  22 " =    1.791
peak=   -4.909 closest distance to pdb=" CG2 VAL B  22 " =    0.772
peak=   -3.925 closest distance to pdb=" CA  GLY B  25 " =    2.126
peak=   -3.629 closest distance to pdb=" CD2 LEU B  39 " =    2.038
peak=   -6.503 closest distance to pdb=" CD2 LEU B  41 " =    0.739
peak=   -4.224 closest distance to pdb=" NE2 GLN B  44 " =    0.775
peak=   -5.608 closest distance to pdb=" CD1 ILE B  45 " =    0.757
peak=   -3.937 closest distance to pdb=" CA  GLY B  47 " =    2.091
peak=   -3.674 closest distance to pdb=" O   ASN B  55 " =    2.815
peak=   -5.374 closest distance to pdb=" CG  ASN B  55 " =    0.853
peak=   -4.368 closest distance to pdb=" OD1 ASN B  55 " =    0.807
peak=   -3.732 closest distance to pdb=" O   GLU B  65 " =    1.613
peak=   -4.643 closest distance to pdb=" CD  GLU B  65 " =    0.791
peak=   -3.990 closest distance to pdb=" N   ILE B  67 " =    2.449
peak=   -3.625 closest distance to pdb=" CZ  ARG B  69 " =    0.994
peak=   -4.696 closest distance to pdb=" N   THR C   1 " =    1.205
peak=   -3.810 closest distance to pdb=" OD2 ASP C   3 " =    1.341
peak=   -3.542 closest distance to pdb=" CE1 TYR C  14 " =    1.682
peak=   -3.726 closest distance to pdb=" O   PHE C  20 " =    1.990
peak=   -3.857 closest distance to pdb=" CE1 PHE C  20 " =    2.414
peak=   -3.675 closest distance to pdb=" N   LYS C  23 " =    1.652
peak=   -3.654 closest distance to pdb=" ND2 ASN C  55 " =    4.825
peak=   -4.100 closest distance to pdb=" ND2 ASN C  55 " =    1.096
peak=   -3.766 closest distance to pdb=" O   PHE C  68 " =    1.340
peak=   -5.027 closest distance to pdb=" CB  ASP D  17 " =    2.441
peak=   -3.611 closest distance to pdb=" CB  THR D  21 " =    2.201
peak=   -3.778 closest distance to pdb=" N   TRP D  34 " =    1.761
peak=   -4.176 closest distance to pdb=" NE1 TRP D  34 " =    0.731
peak=   -3.893 closest distance to pdb=" CE3 TRP D  34 " =    1.402
peak=   -4.591 closest distance to pdb=" CZ3 TRP D  34 " =    1.066
peak=   -4.293 closest distance to pdb=" CD2 LEU D  40 " =    2.412
peak=   -4.538 closest distance to pdb=" OD1 ASN D  55 " =    1.002
peak=   -3.759 closest distance to pdb=" C   VAL D  66 " =    2.727
peak=   -4.486 closest distance to pdb=" SG  CYS E   4 " =    1.527
peak=   -4.225 closest distance to pdb=" O   PHE E  20 " =    2.316
peak=   -3.856 closest distance to pdb=" CG2 VAL E  24 " =    3.159
peak=   -3.692 closest distance to pdb=" O   ILE E  45 " =    2.257
peak=   -4.652 closest distance to pdb=" CG2 VAL E  50 " =    2.599
peak=   -3.670 closest distance to pdb=" CD1 ILE E  52 " =    1.150
peak=   -4.105 closest distance to pdb=" O   ASN E  55 " =    1.357
peak=   -4.074 closest distance to pdb=" SG  CYS E  57 " =    1.318
peak=   -3.785 closest distance to pdb=" SG  CYS E  57 " =    0.777
peak=   -3.742 closest distance to pdb=" O   HOH S  16 " =    1.627
peak=   -3.597 closest distance to pdb=" O   HOH S  21 " =    1.497
peak=   -4.066 closest distance to pdb=" O   HOH S  57 " =    2.124
peak=   -3.658 closest distance to pdb=" O   HOH S  73 " =    4.772
peak=   -3.656 closest distance to pdb=" O   HOH S 108 " =    5.000
peak=   -3.847 closest distance to pdb=" O   HOH S 118 " =    2.206

================= 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_wat: ordered solvent update (add / remove)                            
1_occ: refinement of 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    :  0.3422 0.4513   7.569886e+00   7.611066e+00
   1_bss:  0.3051 0.3229   7.432308e+00   7.490608e+00
   1_xyz:  0.2738 0.3063   7.349389e+00   7.441859e+00
   1_adp:  0.2213 0.2560   7.165730e+00   7.297826e+00
   1_occ:  0.2213 0.2560   7.165738e+00   7.297833e+00
   2_bss:  0.2190 0.2538   7.161477e+00   7.296048e+00
   2_xyz:  0.2132 0.2491   7.139369e+00   7.275793e+00
   2_adp:  0.2083 0.2455   7.123104e+00   7.265936e+00
   2_occ:  0.2083 0.2455   7.123138e+00   7.266016e+00
   3_bss:  0.2083 0.2446   7.119218e+00   7.259857e+00
   3_xyz:  0.2031 0.2412   7.104350e+00   7.245623e+00
   3_adp:  0.2009 0.2380   7.095898e+00   7.236237e+00
   3_occ:  0.2009 0.2380   7.095903e+00   7.236245e+00
   3_bss:  0.2009 0.2370   7.093956e+00   7.232358e+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:  0.314  20.003   1.060  -0.264   9.424  -0.000   0.000   0.000
   1_xyz:  0.314  20.003   1.060  -0.264   9.424  -0.000   0.000   0.000
   1_adp:  0.314  20.003   1.060  -0.264   9.424  -0.000   0.000   0.000
   1_occ:  0.314  20.003   1.060  -0.264   9.424  -0.000   0.000   0.000
   2_bss:  0.315  33.418  -0.042  -0.729   8.266  -0.000   0.000   0.000
   2_xyz:  0.315  33.418  -0.042  -0.729   8.266  -0.000   0.000   0.000
   2_adp:  0.315  33.418  -0.042  -0.729   8.266  -0.000   0.000   0.000
   2_occ:  0.315  33.418  -0.042  -0.729   8.266  -0.000   0.000   0.000
   3_bss:  0.324  33.418  -0.042  -0.729   8.266  -0.000   0.000   0.000
   3_xyz:  0.324  33.418  -0.042  -0.729   8.266  -0.000   0.000   0.000
   3_adp:  0.324  33.418  -0.042  -0.729   8.266  -0.000   0.000   0.000
   3_occ:  0.324  33.418  -0.042  -0.729   8.266  -0.000   0.000   0.000
   3_bss:  0.324  35.916  -2.540  -3.227   5.767  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.618 0.5156  3.7109  1756765.511
   1_bss:  39.065 0.6530  4.5548   626053.967
   1_xyz:  35.506 0.6965  4.8119   556075.669
   1_adp:  27.957 0.7836  5.0553   397174.250
   1_occ:  27.958 0.7836  5.0555   397302.328
   2_bss:  27.708 0.7865  4.9554   398664.748
   2_xyz:  26.665 0.7986  5.0222   386957.855
   2_adp:  26.109 0.8049  5.0575   380461.932
   2_occ:  26.109 0.8049  5.0575   380543.677
   3_bss:  25.905 0.8068  5.0685   367348.501
   3_xyz:  25.379 0.8126  5.0738   356187.236
   3_adp:  25.135 0.8152  5.0770   349063.616
   3_occ:  25.134 0.8152  5.0770   349071.908
   3_bss:  25.059 0.8157  5.0757   341048.595
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  15.591  0.249  1.194 23.952  0.090  4.104   2.3220e+01
   1_bss:  15.591  0.249  1.194 23.952  0.090  4.104   2.3220e+01
   1_xyz:   1.588  0.022  0.100 16.778  0.006  4.119   2.2455e-01
   1_adp:   1.588  0.022  0.100 16.778  0.006  4.119   2.2455e-01
   1_occ:   1.588  0.022  0.100 16.778  0.006  4.119   2.2455e-01
   2_bss:   1.588  0.022  0.100 16.778  0.006  4.119   2.2455e-01
   2_xyz:   1.261  0.011  0.094 15.944  0.005  4.120   1.2221e-01
   2_adp:   1.261  0.011  0.094 15.944  0.005  4.120   1.2221e-01
   2_occ:   1.261  0.011  0.094 15.944  0.005  4.120   1.2221e-01
   3_bss:   1.261  0.011  0.094 15.944  0.005  4.120   1.2221e-01
   3_xyz:   1.060  0.008  0.084 14.648  0.003  4.119   8.6918e-02
   3_adp:   1.060  0.008  0.084 14.648  0.003  4.119   8.6918e-02
   3_occ:   1.060  0.008  0.084 14.648  0.003  4.119   8.6918e-02
   3_bss:   1.060  0.008  0.084 14.648  0.003  4.120   8.6911e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  55.793  0.769  5.428 85.244  0.211  1.457   4.5608e+00
   1_bss:  55.793  0.769  5.428 85.244  0.211  1.457   4.5608e+00
   1_xyz:  10.085  0.192  0.912 72.248  0.037  1.666   2.1180e-01
   1_adp:  10.085  0.192  0.912 72.248  0.037  1.666   2.1180e-01
   1_occ:  10.085  0.192  0.912 72.248  0.037  1.666   2.1180e-01
   2_bss:  10.085  0.192  0.912 72.248  0.037  1.666   2.1180e-01
   2_xyz:   9.678  0.080  1.059 68.434  0.022  1.852   1.1175e-01
   2_adp:   9.678  0.080  1.059 68.434  0.022  1.852   1.1175e-01
   2_occ:   9.678  0.080  1.059 68.434  0.022  1.852   1.1175e-01
   3_bss:   9.678  0.080  1.059 68.434  0.022  1.852   1.1175e-01
   3_xyz:  11.554  0.068  1.065 65.290  0.014  1.925   9.8823e-02
   3_adp:  11.554  0.068  1.065 65.290  0.014  1.925   9.8823e-02
   3_occ:  11.554  0.068  1.065 65.290  0.014  1.925   9.8823e-02
   3_bss:  11.554  0.068  1.065 65.290  0.014  1.925   9.8815e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  25.00  25.00  25.00  25.00  25.00  25.00  25.00  25.00  25.00
   1_bss:  34.00  14.00  24.04  33.99  14.01  24.05  34.00  14.00  23.88
   1_xyz:  34.00  14.00  24.04  33.99  14.01  24.05  34.00  14.00  23.88
   1_adp:  79.66   8.30  23.48  79.66   8.30  22.94  56.81  11.94  31.92
   1_occ:  79.66   8.30  23.48  79.66   8.30  22.94  56.81  11.94  31.92
   2_bss:  79.66   8.30  23.48  79.66   8.30  22.94  56.81  11.94  31.92
   2_xyz:  79.66   8.30  23.41  79.66   8.30  22.94  59.54  10.91  32.11
   2_adp:  84.46   7.63  23.70  84.46   7.63  23.30  48.19  11.92  31.02
   2_occ:  84.46   7.63  23.70  84.46   7.63  23.30  48.19  11.92  31.02
   3_bss:  84.46   7.63  23.70  84.46   7.63  23.30  48.19  11.92  31.02
   3_xyz:  84.46   7.63  23.90  84.46   7.63  23.30  54.90  11.85  33.87
   3_adp:  84.90   7.79  23.68  84.90   7.79  23.17  56.20  10.88  32.13
   3_occ:  84.90   7.79  23.68  84.90   7.79  23.17  56.20  10.88  32.13
   3_bss:  87.40  10.29  26.17  87.40  10.29  25.67  58.70  13.38  34.57
------------------------------------------------------------------------
 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:    2.171    0.030    0.340
   1_adp:    2.171    0.030    0.340
   1_occ:    2.171    0.030    0.340
   2_bss:    2.171    0.030    0.340
   2_xyz:    2.419    0.013    0.352
   2_adp:    2.419    0.013    0.352
   2_occ:    2.419    0.013    0.352
   3_bss:    2.419    0.013    0.352
   3_xyz:    2.571    0.022    0.358
   3_adp:    2.571    0.022    0.358
   3_occ:    2.571    0.022    0.358
   3_bss:    2.571    0.022    0.358
------------------------------------------------------------------------
 stage  number of ordered solvent
     0    :              176
     1_bss:              176
     1_xyz:              176
     1_adp:              176
     1_occ:              176
     2_bss:              176
     2_xyz:              149
     2_adp:              149
     2_occ:              149
     3_bss:              149
     3_xyz:              163
     3_adp:              163
     3_occ:              163
     3_bss:              161
------------------------------------------------------------------------

===================== NCS restraints at end of refinement =====================

NCS restraint group 1:
  NCS operator 1:
    Reference selection: "chain A and (resseq 1:69 )"
        Other selection: "chain B and (resseq 1:69 )"
    Number of atom pairs: 540
    Rotation={{0.666766, -0.507974, -0.545331},
              {0.742807, 0.393562, 0.541614},
              {-0.0605044, -0.766206, 0.63974}}
    Translation={{6.51528}, {6.01671}, {18.0545}}
    Histogram of differences:
      0.004062 - 0.090918: 449
      0.090918 - 0.177774: 80
      0.177774 - 0.264629: 7
      0.264629 - 0.351485: 2
      0.351485 - 0.438341: 1
      0.438341 - 0.525197: 1
    RMS difference with respect to the reference: 0.075773
  NCS operator 2:
    Reference selection: "chain A and (resseq 1:69 )"
        Other selection: "chain C and (resseq 1:69 )"
    Number of atom pairs: 540
    Rotation={{0.0979997, -0.152695, -0.983402},
              {0.697938, -0.693866, 0.17729},
              {-0.709421, -0.703728, 0.0385731}}
    Translation={{3.52354}, {27.2313}, {18.6043}}
    Histogram of differences:
      0.005466 - 0.090803: 462
      0.090803 - 0.176140: 67
      0.176140 - 0.261477: 8
      0.261477 - 0.346814: 0
      0.346814 - 0.432151: 2
      0.432151 - 0.517488: 1
    RMS difference with respect to the reference: 0.071582
  NCS operator 3:
    Reference selection: "chain A and (resseq 1:69 )"
        Other selection: "chain D and (resseq 1:69 )"
    Number of atom pairs: 540
    Rotation={{0.0825987, 0.634745, -0.768295},
              {-0.0758545, -0.764688, -0.63992},
              {-0.993692, 0.111135, -0.0150139}}
    Translation={{-10.352}, {31.3169}, {3.3193}}
    Histogram of differences:
      0.004029 - 0.093252: 490
      0.093252 - 0.182474: 41
      0.182474 - 0.271697: 5
      0.271697 - 0.360919: 2
      0.360919 - 0.450142: 1
      0.450142 - 0.539364: 1
    RMS difference with respect to the reference: 0.066888
  NCS operator 4:
    Reference selection: "chain A and (resseq 1:69 )"
        Other selection: "chain E and (resseq 1:69 )"
    Number of atom pairs: 529
    Rotation={{0.6269, 0.769085, -0.124516},
              {-0.534456, 0.308233, -0.786988},
              {-0.56688, 0.559911, 0.604273}}
    Translation={{-13.1065}, {13.7676}, {-7.02024}}
    Histogram of differences:
      0.001613 - 0.089278: 486
      0.089278 - 0.176943: 37
      0.176943 - 0.264608: 3
      0.264608 - 0.352272: 1
      0.352272 - 0.439937: 1
      0.439937 - 0.527602: 1
    RMS difference with respect to the reference: 0.060767

CPU time actual refinement: 235.52


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

Writing refined structure to PDB file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/ncs/1bov_refine_001.pdb
n_use            =  2875
n_use_u_iso      =  2875
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  24
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2875

Writing 2mFo-DFc XPLOR map to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/ncs/1bov_refine_001_2mFo-DFc.map
Writing mFo-DFc XPLOR map to file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/ncs/1bov_refine_001_mFo-DFc.map
Writing map coefficients to MTZ file:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/ncs/1bov_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/chevy/raid1/afonine/PROJ/als_demo_2008/refinement/ncs/1bov_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 235.39 
  Macro-tasks:
    bulk solvent and scale       = 26.46  
    weights calculation          = 15.58  
    collect and process          = 5.30   
    model show statistics        = 0.67   
    TOTAL for macro-tasks        = 48.01  
  Micro-tasks:
    mask                            = 4.49   
    f_calc                          = 71.09  
    alpha_beta                      = 3.80   
    target                          = 0.51   
    gradients_wrt_atomic_parameters = 69.08  
    fmodel                         = 5.44   
    r_factors                      = 0.44   
    phase_errors                   = 6.18   
    foms                           = 0.21   
    TOTAL for micro-tasks          = 161.24 
NUMBER OF MASK CALCS=  10
Time per interpreted Python bytecode instruction: 3.168 micro seconds
Total CPU time: 4.10 minutes
from_scatterers_fft:    462 calls, 70.95 s
gradients_fft:          398 calls, 63.82 s

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

# Date 2008-10-14 Time 09:48:29 PDT -0700 (1224002909.22 s)
wall clock time: 245.02 s

Start R-work = 0.3422, R-free = 0.4513 (no bulk solvent and anisotropic scale)
Final R-work = 0.2611, R-free = 0.4230 (no bulk solvent and anisotropic scale)

Start R-work = 0.3051, R-free = 0.3229
Final R-work = 0.2009, R-free = 0.2370