Starting phenix.real_space_refine
on Tue Nov 18 10:45:55 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9g8q_51136/11_2025/9g8q_51136.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g8q_51136/11_2025/9g8q_51136.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g8q_51136/11_2025/9g8q_51136.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g8q_51136/11_2025/9g8q_51136.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g8q_51136/11_2025/9g8q_51136.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g8q_51136/11_2025/9g8q_51136.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    8460      2.51       5
     N    2267      2.21       5
     O    2526      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13313
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1268
          Classifications: {'peptide': 163}
          Link IDs: {'PTRANS': 20, 'TRANS': 142}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 7299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 934, 7299
          Classifications: {'peptide': 934}
          Link IDs: {'PTRANS': 22, 'TRANS': 911}
    Chain: "C"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2373
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 8, 'TRANS': 296}
    Chain: "D"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2373
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 8, 'TRANS': 296}
  Time building chain proxies: 3.14, per 1000 atoms: 0.24
  Number of scatterers: 13313
  At special positions: 0
  Unit cell: (92.7808, 157.472, 114.061, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    2526      8.00
     N    2267      7.00
     C    8460      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 581.1 milliseconds
  

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3200

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 16 sheets defined
      47.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.927A  pdb=" N   SER A  64 " --> pdb=" O   GLN A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 73
      removed outlier: 4.402A  pdb=" N   TRP A  68 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      Proline residue:  A  70  - end of helix
      removed outlier: 3.511A  pdb=" N   GLY A  73 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.649A  pdb=" N   SER A  89 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A  91 " --> pdb=" O   TRP A  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 645
    Processing helix  chain 'B' and resid 647 through 662
      removed outlier: 3.788A  pdb=" N   LYS B 661 " --> pdb=" O   MET B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 686
      removed outlier: 3.660A  pdb=" N   LEU B 669 " --> pdb=" O   TYR B 665 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP B 686 " --> pdb=" O   ALA B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 710
      removed outlier: 4.011A  pdb=" N   HIS B 709 " --> pdb=" O   CYS B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 727
      removed outlier: 4.360A  pdb=" N   LEU B 727 " --> pdb=" O   ALA B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 742 through 744
      No H-bonds generated for 'chain 'B' and resid 742 through 744'
    Processing helix  chain 'B' and resid 754 through 773
    Processing helix  chain 'B' and resid 775 through 796
      removed outlier: 3.584A  pdb=" N   THR B 796 " --> pdb=" O   HIS B 792 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 821
    Processing helix  chain 'B' and resid 824 through 836
    Processing helix  chain 'B' and resid 842 through 857
    Processing helix  chain 'B' and resid 860 through 874
    Processing helix  chain 'B' and resid 876 through 891
    Processing helix  chain 'B' and resid 894 through 909
      removed outlier: 3.921A  pdb=" N   TRP B 898 " --> pdb=" O   TYR B 894 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 912 through 925
      removed outlier: 3.641A  pdb=" N   ASN B 924 " --> pdb=" O   THR B 920 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 926 through 943
    Processing helix  chain 'B' and resid 950 through 958
      removed outlier: 3.815A  pdb=" N   TYR B 954 " --> pdb=" O   GLU B 950 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 960 through 976
      removed outlier: 3.907A  pdb=" N   ALA B 964 " --> pdb=" O   ASN B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 979 through 993
    Processing helix  chain 'B' and resid 995 through 1011
    Processing helix  chain 'B' and resid 1017 through 1033
    Processing helix  chain 'B' and resid 1035 through 1045
    Processing helix  chain 'B' and resid 1050 through 1065
    Processing helix  chain 'B' and resid 1066 through 1081
      removed outlier: 3.645A  pdb=" N   SER B1070 " --> pdb=" O   LEU B1066 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1083 through 1101
      removed outlier: 3.667A  pdb=" N   LYS B1087 " --> pdb=" O   SER B1083 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1103 through 1117
      removed outlier: 3.915A  pdb=" N   ALA B1107 " --> pdb=" O   LYS B1103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1121 through 1135
      removed outlier: 3.504A  pdb=" N   MET B1135 " --> pdb=" O   LEU B1131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1139 through 1152
      removed outlier: 3.855A  pdb=" N   HIS B1151 " --> pdb=" O   GLU B1147 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE B1152 " --> pdb=" O   LEU B1148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1157 through 1172
      removed outlier: 3.869A  pdb=" N   ARG B1161 " --> pdb=" O   SER B1157 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLN B1172 " --> pdb=" O   ILE B1168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1176 through 1189
      removed outlier: 3.733A  pdb=" N   LYS B1180 " --> pdb=" O   VAL B1176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1192 through 1206
      removed outlier: 3.761A  pdb=" N   TRP B1196 " --> pdb=" O   ASP B1192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1210 through 1225
      removed outlier: 3.893A  pdb=" N   ASP B1225 " --> pdb=" O   ALA B1221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1228 through 1244
    Processing helix  chain 'B' and resid 1254 through 1266
    Processing helix  chain 'B' and resid 1269 through 1291
      removed outlier: 4.181A  pdb=" N   TRP B1273 " --> pdb=" O   ASP B1269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1299 through 1312
    Processing helix  chain 'B' and resid 1317 through 1340
    Processing helix  chain 'B' and resid 1341 through 1356
      removed outlier: 3.681A  pdb=" N   ASN B1356 " --> pdb=" O   ASN B1352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1359 through 1371
    Processing helix  chain 'B' and resid 1382 through 1396
      removed outlier: 3.612A  pdb=" N   ASN B1396 " --> pdb=" O   THR B1392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1399 through 1414
      removed outlier: 3.618A  pdb=" N   TRP B1403 " --> pdb=" O   SER B1399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1415 through 1433
    Processing helix  chain 'B' and resid 1436 through 1456
    Processing helix  chain 'B' and resid 1462 through 1478
    Processing helix  chain 'B' and resid 1480 through 1495
    Processing helix  chain 'B' and resid 1498 through 1511
      removed outlier: 4.172A  pdb=" N   ARG B1502 " --> pdb=" O   ALA B1498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1515 through 1534
    Processing helix  chain 'B' and resid 1535 through 1549
      removed outlier: 3.513A  pdb=" N   HIS B1549 " --> pdb=" O   ASN B1545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1552 through 1563
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
      removed outlier: 3.558A  pdb=" N   ARG A  20 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 737 through 740
      removed outlier: 3.759A  pdb=" N   VAL B 737 " --> pdb=" O   LEU B 753 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 10
      removed outlier: 6.044A  pdb=" N   ILE C   7 " --> pdb=" O   ASP C 302 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ASP C 302 " --> pdb=" O   ILE C   7 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   PHE C   9 " --> pdb=" O   ILE C 300 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE C 300 " --> pdb=" O   PHE C   9 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 21 through 25
      removed outlier: 6.927A  pdb=" N   VAL C  46 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 72
      removed outlier: 7.244A  pdb=" N   SER C  82 " --> pdb=" O   VAL C  68 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   VAL C  70 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ALA C  80 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER C  81 " --> pdb=" O   ARG C  89 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ARG C  89 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   SER C  83 " --> pdb=" O   HIS C  87 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   HIS C  87 " --> pdb=" O   SER C  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 130 through 134
      removed outlier: 3.547A  pdb=" N   LEU C 144 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   TYR C 142 " --> pdb=" O   ILE C 132 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   GLY C 134 " --> pdb=" O   LYS C 140 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LYS C 140 " --> pdb=" O   GLY C 134 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 151 through 156
      removed outlier: 6.482A  pdb=" N   GLY C 166 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ILE C 154 " --> pdb=" O   ALA C 164 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ALA C 164 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   HIS C 184 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 196 through 197
      removed outlier: 3.909A  pdb=" N   THR C 197 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL C 206 " --> pdb=" O   THR C 197 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ILE C 214 " --> pdb=" O   THR C 227 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   THR C 227 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE C 216 " --> pdb=" O   ALA C 225 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 235 through 240
      removed outlier: 3.783A  pdb=" N   VAL C 256 " --> pdb=" O   PHE C 270 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL C 258 " --> pdb=" O   HIS C 268 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   HIS C 268 " --> pdb=" O   VAL C 258 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   ASP C 260 " --> pdb=" O   CYS C 266 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   CYS C 266 " --> pdb=" O   ASP C 260 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 6 through 10
      removed outlier: 6.108A  pdb=" N   ILE D   7 " --> pdb=" O   ASP D 302 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ASP D 302 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   PHE D   9 " --> pdb=" O   ILE D 300 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE D 300 " --> pdb=" O   PHE D   9 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE D 289 " --> pdb=" O   TYR D 301 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 21 through 25
      removed outlier: 6.947A  pdb=" N   VAL D  46 " --> pdb=" O   GLN D  57 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 67 through 72
      removed outlier: 7.190A  pdb=" N   SER D  82 " --> pdb=" O   VAL D  68 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   VAL D  70 " --> pdb=" O   ALA D  80 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ALA D  80 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER D  81 " --> pdb=" O   ARG D  89 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   SER D  83 " --> pdb=" O   HIS D  87 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   HIS D  87 " --> pdb=" O   SER D  83 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 122 through 124
      removed outlier: 3.953A  pdb=" N   TYR D 142 " --> pdb=" O   ILE D 132 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   GLY D 134 " --> pdb=" O   LYS D 140 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LYS D 140 " --> pdb=" O   GLY D 134 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 156
      removed outlier: 6.399A  pdb=" N   GLY D 166 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   ILE D 154 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA D 164 " --> pdb=" O   ILE D 154 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ILE D 174 " --> pdb=" O   HIS D 184 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   HIS D 184 " --> pdb=" O   ILE D 174 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 196 through 197
      removed outlier: 3.630A  pdb=" N   THR D 197 " --> pdb=" O   VAL D 206 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   GLY D 226 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 235 through 240
      removed outlier: 3.824A  pdb=" N   HIS D 268 " --> pdb=" O   VAL D 258 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ASP D 260 " --> pdb=" O   CYS D 266 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   CYS D 266 " --> pdb=" O   ASP D 260 " (cutoff:3.500A)

    685 hydrogen bonds defined for protein.
    1995 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 1.44 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2584
        1.33 -     1.45: 3240
        1.45 -     1.57: 7683
        1.57 -     1.69: 1
        1.69 -     1.81: 89
  Bond restraints: 13597
  Sorted by residual:
  bond pdb=" CG  PRO B1120 "
       pdb=" CD  PRO B1120 "
    ideal  model  delta    sigma   weight residual
    1.503  1.396  0.107 3.40e-02 8.65e+02 9.93e+00
  bond pdb=" CG  GLU B1388 "
       pdb=" CD  GLU B1388 "
    ideal  model  delta    sigma   weight residual
    1.516  1.459  0.057 2.50e-02 1.60e+03 5.19e+00
  bond pdb=" CB  PRO B1120 "
       pdb=" CG  PRO B1120 "
    ideal  model  delta    sigma   weight residual
    1.492  1.595 -0.103 5.00e-02 4.00e+02 4.20e+00
  bond pdb=" CA  LEU B1375 "
       pdb=" C   LEU B1375 "
    ideal  model  delta    sigma   weight residual
    1.524  1.554 -0.030 1.50e-02 4.44e+03 3.91e+00
  bond pdb=" CG1 ILE B 696 "
       pdb=" CD1 ILE B 696 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.41e+00
  ... (remaining 13592 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 17948
        2.36 -     4.73: 407
        4.73 -     7.09: 81
        7.09 -     9.46: 17
        9.46 -    11.82: 9
  Bond angle restraints: 18462
  Sorted by residual:
  angle pdb=" CA  PRO B1120 "
        pdb=" N   PRO B1120 "
        pdb=" CD  PRO B1120 "
      ideal   model   delta    sigma   weight residual
     112.00  102.49    9.51 1.40e+00 5.10e-01 4.61e+01
  angle pdb=" N   PRO B1120 "
        pdb=" CD  PRO B1120 "
        pdb=" CG  PRO B1120 "
      ideal   model   delta    sigma   weight residual
     103.20   93.75    9.45 1.50e+00 4.44e-01 3.97e+01
  angle pdb=" N   GLU B1075 "
        pdb=" CA  GLU B1075 "
        pdb=" CB  GLU B1075 "
      ideal   model   delta    sigma   weight residual
     110.16  118.42   -8.26 1.48e+00 4.57e-01 3.11e+01
  angle pdb=" C   ILE D 168 "
        pdb=" N   ASP D 169 "
        pdb=" CA  ASP D 169 "
      ideal   model   delta    sigma   weight residual
     125.66  135.34   -9.68 1.85e+00 2.92e-01 2.74e+01
  angle pdb=" C   GLU B1014 "
        pdb=" N   ASP B1015 "
        pdb=" CA  ASP B1015 "
      ideal   model   delta    sigma   weight residual
     124.31  132.63   -8.32 1.67e+00 3.59e-01 2.48e+01
  ... (remaining 18457 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 7243
       17.48 -    34.97: 735
       34.97 -    52.45: 112
       52.45 -    69.94: 18
       69.94 -    87.42: 16
  Dihedral angle restraints: 8124
    sinusoidal: 3159
      harmonic: 4965
  Sorted by residual:
  dihedral pdb=" CA  ASN A  34 "
           pdb=" C   ASN A  34 "
           pdb=" N   LEU A  35 "
           pdb=" CA  LEU A  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.41  -26.59     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CA  ASP D 201 "
           pdb=" C   ASP D 201 "
           pdb=" N   SER D 202 "
           pdb=" CA  SER D 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.25  -25.75     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  GLU A 174 "
           pdb=" C   GLU A 174 "
           pdb=" N   GLU A 175 "
           pdb=" CA  GLU A 175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.38   25.62     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 8121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1588
       0.051 -    0.101: 387
       0.101 -    0.152: 100
       0.152 -    0.203: 12
       0.203 -    0.253: 6
  Chirality restraints: 2093
  Sorted by residual:
  chirality pdb=" CA  GLU B1388 "
            pdb=" N   GLU B1388 "
            pdb=" C   GLU B1388 "
            pdb=" CB  GLU B1388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  ASP B1015 "
            pdb=" N   ASP B1015 "
            pdb=" C   ASP B1015 "
            pdb=" CB  ASP B1015 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  GLU B1075 "
            pdb=" N   GLU B1075 "
            pdb=" C   GLU B1075 "
            pdb=" CB  GLU B1075 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 2090 not shown)

  Planarity restraints: 2349
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  69 "   -0.073 5.00e-02 4.00e+02   1.12e-01 1.99e+01
        pdb=" N   PRO A  70 "    0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B1119 "   -0.070 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO B1120 "    0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO B1120 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B1120 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B1014 "   -0.017 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   GLU B1014 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLU B1014 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ASP B1015 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 2346 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 323
        2.69 -     3.24: 13302
        3.24 -     3.79: 20551
        3.79 -     4.35: 25869
        4.35 -     4.90: 43909
  Nonbonded interactions: 103954
  Sorted by model distance:
  nonbonded pdb=" O   VAL C 107 "
            pdb=" OG1 THR C 125 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" O   VAL D 107 "
            pdb=" OG1 THR D 125 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OD1 ASP B 722 "
            pdb=" OH  TYR B 766 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG  SER D 115 "
            pdb=" OD1 ASP D 117 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ALA A  51 "
            pdb=" NE2 GLN B1205 "
     model   vdw
     2.210 3.120
  ... (remaining 103949 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             54.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.760
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   68.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.107  13597  Z= 0.167
  Angle     :  0.898  11.824  18462  Z= 0.474
  Chirality :  0.049   0.253   2093
  Planarity :  0.006   0.112   2349
  Dihedral  : 14.467  87.422   4924
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.24 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.21), residues: 1697
  helix:  2.74 (0.18), residues: 779
  sheet: -1.14 (0.37), residues: 186
  loop : -3.05 (0.18), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B1005 
 TYR   0.030   0.002   TYR B 648 
 PHE   0.027   0.002   PHE A 196 
 TRP   0.034   0.002   TRP A  30 
 HIS   0.009   0.001   HIS B 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (13597)
  covalent geometry    : angle       0.89822 (18462)
  hydrogen bonds       : bond        0.15352 (  685)
  hydrogen bonds       : angle       5.23678 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7149 (tmm) cc_final: 0.6299 (tmm)
REVERT: B  781 ASP cc_start: 0.8415 (m-30) cc_final: 0.8089 (m-30)
REVERT: B  896 MET cc_start: 0.8675 (mpp) cc_final: 0.8204 (mpp)
REVERT: B  985 MET cc_start: 0.8256 (mpp) cc_final: 0.7851 (mpp)
REVERT: B 1316 PHE cc_start: 0.6849 (p90) cc_final: 0.6264 (p90)
REVERT: B 1415 MET cc_start: 0.7181 (mpp) cc_final: 0.6213 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1044
  time to fit residues: 26.7570
Evaluate side-chains
  117 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 98 optimal weight:    0.0370
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    0.9980
   overall best weight:    0.6460

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 643 GLN
B 676 HIS
** B 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1564 GLN
D 131 ASN
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.075257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.062409 restraints weight = 73258.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.064110 restraints weight = 45025.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.065270 restraints weight = 32394.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.066102 restraints weight = 25632.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.066647 restraints weight = 21596.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13597  Z= 0.175
  Angle     :  0.688  10.782  18462  Z= 0.362
  Chirality :  0.044   0.193   2093
  Planarity :  0.005   0.054   2349
  Dihedral  :  4.864  23.679   1815
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.31 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  5.21 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.21), residues: 1697
  helix:  2.33 (0.18), residues: 785
  sheet: -1.00 (0.34), residues: 224
  loop : -2.96 (0.20), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 264 
 TYR   0.018   0.002   TYR B1320 
 PHE   0.014   0.002   PHE D 247 
 TRP   0.010   0.001   TRP A  30 
 HIS   0.006   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (13597)
  covalent geometry    : angle       0.68755 (18462)
  hydrogen bonds       : bond        0.04327 (  685)
  hydrogen bonds       : angle       4.12121 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 142
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ASP cc_start: 0.8532 (p0) cc_final: 0.8175 (t0)
REVERT: B  781 ASP cc_start: 0.8525 (m-30) cc_final: 0.8117 (m-30)
REVERT: B  896 MET cc_start: 0.8893 (mpp) cc_final: 0.8605 (mpp)
REVERT: B  914 MET cc_start: 0.8559 (pmm) cc_final: 0.8275 (pmm)
REVERT: B 1277 MET cc_start: 0.7607 (mmm) cc_final: 0.7127 (mtt)
REVERT: B 1394 MET cc_start: 0.8823 (mmm) cc_final: 0.8616 (mmm)
REVERT: B 1415 MET cc_start: 0.7674 (mpp) cc_final: 0.7337 (mpp)
REVERT: C  195 SER cc_start: 0.7383 (t) cc_final: 0.6513 (m)
  outliers start: 5
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0963
  time to fit residues: 22.0385
Evaluate side-chains
  103 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0020
   chunk 150 optimal weight:    0.7980
   chunk 164 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 128 optimal weight:    0.9980
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.6988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
B 643 GLN
** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.073005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.060119 restraints weight = 75248.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.061742 restraints weight = 46404.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.062906 restraints weight = 33549.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.063590 restraints weight = 26594.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.064262 restraints weight = 22607.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13597  Z= 0.174
  Angle     :  0.662  11.818  18462  Z= 0.350
  Chirality :  0.043   0.188   2093
  Planarity :  0.005   0.053   2349
  Dihedral  :  4.973  27.315   1815
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.37 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  6.04 %
    Favored  : 93.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.20), residues: 1697
  helix:  2.09 (0.18), residues: 783
  sheet: -1.19 (0.32), residues: 236
  loop : -2.85 (0.20), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 147 
 TYR   0.017   0.001   TYR B1320 
 PHE   0.014   0.002   PHE D 247 
 TRP   0.013   0.001   TRP A  30 
 HIS   0.010   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (13597)
  covalent geometry    : angle       0.66249 (18462)
  hydrogen bonds       : bond        0.04283 (  685)
  hydrogen bonds       : angle       4.00804 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 142
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7471 (tmm) cc_final: 0.6587 (tmm)
REVERT: A  195 ASP cc_start: 0.8510 (p0) cc_final: 0.8205 (t0)
REVERT: B  657 MET cc_start: 0.9170 (tmm) cc_final: 0.8949 (tmm)
REVERT: B  914 MET cc_start: 0.8584 (pmm) cc_final: 0.8280 (pmm)
REVERT: B 1228 HIS cc_start: 0.5980 (m170) cc_final: 0.5770 (m170)
REVERT: B 1394 MET cc_start: 0.8895 (mmm) cc_final: 0.8688 (mmm)
REVERT: B 1415 MET cc_start: 0.7974 (mpp) cc_final: 0.7635 (mpp)
REVERT: C  195 SER cc_start: 0.7464 (t) cc_final: 0.6589 (m)
  outliers start: 4
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1001
  time to fit residues: 22.3593
Evaluate side-chains
  98 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 160 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 115 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 127 optimal weight:    3.9990
   chunk 111 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 124 optimal weight:    0.8980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
B1321 ASN
B1413 GLN
C  98 GLN
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 GLN
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.071355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.058362 restraints weight = 75372.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.060015 restraints weight = 47332.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.061163 restraints weight = 34482.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.061945 restraints weight = 27493.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.062436 restraints weight = 23310.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  13597  Z= 0.195
  Angle     :  0.698  11.560  18462  Z= 0.363
  Chirality :  0.044   0.175   2093
  Planarity :  0.005   0.042   2349
  Dihedral  :  5.083  26.510   1815
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.84 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.47 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.20), residues: 1697
  helix:  1.98 (0.18), residues: 785
  sheet: -1.11 (0.32), residues: 236
  loop : -2.94 (0.20), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B1560 
 TYR   0.017   0.002   TYR B1320 
 PHE   0.013   0.002   PHE C 150 
 TRP   0.013   0.001   TRP B1436 
 HIS   0.012   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (13597)
  covalent geometry    : angle       0.69764 (18462)
  hydrogen bonds       : bond        0.04244 (  685)
  hydrogen bonds       : angle       4.06791 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 137
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7763 (tmm) cc_final: 0.6929 (tmm)
REVERT: A  195 ASP cc_start: 0.8561 (p0) cc_final: 0.8209 (t0)
REVERT: B  657 MET cc_start: 0.9177 (tmm) cc_final: 0.8970 (tmm)
REVERT: B  781 ASP cc_start: 0.8489 (m-30) cc_final: 0.8090 (m-30)
REVERT: B  914 MET cc_start: 0.8570 (pmm) cc_final: 0.8280 (pmm)
REVERT: B  985 MET cc_start: 0.8490 (mpp) cc_final: 0.7488 (mpp)
REVERT: B 1228 HIS cc_start: 0.6272 (m170) cc_final: 0.5992 (m170)
REVERT: B 1394 MET cc_start: 0.8953 (mmm) cc_final: 0.8747 (mmm)
REVERT: B 1415 MET cc_start: 0.8063 (mpp) cc_final: 0.7689 (mpp)
REVERT: B 1496 MET cc_start: 0.8414 (mmm) cc_final: 0.8156 (mmp)
REVERT: C  142 TYR cc_start: 0.7907 (p90) cc_final: 0.7677 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1055
  time to fit residues: 22.4043
Evaluate side-chains
  100 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 151 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 149 optimal weight:    1.9990
   chunk 168 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0050
   overall best weight:    1.3200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 791 GLN
** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1356 ASN
** B1368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1549 HIS
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  87 HIS
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.067299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.054736 restraints weight = 78458.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.056197 restraints weight = 49830.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.057243 restraints weight = 36723.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.057950 restraints weight = 29681.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.058376 restraints weight = 25540.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.4100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  13597  Z= 0.286
  Angle     :  0.807  10.855  18462  Z= 0.426
  Chirality :  0.048   0.181   2093
  Planarity :  0.005   0.042   2349
  Dihedral  :  5.784  27.592   1815
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.61 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.93 %
    Favored  : 94.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.20), residues: 1697
  helix:  1.31 (0.18), residues: 787
  sheet: -1.41 (0.32), residues: 234
  loop : -3.15 (0.20), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 819 
 TYR   0.020   0.002   TYR B1320 
 PHE   0.020   0.002   PHE D 247 
 TRP   0.016   0.002   TRP C  91 
 HIS   0.015   0.002   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 (13597)
  covalent geometry    : angle       0.80684 (18462)
  hydrogen bonds       : bond        0.05300 (  685)
  hydrogen bonds       : angle       4.56019 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8094 (tmm) cc_final: 0.7582 (tmm)
REVERT: A  194 MET cc_start: 0.5636 (tmm) cc_final: 0.5308 (tmm)
REVERT: A  195 ASP cc_start: 0.8698 (p0) cc_final: 0.8296 (t0)
REVERT: B  914 MET cc_start: 0.8561 (pmm) cc_final: 0.8301 (pmm)
REVERT: B 1063 MET cc_start: 0.8035 (tpp) cc_final: 0.7832 (tpp)
REVERT: B 1243 MET cc_start: 0.8688 (ptp) cc_final: 0.8389 (ptm)
REVERT: B 1365 LEU cc_start: 0.9433 (tp) cc_final: 0.9218 (tp)
REVERT: B 1369 VAL cc_start: 0.8421 (t) cc_final: 0.8121 (t)
REVERT: B 1415 MET cc_start: 0.8152 (mpp) cc_final: 0.7441 (mpp)
REVERT: B 1496 MET cc_start: 0.8462 (mmm) cc_final: 0.8172 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0992
  time to fit residues: 19.4142
Evaluate side-chains
  86 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 152 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 137 optimal weight:    0.5980
   chunk 110 optimal weight:    0.3980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
B1205 GLN
B1260 GLN
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1368 GLN
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 HIS
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.069655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.056696 restraints weight = 76377.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.058213 restraints weight = 48144.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.059353 restraints weight = 35277.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.060147 restraints weight = 28580.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.060645 restraints weight = 24399.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13597  Z= 0.156
  Angle     :  0.679  12.417  18462  Z= 0.355
  Chirality :  0.044   0.178   2093
  Planarity :  0.004   0.045   2349
  Dihedral  :  5.307  26.652   1815
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.55 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.20), residues: 1697
  helix:  1.85 (0.18), residues: 783
  sheet: -1.13 (0.33), residues: 226
  loop : -3.02 (0.20), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B1560 
 TYR   0.015   0.001   TYR B1320 
 PHE   0.013   0.001   PHE C 150 
 TRP   0.016   0.001   TRP B1436 
 HIS   0.011   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (13597)
  covalent geometry    : angle       0.67869 (18462)
  hydrogen bonds       : bond        0.04031 (  685)
  hydrogen bonds       : angle       4.08165 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7946 (tmm) cc_final: 0.7390 (tmm)
REVERT: A   16 ASP cc_start: 0.8850 (m-30) cc_final: 0.7874 (t0)
REVERT: A  194 MET cc_start: 0.5765 (tmm) cc_final: 0.5448 (tmm)
REVERT: A  195 ASP cc_start: 0.8683 (p0) cc_final: 0.8307 (t0)
REVERT: B  781 ASP cc_start: 0.8485 (m-30) cc_final: 0.8072 (m-30)
REVERT: B  914 MET cc_start: 0.8517 (pmm) cc_final: 0.8255 (pmm)
REVERT: B 1063 MET cc_start: 0.8030 (tpp) cc_final: 0.7785 (tpp)
REVERT: B 1316 PHE cc_start: 0.7950 (p90) cc_final: 0.7231 (p90)
REVERT: B 1415 MET cc_start: 0.8026 (mpp) cc_final: 0.7533 (mpp)
REVERT: B 1496 MET cc_start: 0.8606 (mmm) cc_final: 0.8345 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1012
  time to fit residues: 20.3874
Evaluate side-chains
  95 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 137 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 88 optimal weight:    0.4980
   chunk 78 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 117 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 128 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0870
   chunk 124 optimal weight:    0.5980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
B1187 HIS
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.070401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.057614 restraints weight = 76116.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.059218 restraints weight = 47062.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.060382 restraints weight = 33966.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.061175 restraints weight = 27030.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.061668 restraints weight = 22941.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.4174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13597  Z= 0.146
  Angle     :  0.664  11.246  18462  Z= 0.344
  Chirality :  0.044   0.177   2093
  Planarity :  0.004   0.042   2349
  Dihedral  :  5.138  26.706   1815
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.14 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.21), residues: 1697
  helix:  1.96 (0.18), residues: 784
  sheet: -1.21 (0.32), residues: 252
  loop : -2.96 (0.21), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  89 
 TYR   0.015   0.001   TYR B1320 
 PHE   0.013   0.001   PHE C 150 
 TRP   0.013   0.001   TRP B1436 
 HIS   0.005   0.001   HIS B 926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (13597)
  covalent geometry    : angle       0.66402 (18462)
  hydrogen bonds       : bond        0.03857 (  685)
  hydrogen bonds       : angle       3.94410 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7941 (tmm) cc_final: 0.7363 (tmm)
REVERT: A   16 ASP cc_start: 0.8793 (m-30) cc_final: 0.7953 (t0)
REVERT: A  195 ASP cc_start: 0.8631 (p0) cc_final: 0.8255 (t0)
REVERT: B  781 ASP cc_start: 0.8433 (m-30) cc_final: 0.8045 (m-30)
REVERT: B  914 MET cc_start: 0.8467 (pmm) cc_final: 0.8212 (pmm)
REVERT: B 1063 MET cc_start: 0.8013 (tpp) cc_final: 0.7670 (tpp)
REVERT: B 1103 LYS cc_start: 0.8693 (ptpt) cc_final: 0.8343 (ptpp)
REVERT: B 1135 MET cc_start: 0.8026 (mmt) cc_final: 0.7677 (mmp)
REVERT: B 1243 MET cc_start: 0.8540 (ptp) cc_final: 0.8325 (ptm)
REVERT: B 1316 PHE cc_start: 0.7819 (p90) cc_final: 0.7158 (p90)
REVERT: B 1415 MET cc_start: 0.8075 (mpp) cc_final: 0.7589 (mpp)
REVERT: C   71 ASP cc_start: 0.9031 (p0) cc_final: 0.8809 (p0)
REVERT: C  195 SER cc_start: 0.7481 (t) cc_final: 0.6654 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0992
  time to fit residues: 20.6727
Evaluate side-chains
  93 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 112 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 162 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0980
   chunk 7 optimal weight:    0.3980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.070635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.057964 restraints weight = 77782.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.059440 restraints weight = 49905.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.060515 restraints weight = 37132.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.061244 restraints weight = 30239.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.061706 restraints weight = 26015.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13597  Z= 0.151
  Angle     :  0.658  10.975  18462  Z= 0.343
  Chirality :  0.043   0.177   2093
  Planarity :  0.004   0.043   2349
  Dihedral  :  5.074  26.165   1815
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.96 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.21), residues: 1697
  helix:  1.98 (0.18), residues: 782
  sheet: -1.05 (0.33), residues: 242
  loop : -2.93 (0.21), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  89 
 TYR   0.015   0.001   TYR B1320 
 PHE   0.014   0.001   PHE C 150 
 TRP   0.013   0.001   TRP B1463 
 HIS   0.005   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (13597)
  covalent geometry    : angle       0.65820 (18462)
  hydrogen bonds       : bond        0.03817 (  685)
  hydrogen bonds       : angle       3.93081 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7956 (tmm) cc_final: 0.7374 (tmm)
REVERT: A   16 ASP cc_start: 0.8784 (m-30) cc_final: 0.8053 (t0)
REVERT: A  195 ASP cc_start: 0.8573 (p0) cc_final: 0.8258 (t0)
REVERT: B  781 ASP cc_start: 0.8452 (m-30) cc_final: 0.8064 (m-30)
REVERT: B  914 MET cc_start: 0.8444 (pmm) cc_final: 0.8157 (pmm)
REVERT: B 1063 MET cc_start: 0.8045 (tpp) cc_final: 0.7674 (tpp)
REVERT: B 1103 LYS cc_start: 0.8776 (ptpt) cc_final: 0.8425 (ptpp)
REVERT: B 1135 MET cc_start: 0.8009 (mmt) cc_final: 0.7660 (mmp)
REVERT: B 1316 PHE cc_start: 0.7727 (p90) cc_final: 0.7080 (p90)
REVERT: B 1415 MET cc_start: 0.8133 (mpp) cc_final: 0.7608 (mpp)
REVERT: C  195 SER cc_start: 0.7518 (t) cc_final: 0.6729 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0985
  time to fit residues: 19.3240
Evaluate side-chains
  95 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 142 optimal weight:    0.4980
   chunk 123 optimal weight:    0.5980
   chunk 161 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1101 GLN
B1151 HIS
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 ASN
C 296 GLN
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.068760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.055835 restraints weight = 76934.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.057453 restraints weight = 47716.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.058579 restraints weight = 34567.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.059288 restraints weight = 27690.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.059873 restraints weight = 23721.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13597  Z= 0.175
  Angle     :  0.698  13.258  18462  Z= 0.361
  Chirality :  0.044   0.176   2093
  Planarity :  0.004   0.045   2349
  Dihedral  :  5.137  26.464   1815
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.31 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.56 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.21), residues: 1697
  helix:  1.87 (0.18), residues: 785
  sheet: -1.11 (0.34), residues: 228
  loop : -2.96 (0.21), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  89 
 TYR   0.022   0.002   TYR B1423 
 PHE   0.016   0.002   PHE C 150 
 TRP   0.012   0.001   TRP B1463 
 HIS   0.010   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (13597)
  covalent geometry    : angle       0.69842 (18462)
  hydrogen bonds       : bond        0.04047 (  685)
  hydrogen bonds       : angle       4.01668 ( 1995)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8063 (tmm) cc_final: 0.7498 (tmm)
REVERT: A   16 ASP cc_start: 0.8963 (m-30) cc_final: 0.8309 (t0)
REVERT: A  159 MET cc_start: 0.7155 (tmm) cc_final: 0.6936 (mmt)
REVERT: B  679 MET cc_start: 0.8954 (ptt) cc_final: 0.8341 (ptp)
REVERT: B  781 ASP cc_start: 0.8502 (m-30) cc_final: 0.8110 (m-30)
REVERT: B  896 MET cc_start: 0.8989 (mmt) cc_final: 0.8671 (mpp)
REVERT: B  914 MET cc_start: 0.8528 (pmm) cc_final: 0.8233 (pmm)
REVERT: B  985 MET cc_start: 0.8604 (mpp) cc_final: 0.7505 (mpp)
REVERT: B 1063 MET cc_start: 0.7948 (tpp) cc_final: 0.7656 (tpp)
REVERT: B 1135 MET cc_start: 0.7914 (mmt) cc_final: 0.7594 (mmp)
REVERT: B 1415 MET cc_start: 0.8074 (mpp) cc_final: 0.7518 (mpp)
REVERT: C  195 SER cc_start: 0.7479 (t) cc_final: 0.6577 (m)
REVERT: C  296 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5149 (mt0)
REVERT: D   61 GLU cc_start: 0.8846 (pp20) cc_final: 0.8442 (pp20)
  outliers start: 2
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0996
  time to fit residues: 19.7160
Evaluate side-chains
  91 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 144 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 127 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 162 optimal weight:    1.9990
   chunk 154 optimal weight:    0.9990
   chunk 116 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 ASN
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.068327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.055329 restraints weight = 76670.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.056946 restraints weight = 46890.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.057983 restraints weight = 33834.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.058817 restraints weight = 27148.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.059357 restraints weight = 23076.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13597  Z= 0.186
  Angle     :  0.721  12.918  18462  Z= 0.373
  Chirality :  0.045   0.176   2093
  Planarity :  0.004   0.050   2349
  Dihedral  :  5.266  27.981   1815
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.49 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.35 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.20), residues: 1697
  helix:  1.78 (0.18), residues: 783
  sheet: -1.18 (0.34), residues: 228
  loop : -2.97 (0.21), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  53 
 TYR   0.017   0.002   TYR B1320 
 PHE   0.017   0.002   PHE C 150 
 TRP   0.016   0.001   TRP B1463 
 HIS   0.008   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (13597)
  covalent geometry    : angle       0.72083 (18462)
  hydrogen bonds       : bond        0.04207 (  685)
  hydrogen bonds       : angle       4.13426 ( 1995)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3394 Ramachandran restraints generated.
    1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8100 (tmm) cc_final: 0.7572 (tmm)
REVERT: A   16 ASP cc_start: 0.9036 (m-30) cc_final: 0.8443 (t0)
REVERT: A  159 MET cc_start: 0.7076 (tmm) cc_final: 0.6714 (mmt)
REVERT: A  195 ASP cc_start: 0.8809 (p0) cc_final: 0.8210 (t70)
REVERT: B  781 ASP cc_start: 0.8502 (m-30) cc_final: 0.8109 (m-30)
REVERT: B  896 MET cc_start: 0.8988 (mmt) cc_final: 0.8683 (mpp)
REVERT: B  914 MET cc_start: 0.8501 (pmm) cc_final: 0.8193 (pmm)
REVERT: B 1063 MET cc_start: 0.7984 (tpp) cc_final: 0.7619 (tpp)
REVERT: B 1135 MET cc_start: 0.7952 (mmt) cc_final: 0.7655 (mmp)
REVERT: B 1296 ARG cc_start: 0.6516 (mtt90) cc_final: 0.6226 (mpt180)
REVERT: B 1394 MET cc_start: 0.9060 (mmm) cc_final: 0.8756 (mmm)
REVERT: B 1415 MET cc_start: 0.8149 (mpp) cc_final: 0.7765 (mpp)
REVERT: C  195 SER cc_start: 0.7498 (t) cc_final: 0.6599 (m)
REVERT: D   61 GLU cc_start: 0.8810 (pp20) cc_final: 0.8191 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1048
  time to fit residues: 19.6859
Evaluate side-chains
  92 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 14 optimal weight:    0.1980
   chunk 86 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 115 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1151 HIS
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1462 HIS
C  31 ASN
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.069065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.056400 restraints weight = 75976.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.057927 restraints weight = 47380.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.059018 restraints weight = 34444.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.059774 restraints weight = 27704.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.060177 restraints weight = 23630.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.4701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13597  Z= 0.152
  Angle     :  0.691  12.969  18462  Z= 0.356
  Chirality :  0.044   0.178   2093
  Planarity :  0.004   0.048   2349
  Dihedral  :  5.150  27.890   1815
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.08 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.14 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.21), residues: 1697
  helix:  1.95 (0.18), residues: 784
  sheet: -1.09 (0.34), residues: 228
  loop : -2.93 (0.21), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B1417 
 TYR   0.015   0.001   TYR B1320 
 PHE   0.014   0.001   PHE C 150 
 TRP   0.019   0.001   TRP B1463 
 HIS   0.007   0.001   HIS B 926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (13597)
  covalent geometry    : angle       0.69144 (18462)
  hydrogen bonds       : bond        0.03881 (  685)
  hydrogen bonds       : angle       3.98731 ( 1995)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3208.62 seconds
wall clock time: 56 minutes 35.92 seconds (3395.92 seconds total)