Starting phenix.real_space_refine
on Fri Jun 13 10:21:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g8r_51137/06_2025/9g8r_51137.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g8r_51137/06_2025/9g8r_51137.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g8r_51137/06_2025/9g8r_51137.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g8r_51137/06_2025/9g8r_51137.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g8r_51137/06_2025/9g8r_51137.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g8r_51137/06_2025/9g8r_51137.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001
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      67      5.16       5
     C    9426      2.51       5
     N    2524      2.21       5
     O    2820      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14837
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 8718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1113, 8718
          Classifications: {'peptide': 1113}
          Link IDs: {'PTRANS': 24, 'TRANS': 1088}
    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}
    Chain: "E"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 105
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
    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
  Time building chain proxies: 19.02, per 1000 atoms: 1.28
  Number of scatterers: 14837
  At special positions: 0
  Unit cell: (93.632, 173.645, 144.704, 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      67     16.00
     O    2820      8.00
     N    2524      7.00
     C    9426      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: 3.75
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3560

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 16 sheets defined
      51.7% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'B' and resid 453 through 468
      removed outlier: 4.156A  pdb=" N   GLY B 468 " --> pdb=" O   TYR B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 474
    Processing helix  chain 'B' and resid 477 through 489
    Processing helix  chain 'B' and resid 492 through 506
      removed outlier: 3.664A  pdb=" N   PHE B 496 " --> pdb=" O   MET B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 524
    Processing helix  chain 'B' and resid 527 through 541
    Processing helix  chain 'B' and resid 543 through 558
    Processing helix  chain 'B' and resid 563 through 577
    Processing helix  chain 'B' and resid 579 through 592
    Processing helix  chain 'B' and resid 597 through 612
      removed outlier: 3.745A  pdb=" N   TRP B 601 " --> pdb=" O   ASP B 597 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER B 603 " --> pdb=" O   ASN B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 615 through 628
    Processing helix  chain 'B' and resid 632 through 645
    Processing helix  chain 'B' and resid 647 through 662
      removed outlier: 3.539A  pdb=" N   ALA B 651 " --> pdb=" O   LYS B 647 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LYS B 661 " --> pdb=" O   MET B 657 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS B 662 " --> pdb=" O   ILE B 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 686
      removed outlier: 3.522A  pdb=" N   LEU B 669 " --> pdb=" O   TYR B 665 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASP B 686 " --> pdb=" O   ALA B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 710
      removed outlier: 3.936A  pdb=" N   HIS B 709 " --> pdb=" O   CYS B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 727
      removed outlier: 4.394A  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: 3.617A  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
      removed outlier: 3.531A  pdb=" N   GLU B 857 " --> pdb=" O   SER B 853 " (cutoff:3.500A)
    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: 3.951A  pdb=" N   TRP B 898 " --> pdb=" O   TYR B 894 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 912 through 925
      removed outlier: 3.620A  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: 3.659A  pdb=" N   TYR B 954 " --> pdb=" O   GLU B 950 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 960 through 976
      removed outlier: 3.828A  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
    Processing helix  chain 'B' and resid 1083 through 1101
      removed outlier: 3.719A  pdb=" N   LYS B1087 " --> pdb=" O   SER B1083 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1103 through 1117
      removed outlier: 3.770A  pdb=" N   ALA B1107 " --> pdb=" O   LYS B1103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1121 through 1135
    Processing helix  chain 'B' and resid 1139 through 1152
      removed outlier: 3.690A  pdb=" N   HIS B1151 " --> pdb=" O   GLU B1147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1157 through 1172
      removed outlier: 3.744A  pdb=" N   ARG B1161 " --> pdb=" O   SER B1157 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLN B1172 " --> pdb=" O   ILE B1168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1176 through 1189
      removed outlier: 3.655A  pdb=" N   LYS B1180 " --> pdb=" O   VAL B1176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1192 through 1206
      removed outlier: 3.839A  pdb=" N   TRP B1196 " --> pdb=" O   ASP B1192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1210 through 1225
      removed outlier: 3.812A  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: 4.151A  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: 3.554A  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: 3.712A  pdb=" N   ASN B1396 " --> pdb=" O   THR B1392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1399 through 1414
      removed outlier: 3.606A  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: 3.995A  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
    Processing helix  chain 'B' and resid 1552 through 1563
    Processing helix  chain 'E' and resid 453 through 464
    Processing helix  chain 'A' and resid 53 through 62
    Processing helix  chain 'A' and resid 65 through 73
      removed outlier: 4.388A  pdb=" N   TRP A  68 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      Proline residue:  A  70  - end of helix
      removed outlier: 3.715A  pdb=" N   GLY A  73 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.629A  pdb=" N   SER A  89 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A  91 " --> pdb=" O   TRP A  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 737 through 740
    Processing sheet with id=AA2, first strand: chain 'C' and resid 6 through 10
      removed outlier: 3.669A  pdb=" N   GLY C   6 " --> pdb=" O   ASP C 302 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LEU C   8 " --> pdb=" O   ILE C 300 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ILE C 300 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   LYS C  10 " --> pdb=" O   ILE C 298 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE C 298 " --> pdb=" O   LYS C  10 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 25
      removed outlier: 6.509A  pdb=" N   VAL C  46 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 67 through 72
      removed outlier: 3.814A  pdb=" N   SER C  81 " --> pdb=" O   ARG C  89 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ARG C  89 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   SER C  83 " --> pdb=" O   HIS C  87 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   HIS C  87 " --> pdb=" O   SER C  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 124
      removed outlier: 3.623A  pdb=" N   TYR C 142 " --> pdb=" O   ILE C 132 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   GLY C 134 " --> pdb=" O   LYS C 140 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LYS C 140 " --> pdb=" O   GLY C 134 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 151 through 156
      removed outlier: 6.560A  pdb=" N   GLY C 166 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ILE C 154 " --> pdb=" O   ALA C 164 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ALA C 164 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE C 174 " --> pdb=" O   HIS C 184 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   HIS C 184 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 196 through 197
      removed outlier: 3.572A  pdb=" N   THR C 197 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   ILE C 214 " --> pdb=" O   THR C 227 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   THR C 227 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ILE C 216 " --> pdb=" O   ALA C 225 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 240
      removed outlier: 3.614A  pdb=" N   HIS C 268 " --> pdb=" O   VAL C 258 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ASP C 260 " --> pdb=" O   CYS C 266 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   CYS C 266 " --> pdb=" O   ASP C 260 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 11
      removed outlier: 5.996A  pdb=" N   ILE D   7 " --> pdb=" O   ASP D 302 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASP D 302 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   PHE D   9 " --> pdb=" O   ILE D 300 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE D 298 " --> pdb=" O   GLN D  11 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 25
      removed outlier: 6.678A  pdb=" N   LYS D  48 " --> pdb=" O   LEU D  56 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   LEU D  56 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 67 through 72
      removed outlier: 3.723A  pdb=" N   SER D  81 " --> pdb=" O   ARG D  89 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ARG D  89 " --> pdb=" O   SER D  81 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   SER D  83 " --> pdb=" O   HIS D  87 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   HIS D  87 " --> pdb=" O   SER D  83 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 112 through 113
      removed outlier: 3.799A  pdb=" N   TYR D 142 " --> pdb=" O   ILE D 132 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   GLY D 134 " --> pdb=" O   LYS D 140 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   LYS D 140 " --> pdb=" O   GLY D 134 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 151 through 156
      removed outlier: 6.548A  pdb=" N   GLY D 166 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   ILE D 154 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ALA D 164 " --> pdb=" O   ILE D 154 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE D 174 " --> pdb=" O   HIS D 184 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   HIS D 184 " --> pdb=" O   ILE D 174 " (cutoff:3.500A)
    Processing sheet with id=AB5, 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: 6.288A  pdb=" N   ILE D 214 " --> pdb=" O   THR D 227 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   THR D 227 " --> pdb=" O   ILE D 214 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE D 216 " --> pdb=" O   ALA D 225 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 235 through 240
      removed outlier: 3.613A  pdb=" N   HIS D 268 " --> pdb=" O   VAL D 258 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ASP D 260 " --> pdb=" O   CYS D 266 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   CYS D 266 " --> pdb=" O   ASP D 260 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 20 through 23

    817 hydrogen bonds defined for protein.
    2379 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: 6.02

  Time building geometry restraints manager: 4.49 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: 3422
        1.33 -     1.45: 3229
        1.45 -     1.58: 8401
        1.58 -     1.70: 0
        1.70 -     1.82: 100
  Bond restraints: 15152
  Sorted by residual:
  bond pdb=" N   ASP B1015 "
       pdb=" CA  ASP B1015 "
    ideal  model  delta    sigma   weight residual
    1.459  1.478 -0.019 1.32e-02 5.74e+03 2.14e+00
  bond pdb=" CG  ARG B 512 "
       pdb=" CD  ARG B 512 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.13e+00
  bond pdb=" N   ASP D 169 "
       pdb=" CA  ASP D 169 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.025 1.77e-02 3.19e+03 2.02e+00
  bond pdb=" N   ASP C 169 "
       pdb=" CA  ASP C 169 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.024 1.77e-02 3.19e+03 1.90e+00
  bond pdb=" CG  GLN B 588 "
       pdb=" CD  GLN B 588 "
    ideal  model  delta    sigma   weight residual
    1.516  1.482  0.034 2.50e-02 1.60e+03 1.89e+00
  ... (remaining 15147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.29: 20337
        3.29 -     6.59: 199
        6.59 -     9.88: 18
        9.88 -    13.17: 7
       13.17 -    16.47: 3
  Bond angle restraints: 20564
  Sorted by residual:
  angle pdb=" C   PRO A  12 "
        pdb=" N   ASP A  13 "
        pdb=" CA  ASP A  13 "
      ideal   model   delta    sigma   weight residual
     121.80  133.84  -12.04 2.44e+00 1.68e-01 2.44e+01
  angle pdb=" CB  ARG B 512 "
        pdb=" CG  ARG B 512 "
        pdb=" CD  ARG B 512 "
      ideal   model   delta    sigma   weight residual
     111.30  100.12   11.18 2.30e+00 1.89e-01 2.36e+01
  angle pdb=" C   GLU B1014 "
        pdb=" N   ASP B1015 "
        pdb=" CA  ASP B1015 "
      ideal   model   delta    sigma   weight residual
     124.31  132.41   -8.10 1.67e+00 3.59e-01 2.35e+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  134.47   -8.81 1.85e+00 2.92e-01 2.27e+01
  angle pdb=" N   GLN B 588 "
        pdb=" CA  GLN B 588 "
        pdb=" CB  GLN B 588 "
      ideal   model   delta    sigma   weight residual
     110.12  117.10   -6.98 1.47e+00 4.63e-01 2.25e+01
  ... (remaining 20559 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 8070
       17.77 -    35.54: 802
       35.54 -    53.31: 125
       53.31 -    71.07: 30
       71.07 -    88.84: 15
  Dihedral angle restraints: 9042
    sinusoidal: 3513
      harmonic: 5529
  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 -152.95  -27.05     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  ASP C 201 "
           pdb=" C   ASP C 201 "
           pdb=" N   SER C 202 "
           pdb=" CA  SER C 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.81  -25.19     0      5.00e+00 4.00e-02 2.54e+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 -154.96  -25.04     0      5.00e+00 4.00e-02 2.51e+01
  ... (remaining 9039 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1834
       0.052 -    0.104: 377
       0.104 -    0.156: 98
       0.156 -    0.208: 9
       0.208 -    0.260: 4
  Chirality restraints: 2322
  Sorted by residual:
  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    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  ASN B1356 "
            pdb=" N   ASN B1356 "
            pdb=" C   ASN B1356 "
            pdb=" CB  ASN B1356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  ILE D  78 "
            pdb=" N   ILE D  78 "
            pdb=" C   ILE D  78 "
            pdb=" CB  ILE D  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 2319 not shown)

  Planarity restraints: 2616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  69 "   -0.074 5.00e-02 4.00e+02   1.13e-01 2.05e+01
        pdb=" N   PRO A  70 "    0.196 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B1381 "   -0.066 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO B1382 "    0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO B1382 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO B1382 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B1014 "   -0.018 2.00e-02 2.50e+03   3.60e-02 1.29e+01
        pdb=" C   GLU B1014 "    0.062 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 2613 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 313
        2.68 -     3.24: 14446
        3.24 -     3.79: 22426
        3.79 -     4.35: 28963
        4.35 -     4.90: 49690
  Nonbonded interactions: 115838
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 722 "
            pdb=" OH  TYR B 766 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OG  SER C 251 "
            pdb=" OD1 ASP C 253 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OG  SER D 251 "
            pdb=" OD1 ASP D 253 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" O   VAL C 107 "
            pdb=" OG1 THR C 125 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O   VAL D 107 "
            pdb=" OG1 THR D 125 "
     model   vdw
     2.178 3.040
  ... (remaining 115833 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 individual isotropic
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:             536.820
  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:             0.020
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     46.610
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.080
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  587.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
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      :  0.003   0.049  15152  Z= 0.155
  Angle     :  0.838  16.468  20564  Z= 0.446
  Chirality :  0.046   0.260   2322
  Planarity :  0.006   0.113   2616
  Dihedral  : 14.720  88.843   5482
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.34 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.20), residues: 1888
  helix:  2.41 (0.16), residues: 953
  sheet: -1.13 (0.34), residues: 218
  loop : -2.88 (0.19), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 601 
 HIS   0.011   0.001   HIS D 126 
 PHE   0.022   0.002   PHE C 114 
 TYR   0.042   0.002   TYR B1525 
 ARG   0.024   0.001   ARG B 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11346 (  817)
  hydrogen bonds       : angle       4.63177 ( 2379)
  covalent geometry    : bond        0.00316 (15152)
  covalent geometry    : angle       0.83792 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  567 TRP cc_start: 0.8182 (m100) cc_final: 0.7807 (m100)
REVERT: B  598 PHE cc_start: 0.8330 (p90) cc_final: 0.8056 (p90)
REVERT: B 1063 MET cc_start: 0.9044 (mmt) cc_final: 0.8827 (mmm)
REVERT: E  456 GLU cc_start: 0.7466 (mp0) cc_final: 0.7186 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2664
  time to fit residues: 65.3383
Evaluate side-chains
  129 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 158 optimal weight:    1.9990
   chunk 142 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0870
   chunk 48 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0870
   chunk 147 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9980
   chunk 170 optimal weight:    0.6980
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
B 791 GLN
** B 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  98 GLN
D 126 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.097886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.066956 restraints weight = 31903.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 3.09
r_work: 0.2690 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8767
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  15152  Z= 0.194
  Angle     :  0.714  11.549  20564  Z= 0.371
  Chirality :  0.045   0.185   2322
  Planarity :  0.005   0.067   2616
  Dihedral  :  4.941  32.915   2029
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.16 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  9.97 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.20), residues: 1888
  helix:  2.57 (0.17), residues: 954
  sheet: -1.65 (0.31), residues: 250
  loop : -2.68 (0.20), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D  47 
 HIS   0.012   0.001   HIS D 126 
 PHE   0.016   0.002   PHE B1317 
 TYR   0.014   0.002   TYR C 156 
 ARG   0.012   0.001   ARG B 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05814 (  817)
  hydrogen bonds       : angle       3.92641 ( 2379)
  covalent geometry    : bond        0.00452 (15152)
  covalent geometry    : angle       0.71366 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.609 
Fit side-chains
REVERT: B  546 MET cc_start: 0.8319 (mpp) cc_final: 0.7914 (ttm)
REVERT: B  567 TRP cc_start: 0.8138 (m100) cc_final: 0.7616 (m100)
REVERT: B  598 PHE cc_start: 0.8407 (p90) cc_final: 0.8118 (p90)
REVERT: B  679 MET cc_start: 0.9431 (mtp) cc_final: 0.9215 (mtp)
REVERT: B 1063 MET cc_start: 0.9393 (mmt) cc_final: 0.9187 (mmm)
REVERT: B 1489 LEU cc_start: 0.8922 (mm) cc_final: 0.8716 (mm)
REVERT: C   50 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7436 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8400 (pm20) cc_final: 0.7942 (pm20)
REVERT: E  456 GLU cc_start: 0.7616 (mp0) cc_final: 0.7335 (mp0)
  outliers start: 17
  outliers final: 8
  residues processed: 142
  average time/residue: 0.2750
  time to fit residues: 58.4177
Evaluate side-chains
  123 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 1.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain E residue  455 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 65 optimal weight:    0.2980
   chunk 48 optimal weight:    0.1980
   chunk 67 optimal weight:    0.5980
   chunk 153 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.096794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.065803 restraints weight = 31890.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 3.09
r_work: 0.2667 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15152  Z= 0.189
  Angle     :  0.678  11.300  20564  Z= 0.354
  Chirality :  0.044   0.176   2322
  Planarity :  0.005   0.054   2616
  Dihedral  :  5.036  34.276   2029
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.69 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.23 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.20), residues: 1888
  helix:  2.55 (0.17), residues: 958
  sheet: -1.31 (0.31), residues: 238
  loop : -2.73 (0.20), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B1524 
 HIS   0.010   0.001   HIS D 126 
 PHE   0.014   0.002   PHE D 150 
 TYR   0.014   0.001   TYR B 954 
 ARG   0.008   0.001   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05530 (  817)
  hydrogen bonds       : angle       3.81993 ( 2379)
  covalent geometry    : bond        0.00444 (15152)
  covalent geometry    : angle       0.67764 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 119
  time to evaluate  : 1.765 
Fit side-chains
   revert: symmetry clash
REVERT: B  527 ASP cc_start: 0.7302 (t0) cc_final: 0.6822 (p0)
REVERT: B  567 TRP cc_start: 0.8132 (m100) cc_final: 0.7625 (m100)
REVERT: B  598 PHE cc_start: 0.8461 (p90) cc_final: 0.8168 (p90)
REVERT: B 1489 LEU cc_start: 0.8971 (mm) cc_final: 0.8708 (mm)
REVERT: C   50 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7323 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8499 (pm20) cc_final: 0.8004 (pm20)
REVERT: C  184 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.7775 (p-80)
REVERT: C  240 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8798 (t80)
REVERT: D  297 GLU cc_start: 0.8306 (tt0) cc_final: 0.8022 (tm-30)
REVERT: E  456 GLU cc_start: 0.7633 (mp0) cc_final: 0.7372 (mp0)
  outliers start: 40
  outliers final: 18
  residues processed: 152
  average time/residue: 0.2720
  time to fit residues: 62.6227
Evaluate side-chains
  134 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 1.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  927 THR
Chi-restraints excluded: chain B residue  951 LEU
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  184 HIS
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  207 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9990
   chunk 163 optimal weight:    0.2980
   chunk 31 optimal weight:    0.6980
   chunk 27 optimal weight:    0.3980
   chunk 52 optimal weight:    0.0970
   chunk 125 optimal weight:    0.7980
   chunk 137 optimal weight:    0.7980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
B 791 GLN
B 825 HIS
B 860 ASN
B1291 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.096610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.064967 restraints weight = 31796.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 3.14
r_work: 0.2657 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15152  Z= 0.172
  Angle     :  0.654  14.866  20564  Z= 0.339
  Chirality :  0.043   0.179   2322
  Planarity :  0.005   0.049   2616
  Dihedral  :  4.955  34.087   2029
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.80 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.12 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.20), residues: 1888
  helix:  2.68 (0.16), residues: 950
  sheet: -1.18 (0.31), residues: 238
  loop : -2.75 (0.20), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B1524 
 HIS   0.012   0.001   HIS D 126 
 PHE   0.011   0.002   PHE C 114 
 TYR   0.013   0.001   TYR B 954 
 ARG   0.010   0.001   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05216 (  817)
  hydrogen bonds       : angle       3.70398 ( 2379)
  covalent geometry    : bond        0.00403 (15152)
  covalent geometry    : angle       0.65379 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 1.577 
Fit side-chains
REVERT: B  527 ASP cc_start: 0.7140 (t0) cc_final: 0.6765 (p0)
REVERT: B  546 MET cc_start: 0.8386 (mpp) cc_final: 0.8173 (pmm)
REVERT: B  567 TRP cc_start: 0.8110 (m100) cc_final: 0.7617 (m100)
REVERT: B  598 PHE cc_start: 0.8464 (p90) cc_final: 0.8178 (p90)
REVERT: B 1489 LEU cc_start: 0.8992 (mm) cc_final: 0.8694 (mm)
REVERT: C   50 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7481 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8527 (pm20) cc_final: 0.8065 (pm20)
REVERT: C  184 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.7854 (p-80)
REVERT: C  240 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8772 (t80)
REVERT: D  127 VAL cc_start: 0.7812 (m) cc_final: 0.7511 (t)
REVERT: D  221 HIS cc_start: 0.7545 (m-70) cc_final: 0.7301 (m-70)
REVERT: E  456 GLU cc_start: 0.7599 (mp0) cc_final: 0.7355 (mp0)
  outliers start: 42
  outliers final: 28
  residues processed: 154
  average time/residue: 0.2654
  time to fit residues: 62.0534
Evaluate side-chains
  143 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 1.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  927 THR
Chi-restraints excluded: chain B residue  951 LEU
Chi-restraints excluded: chain B residue  973 VAL
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1400 VAL
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain B residue 1502 ARG
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  184 HIS
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   87 HIS
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain A residue  120 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 81 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9980
   chunk 150 optimal weight:    0.0030
   chunk 113 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 11 optimal weight:    0.6980
   chunk 158 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 184 optimal weight:    0.0060
   chunk 7 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.3006

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
B 582 GLN
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 860 ASN
D  11 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.097898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.067066 restraints weight = 31948.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 3.24
r_work: 0.2692 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15152  Z= 0.136
  Angle     :  0.610  11.581  20564  Z= 0.320
  Chirality :  0.041   0.175   2322
  Planarity :  0.004   0.044   2616
  Dihedral  :  4.841  33.157   2029
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.95 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.50 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.20), residues: 1888
  helix:  2.81 (0.17), residues: 950
  sheet: -0.99 (0.31), residues: 234
  loop : -2.72 (0.20), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1524 
 HIS   0.009   0.001   HIS D 126 
 PHE   0.011   0.001   PHE C 150 
 TYR   0.013   0.001   TYR B 503 
 ARG   0.010   0.000   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04438 (  817)
  hydrogen bonds       : angle       3.58733 ( 2379)
  covalent geometry    : bond        0.00306 (15152)
  covalent geometry    : angle       0.60996 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 115
  time to evaluate  : 1.561 
Fit side-chains
REVERT: B  527 ASP cc_start: 0.7026 (t0) cc_final: 0.6745 (p0)
REVERT: B  567 TRP cc_start: 0.8111 (m100) cc_final: 0.7592 (m100)
REVERT: B 1489 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8668 (mm)
REVERT: C   50 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7455 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8520 (pm20) cc_final: 0.8140 (pt0)
REVERT: C  184 HIS cc_start: 0.8653 (OUTLIER) cc_final: 0.7832 (p-80)
REVERT: C  240 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8748 (t80)
REVERT: D  221 HIS cc_start: 0.7540 (m-70) cc_final: 0.7284 (m-70)
REVERT: E  456 GLU cc_start: 0.7650 (mp0) cc_final: 0.7423 (mp0)
  outliers start: 42
  outliers final: 29
  residues processed: 151
  average time/residue: 0.2506
  time to fit residues: 58.1886
Evaluate side-chains
  138 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 1.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  503 TYR
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  927 THR
Chi-restraints excluded: chain B residue  951 LEU
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1400 VAL
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1502 ARG
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   29 LYS
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  184 HIS
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   87 HIS
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue  453 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 129 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0870
   chunk 27 optimal weight:    0.0970
   chunk 166 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0270
   chunk 149 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.3214

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
** B 588 GLN ** 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 = 0.3439 r_free = 0.3439 target = 0.097604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.066444 restraints weight = 32258.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 3.06
r_work: 0.2685 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15152  Z= 0.140
  Angle     :  0.607  11.699  20564  Z= 0.317
  Chirality :  0.041   0.174   2322
  Planarity :  0.004   0.048   2616
  Dihedral  :  4.787  33.066   2029
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.38 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.87 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.20), residues: 1888
  helix:  2.85 (0.16), residues: 950
  sheet: -0.98 (0.31), residues: 238
  loop : -2.71 (0.20), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1524 
 HIS   0.009   0.001   HIS D 126 
 PHE   0.010   0.001   PHE C 150 
 TYR   0.013   0.001   TYR B 517 
 ARG   0.011   0.000   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04465 (  817)
  hydrogen bonds       : angle       3.51115 ( 2379)
  covalent geometry    : bond        0.00317 (15152)
  covalent geometry    : angle       0.60711 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 114
  time to evaluate  : 1.615 
Fit side-chains
REVERT: B  527 ASP cc_start: 0.7022 (t0) cc_final: 0.6731 (p0)
REVERT: B  567 TRP cc_start: 0.8074 (m100) cc_final: 0.7610 (m100)
REVERT: B 1489 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8672 (mm)
REVERT: C   50 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7490 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8457 (pm20) cc_final: 0.8118 (pt0)
REVERT: C  184 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.7846 (p-80)
REVERT: C  240 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8736 (t80)
REVERT: D  221 HIS cc_start: 0.7488 (m-70) cc_final: 0.7231 (m-70)
REVERT: E  456 GLU cc_start: 0.7708 (mp0) cc_final: 0.7494 (mp0)
  outliers start: 45
  outliers final: 34
  residues processed: 151
  average time/residue: 0.2514
  time to fit residues: 58.9311
Evaluate side-chains
  146 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 109
  time to evaluate  : 1.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  503 TYR
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  927 THR
Chi-restraints excluded: chain B residue  951 LEU
Chi-restraints excluded: chain B residue  973 VAL
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1400 VAL
Chi-restraints excluded: chain B residue 1443 LEU
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1502 ARG
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   29 LYS
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  184 HIS
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   87 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue  453 SER
Chi-restraints excluded: chain A residue  103 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 125 optimal weight:    0.8980
   chunk 180 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0000
   chunk 162 optimal weight:    1.9990
   chunk 163 optimal weight:    0.5980
   chunk 160 optimal weight:    0.3980
   chunk 2 optimal weight:    0.8980
   chunk 157 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
D 184 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.095955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.064281 restraints weight = 32195.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.2788 rms_B_bonded: 3.16
r_work: 0.2642 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15152  Z= 0.175
  Angle     :  0.653  16.644  20564  Z= 0.338
  Chirality :  0.043   0.181   2322
  Planarity :  0.004   0.053   2616
  Dihedral  :  4.933  33.671   2029
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.96 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.93 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.20), residues: 1888
  helix:  2.79 (0.16), residues: 950
  sheet: -0.93 (0.31), residues: 238
  loop : -2.72 (0.20), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B1524 
 HIS   0.012   0.001   HIS D 126 
 PHE   0.038   0.002   PHE B1316 
 TYR   0.013   0.001   TYR C 156 
 ARG   0.011   0.001   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05193 (  817)
  hydrogen bonds       : angle       3.62813 ( 2379)
  covalent geometry    : bond        0.00413 (15152)
  covalent geometry    : angle       0.65299 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 111
  time to evaluate  : 1.667 
Fit side-chains
REVERT: B  527 ASP cc_start: 0.6880 (t0) cc_final: 0.6585 (p0)
REVERT: B  567 TRP cc_start: 0.8045 (m100) cc_final: 0.7581 (m100)
REVERT: B  588 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7141 (pm20)
REVERT: B 1489 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8727 (mm)
REVERT: C   50 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7489 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8482 (pm20) cc_final: 0.8124 (pt0)
REVERT: C  184 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.7890 (p-80)
REVERT: C  240 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8716 (t80)
REVERT: D  221 HIS cc_start: 0.7463 (m-70) cc_final: 0.7210 (m-70)
REVERT: E  456 GLU cc_start: 0.7711 (mp0) cc_final: 0.7500 (mp0)
  outliers start: 47
  outliers final: 37
  residues processed: 151
  average time/residue: 0.2507
  time to fit residues: 58.7028
Evaluate side-chains
  149 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 108
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  503 TYR
Chi-restraints excluded: chain B residue  588 GLN
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  920 THR
Chi-restraints excluded: chain B residue  927 THR
Chi-restraints excluded: chain B residue  951 LEU
Chi-restraints excluded: chain B residue  973 VAL
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1400 VAL
Chi-restraints excluded: chain B residue 1443 LEU
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1502 ARG
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   29 LYS
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  184 HIS
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   87 HIS
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue  453 SER
Chi-restraints excluded: chain A residue  103 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 145 optimal weight:    0.7980
   chunk 175 optimal weight:    0.0270
   chunk 3 optimal weight:    3.9990
   chunk 120 optimal weight:    0.7980
   chunk 123 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   chunk 152 optimal weight:    0.8980
   chunk 117 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.094502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.063171 restraints weight = 32121.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 3.02
r_work: 0.2613 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  15152  Z= 0.209
  Angle     :  0.690  15.446  20564  Z= 0.360
  Chirality :  0.044   0.186   2322
  Planarity :  0.005   0.046   2616
  Dihedral  :  5.140  34.904   2029
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.96 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.37 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.20), residues: 1888
  helix:  2.65 (0.16), residues: 951
  sheet: -0.92 (0.32), residues: 250
  loop : -2.80 (0.20), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B1524 
 HIS   0.014   0.001   HIS D 126 
 PHE   0.014   0.002   PHE D   9 
 TYR   0.013   0.001   TYR B 517 
 ARG   0.006   0.001   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05854 (  817)
  hydrogen bonds       : angle       3.76189 ( 2379)
  covalent geometry    : bond        0.00499 (15152)
  covalent geometry    : angle       0.69041 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 112
  time to evaluate  : 1.818 
Fit side-chains
   revert: symmetry clash
REVERT: B  527 ASP cc_start: 0.6769 (t0) cc_final: 0.6531 (p0)
REVERT: B  567 TRP cc_start: 0.8024 (m100) cc_final: 0.7580 (m100)
REVERT: C   50 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7486 (ptp-110)
REVERT: C  184 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.7927 (p-80)
REVERT: C  240 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8848 (t80)
REVERT: D  221 HIS cc_start: 0.7500 (m-70) cc_final: 0.7276 (m-70)
REVERT: D  240 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7624 (t80)
REVERT: E  456 GLU cc_start: 0.7730 (mp0) cc_final: 0.7501 (mp0)
  outliers start: 47
  outliers final: 36
  residues processed: 154
  average time/residue: 0.2695
  time to fit residues: 63.2736
Evaluate side-chains
  148 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 1.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  570 ARG
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  920 THR
Chi-restraints excluded: chain B residue  927 THR
Chi-restraints excluded: chain B residue  951 LEU
Chi-restraints excluded: chain B residue  973 VAL
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1400 VAL
Chi-restraints excluded: chain B residue 1443 LEU
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain B residue 1502 ARG
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   29 LYS
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  184 HIS
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   87 HIS
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue  453 SER
Chi-restraints excluded: chain A residue  120 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 113 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 84 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 150 optimal weight:    0.5980
   chunk 130 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 184 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9980
   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 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
** B 588 GLN ** 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 = 0.3395 r_free = 0.3395 target = 0.094947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.063983 restraints weight = 32021.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.2780 rms_B_bonded: 3.20
r_work: 0.2609 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  15152  Z= 0.192
  Angle     :  0.683  15.762  20564  Z= 0.356
  Chirality :  0.044   0.184   2322
  Planarity :  0.005   0.046   2616
  Dihedral  :  5.125  35.022   2029
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.85 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.81 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.20), residues: 1888
  helix:  2.63 (0.16), residues: 951
  sheet: -0.78 (0.33), residues: 232
  loop : -2.75 (0.20), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 601 
 HIS   0.012   0.001   HIS D 126 
 PHE   0.016   0.002   PHE B 598 
 TYR   0.013   0.001   TYR D 142 
 ARG   0.008   0.001   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05480 (  817)
  hydrogen bonds       : angle       3.73962 ( 2379)
  covalent geometry    : bond        0.00456 (15152)
  covalent geometry    : angle       0.68328 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 110
  time to evaluate  : 1.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  527 ASP cc_start: 0.6702 (t0) cc_final: 0.6500 (p0)
REVERT: B  567 TRP cc_start: 0.8005 (m100) cc_final: 0.7591 (m100)
REVERT: B 1415 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7678 (mpp)
REVERT: B 1489 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8690 (mm)
REVERT: C   50 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7462 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8696 (pp20) cc_final: 0.8241 (pt0)
REVERT: C  184 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.7898 (p-80)
REVERT: C  240 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8834 (t80)
REVERT: D   50 ARG cc_start: 0.8223 (ptp-110) cc_final: 0.7966 (ptp-110)
REVERT: D  203 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8158 (mp10)
REVERT: D  221 HIS cc_start: 0.7517 (m-70) cc_final: 0.7283 (m-70)
REVERT: D  240 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7637 (t80)
  outliers start: 50
  outliers final: 42
  residues processed: 153
  average time/residue: 0.2750
  time to fit residues: 63.6175
Evaluate side-chains
  156 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 108
  time to evaluate  : 1.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  503 TYR
Chi-restraints excluded: chain B residue  570 ARG
Chi-restraints excluded: chain B residue  598 PHE
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  920 THR
Chi-restraints excluded: chain B residue  927 THR
Chi-restraints excluded: chain B residue  951 LEU
Chi-restraints excluded: chain B residue  973 VAL
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1400 VAL
Chi-restraints excluded: chain B residue 1415 MET
Chi-restraints excluded: chain B residue 1443 LEU
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1502 ARG
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   29 LYS
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  184 HIS
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   74 HIS
Chi-restraints excluded: chain D residue   87 HIS
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  289 ILE
Chi-restraints excluded: chain E residue  453 SER
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  194 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 101 optimal weight:    0.4980
   chunk 146 optimal weight:    1.9990
   chunk 173 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   chunk 131 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9990
   chunk 152 optimal weight:    0.6980
   chunk 73 optimal weight:    0.4980
   chunk 120 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 76 optimal weight:    0.1980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 628 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 = 0.3407 r_free = 0.3407 target = 0.095688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.064818 restraints weight = 32082.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 3.24
r_work: 0.2640 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15152  Z= 0.163
  Angle     :  0.658  15.190  20564  Z= 0.342
  Chirality :  0.043   0.180   2322
  Planarity :  0.004   0.045   2616
  Dihedral  :  4.996  33.669   2029
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.59 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.75 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.20), residues: 1888
  helix:  2.72 (0.16), residues: 950
  sheet: -0.74 (0.32), residues: 242
  loop : -2.76 (0.20), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B1524 
 HIS   0.010   0.001   HIS D 126 
 PHE   0.014   0.001   PHE B 598 
 TYR   0.014   0.001   TYR B 517 
 ARG   0.008   0.001   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04889 (  817)
  hydrogen bonds       : angle       3.64049 ( 2379)
  covalent geometry    : bond        0.00380 (15152)
  covalent geometry    : angle       0.65772 (20564)

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

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

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3776 Ramachandran restraints generated.
    1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 113
  time to evaluate  : 1.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  567 TRP cc_start: 0.8030 (m100) cc_final: 0.7604 (m100)
REVERT: B 1415 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7621 (mpp)
REVERT: B 1489 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8697 (mm)
REVERT: C   50 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7518 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8730 (pp20) cc_final: 0.8216 (pt0)
REVERT: C  184 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.7903 (p-80)
REVERT: C  240 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8811 (t80)
REVERT: D   50 ARG cc_start: 0.8252 (ptp-110) cc_final: 0.8024 (ptp-110)
REVERT: D  203 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8142 (mp10)
REVERT: D  221 HIS cc_start: 0.7433 (m-70) cc_final: 0.7219 (m-70)
REVERT: D  240 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7589 (t80)
  outliers start: 50
  outliers final: 39
  residues processed: 157
  average time/residue: 0.2566
  time to fit residues: 61.0563
Evaluate side-chains
  156 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 111
  time to evaluate  : 1.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  503 TYR
Chi-restraints excluded: chain B residue  570 ARG
Chi-restraints excluded: chain B residue  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  920 THR
Chi-restraints excluded: chain B residue  927 THR
Chi-restraints excluded: chain B residue  951 LEU
Chi-restraints excluded: chain B residue  973 VAL
Chi-restraints excluded: chain B residue 1311 ILE
Chi-restraints excluded: chain B residue 1375 LEU
Chi-restraints excluded: chain B residue 1400 VAL
Chi-restraints excluded: chain B residue 1415 MET
Chi-restraints excluded: chain B residue 1443 LEU
Chi-restraints excluded: chain B residue 1462 HIS
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1502 ARG
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   29 LYS
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  184 HIS
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   87 HIS
Chi-restraints excluded: chain D residue  126 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  207 THR
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue  453 SER
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  194 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 142 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 114 optimal weight:    0.2980
   chunk 35 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 148 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 182 optimal weight:    0.0970
   chunk 157 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 628 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 = 0.3396 r_free = 0.3396 target = 0.095037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.064344 restraints weight = 32218.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 2.90
r_work: 0.2641 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  15152  Z= 0.191
  Angle     :  0.684  15.483  20564  Z= 0.357
  Chirality :  0.044   0.213   2322
  Planarity :  0.005   0.045   2616
  Dihedral  :  5.077  34.570   2029
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 10.17 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.06 %
    Favored  : 79.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.20), residues: 1888
  helix:  2.65 (0.16), residues: 949
  sheet: -0.73 (0.32), residues: 242
  loop : -2.78 (0.20), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B1524 
 HIS   0.012   0.001   HIS D 126 
 PHE   0.039   0.002   PHE B1316 
 TYR   0.012   0.001   TYR D 142 
 ARG   0.007   0.001   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05397 (  817)
  hydrogen bonds       : angle       3.71769 ( 2379)
  covalent geometry    : bond        0.00455 (15152)
  covalent geometry    : angle       0.68441 (20564)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9805.32 seconds
wall clock time: 173 minutes 36.94 seconds (10416.94 seconds total)