Starting phenix.real_space_refine
on Tue Nov 18 14:45:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g8r_51137/11_2025/9g8r_51137.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g8r_51137/11_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_51137/11_2025/9g8r_51137.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g8r_51137/11_2025/9g8r_51137.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g8r_51137/11_2025/9g8r_51137.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g8r_51137/11_2025/9g8r_51137.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 3.57, per 1000 atoms: 0.24
  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: 1.23
  Conformation dependent library (CDL) restraints added in 635.7 milliseconds
  

  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: 0.58
  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: 2.88

  Time building geometry restraints manager: 1.59 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:             53.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.210
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   70.550
-------------------------------------------------------------------------------
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 : 10.69
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (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
 ARG   0.024   0.001   ARG B 512 
 TYR   0.042   0.002   TYR B1525 
 PHE   0.022   0.002   PHE C 114 
 TRP   0.034   0.002   TRP B 601 
 HIS   0.011   0.001   HIS D 126 

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

*********************** 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  : 0.694 
Fit side-chains
   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: 0.7187 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1232
  time to fit residues: 30.4630
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  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.4980
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
C  98 GLN
D 126 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.096749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.065691 restraints weight = 32210.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 3.10
r_work: 0.2668 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  15152  Z= 0.229
  Angle     :  0.741  12.140  20564  Z= 0.387
  Chirality :  0.046   0.181   2322
  Planarity :  0.005   0.067   2616
  Dihedral  :  5.035  34.554   2029
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.43 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.66 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.20), residues: 1888
  helix:  2.52 (0.17), residues: 951
  sheet: -1.67 (0.31), residues: 250
  loop : -2.71 (0.20), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 512 
 TYR   0.015   0.002   TYR B 954 
 PHE   0.015   0.002   PHE D 150 
 TRP   0.020   0.002   TRP D  47 
 HIS   0.011   0.002   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (15152)
  covalent geometry    : angle       0.74066 (20564)
  hydrogen bonds       : bond        0.06329 (  817)
  hydrogen bonds       : angle       4.02931 ( 2379)

*********************** 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
  145 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.467 
Fit side-chains
REVERT: B  567 TRP cc_start: 0.8126 (m100) cc_final: 0.7591 (m100)
REVERT: B  598 PHE cc_start: 0.8408 (p90) cc_final: 0.8118 (p90)
REVERT: B  679 MET cc_start: 0.9431 (mtp) cc_final: 0.9217 (mtp)
REVERT: B 1063 MET cc_start: 0.9410 (mmt) cc_final: 0.9210 (mmm)
REVERT: C   50 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7378 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8461 (pm20) cc_final: 0.8090 (pm20)
REVERT: C  184 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.7848 (p-80)
REVERT: E  456 GLU cc_start: 0.7548 (mp0) cc_final: 0.7237 (mp0)
  outliers start: 20
  outliers final: 11
  residues processed: 142
  average time/residue: 0.1300
  time to fit residues: 27.6569
Evaluate side-chains
  124 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  657 MET
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  184 HIS
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 D residue  207 THR
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 138 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0060
   chunk 25 optimal weight:    0.4980
   chunk 112 optimal weight:    0.6980
   chunk 36 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 149 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 50 optimal weight:    0.1980
   chunk 64 optimal weight:    0.2980
   chunk 180 optimal weight:    0.4980
   overall best weight:    0.2796

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
D 126 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.098542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.068484 restraints weight = 32178.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.06
r_work: 0.2697 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8758
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15152  Z= 0.138
  Angle     :  0.638  10.758  20564  Z= 0.331
  Chirality :  0.042   0.180   2322
  Planarity :  0.005   0.052   2616
  Dihedral  :  4.874  33.050   2029
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.53 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.11 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.20), residues: 1888
  helix:  2.63 (0.17), residues: 958
  sheet: -1.35 (0.31), residues: 238
  loop : -2.67 (0.20), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  50 
 TYR   0.014   0.001   TYR B1525 
 PHE   0.010   0.001   PHE B 598 
 TRP   0.014   0.001   TRP D  47 
 HIS   0.008   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (15152)
  covalent geometry    : angle       0.63763 (20564)
  hydrogen bonds       : bond        0.04595 (  817)
  hydrogen bonds       : angle       3.71261 ( 2379)

*********************** 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
  156 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.623 
Fit side-chains
REVERT: B  527 ASP cc_start: 0.7246 (t0) cc_final: 0.6782 (p0)
REVERT: B  567 TRP cc_start: 0.8142 (m100) cc_final: 0.7637 (m100)
REVERT: B  598 PHE cc_start: 0.8446 (p90) cc_final: 0.8160 (p90)
REVERT: B 1293 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7891 (mm-40)
REVERT: B 1489 LEU cc_start: 0.8986 (mm) cc_final: 0.8753 (mm)
REVERT: C   50 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7432 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8449 (pm20) cc_final: 0.8012 (pm20)
REVERT: E  456 GLU cc_start: 0.7654 (mp0) cc_final: 0.7398 (mp0)
  outliers start: 36
  outliers final: 16
  residues processed: 152
  average time/residue: 0.1184
  time to fit residues: 27.6671
Evaluate side-chains
  128 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 TYR
Chi-restraints excluded: chain B residue  927 THR
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 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  125 THR
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  207 THR
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  168 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 114 optimal weight:    0.3980
   chunk 86 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 117 optimal weight:    0.2980
   chunk 51 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 138 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
B 791 GLN
B 825 HIS
B 860 ASN
D  11 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.095860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.065146 restraints weight = 32377.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.89
r_work: 0.2666 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  15152  Z= 0.195
  Angle     :  0.684  17.754  20564  Z= 0.353
  Chirality :  0.044   0.183   2322
  Planarity :  0.005   0.051   2616
  Dihedral  :  5.003  34.647   2029
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.53 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.86 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.20), residues: 1888
  helix:  2.68 (0.16), residues: 952
  sheet: -1.38 (0.31), residues: 246
  loop : -2.79 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  50 
 TYR   0.015   0.001   TYR C 156 
 PHE   0.012   0.002   PHE D 150 
 TRP   0.015   0.001   TRP B1524 
 HIS   0.013   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (15152)
  covalent geometry    : angle       0.68395 (20564)
  hydrogen bonds       : bond        0.05684 (  817)
  hydrogen bonds       : angle       3.76287 ( 2379)

*********************** 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
  154 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: B  527 ASP cc_start: 0.7139 (t0) cc_final: 0.6731 (p0)
REVERT: B  567 TRP cc_start: 0.8112 (m100) cc_final: 0.7631 (m100)
REVERT: B  598 PHE cc_start: 0.8462 (p90) cc_final: 0.8255 (p90)
REVERT: B 1489 LEU cc_start: 0.9019 (mm) cc_final: 0.8693 (mm)
REVERT: C   50 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7358 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8494 (pm20) cc_final: 0.8080 (pm20)
REVERT: C  184 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.7826 (p-80)
REVERT: C  240 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8808 (t80)
REVERT: E  456 GLU cc_start: 0.7591 (mp0) cc_final: 0.7342 (mp0)
  outliers start: 39
  outliers final: 26
  residues processed: 147
  average time/residue: 0.1276
  time to fit residues: 28.2482
Evaluate side-chains
  139 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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  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   29 LYS
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 171 optimal weight:    0.0030
   chunk 10 optimal weight:    0.8980
   chunk 187 optimal weight:    0.0870
   chunk 84 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   chunk 30 optimal weight:    0.5980
   chunk 99 optimal weight:    0.5980
   chunk 125 optimal weight:    0.6980
   chunk 156 optimal weight:    0.1980
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.2368

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.098337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.067419 restraints weight = 32358.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 3.28
r_work: 0.2698 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8758
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15152  Z= 0.127
  Angle     :  0.612  13.616  20564  Z= 0.318
  Chirality :  0.041   0.178   2322
  Planarity :  0.004   0.044   2616
  Dihedral  :  4.805  32.837   2029
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.74 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.99 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.20), residues: 1888
  helix:  2.85 (0.16), residues: 950
  sheet: -1.07 (0.31), residues: 238
  loop : -2.72 (0.20), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  50 
 TYR   0.012   0.001   TYR B1525 
 PHE   0.010   0.001   PHE C 247 
 TRP   0.011   0.001   TRP D  47 
 HIS   0.007   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (15152)
  covalent geometry    : angle       0.61237 (20564)
  hydrogen bonds       : bond        0.04201 (  817)
  hydrogen bonds       : angle       3.55083 ( 2379)

*********************** 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
  149 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: B  527 ASP cc_start: 0.7020 (t0) cc_final: 0.6750 (p0)
REVERT: B  567 TRP cc_start: 0.8109 (m100) cc_final: 0.7606 (m100)
REVERT: B 1489 LEU cc_start: 0.9026 (mm) cc_final: 0.8697 (mm)
REVERT: C   50 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7428 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8483 (pm20) cc_final: 0.8085 (pm20)
REVERT: C  240 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8771 (t80)
REVERT: E  456 GLU cc_start: 0.7633 (mp0) cc_final: 0.7405 (mp0)
  outliers start: 36
  outliers final: 30
  residues processed: 144
  average time/residue: 0.1299
  time to fit residues: 28.3460
Evaluate side-chains
  138 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
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  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  927 THR
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   29 LYS
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  185 THR
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 E residue  453 SER
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  120 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 136 optimal weight:    0.6980
   chunk 78 optimal weight:    0.2980
   chunk 123 optimal weight:    0.9990
   chunk 177 optimal weight:    1.9990
   chunk 163 optimal weight:    0.0010
   chunk 181 optimal weight:    0.2980
   chunk 5 optimal weight:    5.9990
   chunk 133 optimal weight:    0.0020
   chunk 69 optimal weight:    0.9990
   chunk 164 optimal weight:    0.5980
   chunk 159 optimal weight:    1.9990
   overall best weight:    0.2394

-------------------------------------------------------------------------------
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**
B 628 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.098472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.067357 restraints weight = 32022.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 3.08
r_work: 0.2705 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.2604

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= 0.125
  Angle     :  0.602  12.991  20564  Z= 0.311
  Chirality :  0.041   0.175   2322
  Planarity :  0.004   0.044   2616
  Dihedral  :  4.690  31.783   2029
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.63 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.24 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.20), residues: 1888
  helix:  2.92 (0.16), residues: 950
  sheet: -0.98 (0.31), residues: 240
  loop : -2.69 (0.20), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  50 
 TYR   0.012   0.001   TYR B 517 
 PHE   0.032   0.001   PHE B 598 
 TRP   0.010   0.001   TRP D  47 
 HIS   0.006   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (15152)
  covalent geometry    : angle       0.60160 (20564)
  hydrogen bonds       : bond        0.04077 (  817)
  hydrogen bonds       : angle       3.45190 ( 2379)

*********************** 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
  151 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 112
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: B  527 ASP cc_start: 0.7032 (t0) cc_final: 0.6757 (p0)
REVERT: B  567 TRP cc_start: 0.8087 (m100) cc_final: 0.7620 (m100)
REVERT: B 1394 MET cc_start: 0.8933 (tpp) cc_final: 0.8552 (tpt)
REVERT: B 1489 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8691 (mm)
REVERT: C   50 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7449 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8427 (pm20) cc_final: 0.8026 (pm20)
REVERT: C  184 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.7801 (p-80)
REVERT: C  210 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.8996 (m-30)
REVERT: C  240 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8746 (t80)
REVERT: E  456 GLU cc_start: 0.7698 (mp0) cc_final: 0.7493 (mp0)
  outliers start: 39
  outliers final: 31
  residues processed: 145
  average time/residue: 0.1230
  time to fit residues: 27.3665
Evaluate side-chains
  145 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
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  657 MET
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  927 THR
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   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  210 ASP
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 E residue  453 SER
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  120 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 127 optimal weight:    0.1980
   chunk 117 optimal weight:    0.0010
   chunk 107 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 145 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 147 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   overall best weight:    0.4986

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.095504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.064533 restraints weight = 31930.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 3.24
r_work: 0.2633 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15152  Z= 0.181
  Angle     :  0.659  13.612  20564  Z= 0.343
  Chirality :  0.043   0.182   2322
  Planarity :  0.004   0.046   2616
  Dihedral  :  4.976  34.122   2029
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.90 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.75 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.20), residues: 1888
  helix:  2.82 (0.16), residues: 951
  sheet: -0.76 (0.32), residues: 232
  loop : -2.77 (0.20), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  50 
 TYR   0.014   0.001   TYR C 156 
 PHE   0.021   0.002   PHE B 598 
 TRP   0.015   0.001   TRP B1524 
 HIS   0.012   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (15152)
  covalent geometry    : angle       0.65898 (20564)
  hydrogen bonds       : bond        0.05498 (  817)
  hydrogen bonds       : angle       3.65483 ( 2379)

*********************** 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
  157 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 111
  time to evaluate  : 0.461 
Fit side-chains
REVERT: B  527 ASP cc_start: 0.6872 (t0) cc_final: 0.6608 (p0)
REVERT: B  567 TRP cc_start: 0.8043 (m100) cc_final: 0.7660 (m100)
REVERT: B  588 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7174 (pm20)
REVERT: B 1489 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8721 (mm)
REVERT: C   50 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7431 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8471 (pm20) cc_final: 0.8080 (pm20)
REVERT: C  184 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.7926 (p-80)
REVERT: C  240 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8745 (t80)
REVERT: D  221 HIS cc_start: 0.7458 (m-70) cc_final: 0.7218 (m-70)
REVERT: E  456 GLU cc_start: 0.7696 (mp0) cc_final: 0.7477 (mp0)
  outliers start: 46
  outliers final: 37
  residues processed: 148
  average time/residue: 0.1221
  time to fit residues: 27.6003
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  : 0.590 
-------------------------------------------------------------------------------
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  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   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
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  120 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 131 optimal weight:    0.5980
   chunk 108 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 48 optimal weight:    0.0970
   chunk 71 optimal weight:    0.3980
   chunk 61 optimal weight:    0.0870
   chunk 8 optimal weight:    0.2980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.2556

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
A  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.097867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.066368 restraints weight = 31930.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 3.18
r_work: 0.2684 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.2883

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= 0.129
  Angle     :  0.614  12.561  20564  Z= 0.318
  Chirality :  0.041   0.175   2322
  Planarity :  0.004   0.043   2616
  Dihedral  :  4.787  31.653   2029
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.74 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.12 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.20), residues: 1888
  helix:  2.91 (0.16), residues: 950
  sheet: -0.71 (0.32), residues: 230
  loop : -2.68 (0.20), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  50 
 TYR   0.013   0.001   TYR B 517 
 PHE   0.026   0.001   PHE B 598 
 TRP   0.011   0.001   TRP B1524 
 HIS   0.007   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (15152)
  covalent geometry    : angle       0.61378 (20564)
  hydrogen bonds       : bond        0.04172 (  817)
  hydrogen bonds       : angle       3.47560 ( 2379)

*********************** 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
  155 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 112
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
REVERT: B  567 TRP cc_start: 0.8041 (m100) cc_final: 0.7602 (m100)
REVERT: B  588 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7225 (pm20)
REVERT: B  611 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7212 (ttp-110)
REVERT: B 1489 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8741 (mm)
REVERT: C   50 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7468 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8398 (pm20) cc_final: 0.8037 (pm20)
REVERT: C  184 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7921 (p-80)
REVERT: C  240 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8774 (t80)
REVERT: D   50 ARG cc_start: 0.8238 (ptp-110) cc_final: 0.7970 (ptp-110)
REVERT: D  221 HIS cc_start: 0.7452 (m-70) cc_final: 0.7123 (m170)
REVERT: E  456 GLU cc_start: 0.7711 (mp0) cc_final: 0.7495 (mp0)
  outliers start: 43
  outliers final: 35
  residues processed: 149
  average time/residue: 0.1220
  time to fit residues: 27.3980
Evaluate side-chains
  150 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 111
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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  588 GLN
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 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  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  248 VAL
Chi-restraints excluded: chain E residue  453 SER
Chi-restraints excluded: chain A residue  119 VAL
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 61 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 135 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 71 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 176 optimal weight:    0.0980
   chunk 62 optimal weight:    0.3980
   chunk 156 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.096744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.065500 restraints weight = 32265.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 3.07
r_work: 0.2672 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15152  Z= 0.149
  Angle     :  0.632  12.418  20564  Z= 0.328
  Chirality :  0.042   0.229   2322
  Planarity :  0.004   0.044   2616
  Dihedral  :  4.806  31.947   2029
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.43 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.06 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.20), residues: 1888
  helix:  2.88 (0.16), residues: 952
  sheet: -0.76 (0.32), residues: 234
  loop : -2.70 (0.20), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  50 
 TYR   0.010   0.001   TYR D 301 
 PHE   0.041   0.002   PHE B1316 
 TRP   0.012   0.001   TRP B1524 
 HIS   0.008   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (15152)
  covalent geometry    : angle       0.63169 (20564)
  hydrogen bonds       : bond        0.04565 (  817)
  hydrogen bonds       : angle       3.50618 ( 2379)

*********************** 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
  157 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 113
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
REVERT: B  567 TRP cc_start: 0.8033 (m100) cc_final: 0.7624 (m100)
REVERT: B  588 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7245 (pm20)
REVERT: B  611 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7213 (ttp-110)
REVERT: B  628 ASN cc_start: 0.8467 (m-40) cc_final: 0.8252 (m-40)
REVERT: B 1489 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8743 (mm)
REVERT: C   50 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7473 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8400 (pm20) cc_final: 0.7995 (pm20)
REVERT: C  184 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.7953 (p-80)
REVERT: C  240 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8776 (t80)
REVERT: D   50 ARG cc_start: 0.8246 (ptp-110) cc_final: 0.8024 (ptp-110)
REVERT: D  221 HIS cc_start: 0.7355 (m-70) cc_final: 0.7068 (m170)
REVERT: E  456 GLU cc_start: 0.7721 (mp0) cc_final: 0.7512 (mp0)
  outliers start: 44
  outliers final: 37
  residues processed: 150
  average time/residue: 0.1230
  time to fit residues: 28.0010
Evaluate side-chains
  152 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
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  588 GLN
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 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  119 VAL
Chi-restraints excluded: chain A residue  120 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 172 optimal weight:    0.7980
   chunk 150 optimal weight:    0.0000
   chunk 187 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 151 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0170
   chunk 102 optimal weight:    0.2980
   overall best weight:    0.3022

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.097489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.066452 restraints weight = 31989.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 3.05
r_work: 0.2686 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  15152  Z= 0.139
  Angle     :  0.628  12.400  20564  Z= 0.325
  Chirality :  0.042   0.218   2322
  Planarity :  0.004   0.044   2616
  Dihedral  :  4.790  31.288   2029
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.06 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.25 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.20), residues: 1888
  helix:  2.91 (0.16), residues: 952
  sheet: -0.84 (0.31), residues: 250
  loop : -2.73 (0.20), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  50 
 TYR   0.014   0.001   TYR D 301 
 PHE   0.015   0.001   PHE B 598 
 TRP   0.017   0.001   TRP B 601 
 HIS   0.017   0.001   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (15152)
  covalent geometry    : angle       0.62811 (20564)
  hydrogen bonds       : bond        0.04303 (  817)
  hydrogen bonds       : angle       3.48213 ( 2379)

********************** 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
  155 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 111
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  567 TRP cc_start: 0.8020 (m100) cc_final: 0.7626 (m100)
REVERT: B  588 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7238 (pm20)
REVERT: B  611 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.7243 (ttp-110)
REVERT: B 1489 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8744 (mm)
REVERT: C   50 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7474 (ptp-110)
REVERT: C   61 GLU cc_start: 0.8368 (pm20) cc_final: 0.7971 (pm20)
REVERT: C  184 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.7923 (p-80)
REVERT: C  240 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8784 (t80)
REVERT: D   50 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.8084 (ptp-110)
REVERT: D  221 HIS cc_start: 0.7345 (m-70) cc_final: 0.7049 (m170)
REVERT: E  456 GLU cc_start: 0.7712 (mp0) cc_final: 0.7506 (mp0)
  outliers start: 44
  outliers final: 38
  residues processed: 149
  average time/residue: 0.1266
  time to fit residues: 28.6924
Evaluate side-chains
  152 residues out of total 1594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 110
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
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  588 GLN
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  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  119 VAL
Chi-restraints excluded: chain A residue  120 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 173 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   chunk 157 optimal weight:    1.9990
   chunk 156 optimal weight:    0.0370
   chunk 82 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 172 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   chunk 139 optimal weight:    0.0870
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
B 501 HIS
B 860 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.095868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.064604 restraints weight = 31895.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 3.04
r_work: 0.2646 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15152  Z= 0.174
  Angle     :  0.662  12.734  20564  Z= 0.343
  Chirality :  0.043   0.229   2322
  Planarity :  0.004   0.046   2616
  Dihedral  :  4.930  33.051   2029
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.85 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.44 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.20), residues: 1888
  helix:  2.83 (0.16), residues: 952
  sheet: -0.78 (0.32), residues: 250
  loop : -2.77 (0.20), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  50 
 TYR   0.013   0.001   TYR B 517 
 PHE   0.042   0.002   PHE B1316 
 TRP   0.014   0.001   TRP B1524 
 HIS   0.017   0.001   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (15152)
  covalent geometry    : angle       0.66214 (20564)
  hydrogen bonds       : bond        0.05112 (  817)
  hydrogen bonds       : angle       3.59275 ( 2379)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3986.07 seconds
wall clock time: 69 minutes 34.96 seconds (4174.96 seconds total)