Starting phenix.real_space_refine
on Thu Feb 13 04:19:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jlu_22380/02_2025/7jlu_22380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jlu_22380/02_2025/7jlu_22380.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jlu_22380/02_2025/7jlu_22380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jlu_22380/02_2025/7jlu_22380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jlu_22380/02_2025/7jlu_22380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jlu_22380/02_2025/7jlu_22380.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      52      5.16       5
     C    5499      2.51       5
     N    1460      2.21       5
     O    1580      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8592
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 726, 5884
          Classifications: {'peptide': 726}
          Link IDs: {'PTRANS': 31, 'TRANS': 694}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2707
          Classifications: {'peptide': 353}
          Link IDs: {'PTRANS': 24, 'TRANS': 328}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.00, per 1000 atoms: 0.81
  Number of scatterers: 8592
  At special positions: 0
  Unit cell: (96.6758, 108.878, 94.7986, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      52     16.00
     O    1580      8.00
     N    1460      7.00
     C    5499      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: 2.07
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      31.7% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 540 through 546
      removed outlier: 3.885A  pdb=" N   TYR A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 554
    Processing helix  chain 'A' and resid 663 through 669
      removed outlier: 3.549A  pdb=" N   LEU A 669 " --> pdb=" O   VAL A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 742
      removed outlier: 3.853A  pdb=" N   ILE A 736 " --> pdb=" O   PRO A 733 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLU A 737 " --> pdb=" O   ALA A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 763
    Processing helix  chain 'A' and resid 803 through 808
      removed outlier: 3.638A  pdb=" N   ASN A 806 " --> pdb=" O   SER A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 831
      removed outlier: 3.658A  pdb=" N   GLY A 830 " --> pdb=" O   SER A 827 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU A 831 " --> pdb=" O   ILE A 828 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 827 through 831'
    Processing helix  chain 'A' and resid 896 through 901
      removed outlier: 3.827A  pdb=" N   ILE A 899 " --> pdb=" O   PRO A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 949
      removed outlier: 3.520A  pdb=" N   LEU A 949 " --> pdb=" O   VAL A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 976
      removed outlier: 3.855A  pdb=" N   LEU A 976 " --> pdb=" O   SER A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 981
    Processing helix  chain 'A' and resid 1044 through 1052
      removed outlier: 3.590A  pdb=" N   MET A1048 " --> pdb=" O   ALA A1044 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU A1049 " --> pdb=" O   LEU A1045 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1072
      removed outlier: 4.007A  pdb=" N   TYR A1072 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1079
      removed outlier: 3.570A  pdb=" N   ILE A1078 " --> pdb=" O   LEU A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1100
      removed outlier: 4.271A  pdb=" N   GLU A1087 " --> pdb=" O   SER A1083 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASN A1088 " --> pdb=" O   GLU A1084 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN A1090 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   GLN A1092 " --> pdb=" O   ASN A1088 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   GLN A1093 " --> pdb=" O   SER A1089 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A1095 " --> pdb=" O   LYS A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1149
      removed outlier: 4.141A  pdb=" N   THR A1148 " --> pdb=" O   TYR A1145 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLU A1149 " --> pdb=" O   TRP A1146 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1145 through 1149'
    Processing helix  chain 'A' and resid 1166 through 1178
      removed outlier: 3.629A  pdb=" N   ASP A1170 " --> pdb=" O   ALA A1166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1183 through 1190
      removed outlier: 3.716A  pdb=" N   GLU A1189 " --> pdb=" O   TYR A1186 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR A1190 " --> pdb=" O   TRP A1187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 103
    Processing helix  chain 'B' and resid 121 through 136
      removed outlier: 3.706A  pdb=" N   VAL B 125 " --> pdb=" O   PRO B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 168
    Processing helix  chain 'B' and resid 184 through 192
    Processing helix  chain 'B' and resid 195 through 199
      removed outlier: 3.517A  pdb=" N   GLY B 198 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 223
      removed outlier: 3.570A  pdb=" N   GLU B 218 " --> pdb=" O   ARG B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 243
    Processing helix  chain 'B' and resid 245 through 252
    Processing helix  chain 'B' and resid 278 through 284
      removed outlier: 4.160A  pdb=" N   ASP B 284 " --> pdb=" O   ASN B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 298
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'B' and resid 317 through 325
      removed outlier: 3.600A  pdb=" N   GLU B 321 " --> pdb=" O   PRO B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 350
      removed outlier: 3.656A  pdb=" N   GLN B 350 " --> pdb=" O   TRP B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 353
      No H-bonds generated for 'chain 'B' and resid 351 through 353'
    Processing helix  chain 'B' and resid 358 through 366
    Processing helix  chain 'B' and resid 384 through 389
    Processing helix  chain 'B' and resid 390 through 392
      No H-bonds generated for 'chain 'B' and resid 390 through 392'
    Processing helix  chain 'B' and resid 398 through 407
      removed outlier: 3.911A  pdb=" N   THR B 402 " --> pdb=" O   TYR B 398 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 415
      removed outlier: 3.895A  pdb=" N   ARG B 412 " --> pdb=" O   PRO B 408 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   LEU B 413 " --> pdb=" O   GLY B 409 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU B 414 " --> pdb=" O   ALA B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 452
    Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 531
      removed outlier: 3.625A  pdb=" N   LEU A 529 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 561 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 531 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU A 560 " --> pdb=" O   GLU A 584 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LEU A 605 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   SER A 631 " --> pdb=" O   LEU A 605 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   MET A 607 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690
      removed outlier: 3.805A  pdb=" N   ILE A 690 " --> pdb=" O   GLU A 711 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 744 through 748
      removed outlier: 7.046A  pdb=" N   VAL A 795 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU A 790 " --> pdb=" O   GLU A 814 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   CYS A 816 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LEU A 792 " --> pdb=" O   CYS A 816 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU A 813 " --> pdb=" O   LYS A 838 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   LEU A 840 " --> pdb=" O   LEU A 813 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ILE A 815 " --> pdb=" O   LEU A 840 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ILE A 884 " --> pdb=" O   CYS A 909 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   SER A 911 " --> pdb=" O   ILE A 884 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   MET A 886 " --> pdb=" O   SER A 911 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASP A1040 " --> pdb=" O   ILE A1018 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   HIS A1120 " --> pdb=" O   VAL A1063 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A1238 " --> pdb=" O   PHE A1162 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   PHE A1162 " --> pdb=" O   VAL A1238 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A1246 " --> pdb=" O   PHE A1154 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   PHE A1154 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLY A1153 " --> pdb=" O   VAL A1289 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL A1289 " --> pdb=" O   GLY A1153 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA A1155 " --> pdb=" O   ASN A1287 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASN A1287 " --> pdb=" O   ALA A1155 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1139 through 1140
      removed outlier: 3.590A  pdb=" N   CYS A1271 " --> pdb=" O   THR A1206 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS A1223 " --> pdb=" O   ALA A1207 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 174 through 176
      removed outlier: 5.398A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   LEU B 141 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   THR B 111 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   ASP B 143 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASP B 110 " --> pdb=" O   GLY B 228 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   VAL B 230 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LEU B 112 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LEU B 227 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE B 256 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   MET B 229 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   ILE B 258 " --> pdb=" O   MET B 229 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL B 231 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   ARG B 303 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ILE B 256 " --> pdb=" O   ARG B 303 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   LEU B 305 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE B 258 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   LEU B 302 " --> pdb=" O   GLU B 429 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   VAL B 431 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE B 304 " --> pdb=" O   VAL B 431 " (cutoff:3.500A)

    263 hydrogen bonds defined for protein.
    699 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: 3.10

  Time building geometry restraints manager: 2.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2793
        1.34 -     1.46: 1911
        1.46 -     1.58: 3998
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8780
  Sorted by residual:
  bond pdb=" N   THR A1136 "
       pdb=" CA  THR A1136 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.20e+00
  bond pdb=" CA  THR B 147 "
       pdb=" C   THR B 147 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.24e-02 6.50e+03 8.96e-01
  bond pdb=" CB  GLU B 251 "
       pdb=" CG  GLU B 251 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.43e-01
  bond pdb=" CA  ASN A 744 "
       pdb=" CB  ASN A 744 "
    ideal  model  delta    sigma   weight residual
    1.535  1.554 -0.019 2.09e-02 2.29e+03 8.33e-01
  bond pdb=" CB  ASP B 150 "
       pdb=" CG  ASP B 150 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.91e-01
  ... (remaining 8775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 11613
        2.30 -     4.59: 257
        4.59 -     6.89: 28
        6.89 -     9.19: 6
        9.19 -    11.49: 1
  Bond angle restraints: 11905
  Sorted by residual:
  angle pdb=" CA  LEU B 334 "
        pdb=" CB  LEU B 334 "
        pdb=" CG  LEU B 334 "
      ideal   model   delta    sigma   weight residual
     116.30  127.79  -11.49 3.50e+00 8.16e-02 1.08e+01
  angle pdb=" CA  GLU B 251 "
        pdb=" CB  GLU B 251 "
        pdb=" CG  GLU B 251 "
      ideal   model   delta    sigma   weight residual
     114.10  120.41   -6.31 2.00e+00 2.50e-01 9.95e+00
  angle pdb=" CB  MET A1241 "
        pdb=" CG  MET A1241 "
        pdb=" SD  MET A1241 "
      ideal   model   delta    sigma   weight residual
     112.70  120.82   -8.12 3.00e+00 1.11e-01 7.33e+00
  angle pdb=" CB  MET B 383 "
        pdb=" CG  MET B 383 "
        pdb=" SD  MET B 383 "
      ideal   model   delta    sigma   weight residual
     112.70  120.76   -8.06 3.00e+00 1.11e-01 7.22e+00
  angle pdb=" C   ALA B 351 "
        pdb=" N   ASN B 352 "
        pdb=" CA  ASN B 352 "
      ideal   model   delta    sigma   weight residual
     121.54  126.63   -5.09 1.91e+00 2.74e-01 7.09e+00
  ... (remaining 11900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4548
       17.96 -    35.92: 634
       35.92 -    53.89: 117
       53.89 -    71.85: 18
       71.85 -    89.81: 7
  Dihedral angle restraints: 5324
    sinusoidal: 2162
      harmonic: 3162
  Sorted by residual:
  dihedral pdb=" CA  SER A 590 "
           pdb=" C   SER A 590 "
           pdb=" N   ASN A 591 "
           pdb=" CA  ASN A 591 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.98  -22.02     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  TRP A 900 "
           pdb=" C   TRP A 900 "
           pdb=" N   MET A 901 "
           pdb=" CA  MET A 901 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.61   19.39     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  ARG A1133 "
           pdb=" C   ARG A1133 "
           pdb=" N   SER A1134 "
           pdb=" CA  SER A1134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 777
       0.033 -    0.066: 367
       0.066 -    0.099: 137
       0.099 -    0.131: 60
       0.131 -    0.164: 9
  Chirality restraints: 1350
  Sorted by residual:
  chirality pdb=" CA  GLU A 743 "
            pdb=" N   GLU A 743 "
            pdb=" C   GLU A 743 "
            pdb=" CB  GLU A 743 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.74e-01
  chirality pdb=" CG  LEU A 630 "
            pdb=" CB  LEU A 630 "
            pdb=" CD1 LEU A 630 "
            pdb=" CD2 LEU A 630 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.35e-01
  chirality pdb=" CB  THR A1299 "
            pdb=" CA  THR A1299 "
            pdb=" OG1 THR A1299 "
            pdb=" CG2 THR A1299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.56e-01
  ... (remaining 1347 not shown)

  Planarity restraints: 1515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 900 "    0.017 2.00e-02 2.50e+03   1.46e-02 5.32e+00
        pdb=" CG  TRP A 900 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 900 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 900 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 900 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 900 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 900 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 900 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 900 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 900 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 800 "   -0.029 5.00e-02 4.00e+02   4.34e-02 3.01e+00
        pdb=" N   PRO A 801 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 801 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 801 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 385 "   -0.006 2.00e-02 2.50e+03   1.22e-02 2.59e+00
        pdb=" CG  PHE B 385 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 385 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 385 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 385 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 385 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 385 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1512 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 475
        2.73 -     3.27: 8625
        3.27 -     3.81: 13132
        3.81 -     4.36: 15685
        4.36 -     4.90: 26632
  Nonbonded interactions: 64549
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1080 "
            pdb=" OD1 ASP A1081 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O   LEU A 551 "
            pdb=" OG1 THR A 554 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OD1 ASP A1040 "
            pdb=" N   GLU A1041 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   GLU A 543 "
            pdb=" OG  SER A 547 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR B 418 "
            pdb=" OE1 GLU B 435 "
     model   vdw
     2.269 3.040
  ... (remaining 64544 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.210
  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:             0.000
  Extract box with map and model:          1.620
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     23.020
  Find NCS groups from input model:        0.110
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
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   0.031   8780  Z= 0.193
  Angle     :  0.780  11.487  11905  Z= 0.392
  Chirality :  0.046   0.164   1350
  Planarity :  0.004   0.043   1515
  Dihedral  : 16.633  89.810   3272
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.42 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.26), residues: 1067
  helix:  0.08 (0.35), residues: 246
  sheet:  0.28 (0.37), residues: 203
  loop : -2.08 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 900 
 HIS   0.008   0.001   HIS B 430 
 PHE   0.026   0.002   PHE B 385 
 TYR   0.020   0.002   TYR A1186 
 ARG   0.020   0.001   ARG A 882 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: A  551 LEU cc_start: 0.7731 (mm) cc_final: 0.7458 (mt)
REVERT: A  586 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7289 (mtp180)
REVERT: A  607 MET cc_start: 0.6620 (mmm) cc_final: 0.6395 (mtt)
REVERT: A  677 MET cc_start: 0.8016 (mmt) cc_final: 0.7815 (mmt)
REVERT: A 1138 MET cc_start: 0.7502 (ttt) cc_final: 0.7211 (ttt)
  outliers start: 2
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1994
  time to fit residues: 29.7039
Evaluate side-chains
  84 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0000
   chunk 27 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0070
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.6008

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1090 GLN
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 HIS
B 328 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.113816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.101354 restraints weight = 18562.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.103908 restraints weight = 9768.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.105620 restraints weight = 6074.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8780  Z= 0.261
  Angle     :  0.690   7.106  11905  Z= 0.350
  Chirality :  0.047   0.165   1350
  Planarity :  0.005   0.051   1515
  Dihedral  :  5.201  31.837   1177
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.00 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.26), residues: 1067
  helix: -0.21 (0.32), residues: 258
  sheet:  0.20 (0.37), residues: 217
  loop : -2.03 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 582 
 HIS   0.006   0.001   HIS B 430 
 PHE   0.022   0.002   PHE A 704 
 TYR   0.014   0.002   TYR A1145 
 ARG   0.005   0.001   ARG A1233 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A  584 GLU cc_start: 0.7452 (mp0) cc_final: 0.7171 (mp0)
REVERT: A  677 MET cc_start: 0.8214 (mmt) cc_final: 0.7846 (mmt)
REVERT: A 1040 ASP cc_start: 0.8570 (t0) cc_final: 0.8368 (t0)
REVERT: B  107 LEU cc_start: 0.7787 (mp) cc_final: 0.7492 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1769
  time to fit residues: 23.5394
Evaluate side-chains
  86 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain B residue  148 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 103 HIS
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.108869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.096659 restraints weight = 18964.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.099143 restraints weight = 9851.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.100805 restraints weight = 6108.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8780  Z= 0.356
  Angle     :  0.712   7.101  11905  Z= 0.370
  Chirality :  0.048   0.160   1350
  Planarity :  0.005   0.056   1515
  Dihedral  :  5.324  23.162   1173
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.00 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.25), residues: 1067
  helix: -0.45 (0.31), residues: 265
  sheet: -0.17 (0.37), residues: 215
  loop : -2.33 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 582 
 HIS   0.006   0.001   HIS A 663 
 PHE   0.022   0.002   PHE A 704 
 TYR   0.015   0.002   TYR A1186 
 ARG   0.004   0.001   ARG A1233 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8259 (mmt) cc_final: 0.7868 (mmt)
REVERT: A  718 HIS cc_start: 0.7280 (OUTLIER) cc_final: 0.7058 (m-70)
REVERT: A 1040 ASP cc_start: 0.8622 (t0) cc_final: 0.8341 (t0)
REVERT: B  107 LEU cc_start: 0.7850 (mp) cc_final: 0.7611 (mt)
REVERT: B  235 MET cc_start: 0.7725 (mtt) cc_final: 0.7332 (mtt)
  outliers start: 22
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1768
  time to fit residues: 24.5990
Evaluate side-chains
  92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.109354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.097128 restraints weight = 18860.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.099640 restraints weight = 9866.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.101281 restraints weight = 6103.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8780  Z= 0.273
  Angle     :  0.658   7.483  11905  Z= 0.340
  Chirality :  0.046   0.149   1350
  Planarity :  0.005   0.056   1515
  Dihedral  :  5.181  25.212   1173
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.79 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.25), residues: 1067
  helix: -0.37 (0.31), residues: 272
  sheet: -0.28 (0.37), residues: 215
  loop : -2.45 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 900 
 HIS   0.006   0.001   HIS A 663 
 PHE   0.022   0.002   PHE A 704 
 TYR   0.016   0.002   TYR A 575 
 ARG   0.005   0.000   ARG A 621 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8251 (mmt) cc_final: 0.7927 (mmt)
REVERT: A  718 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.7041 (m-70)
REVERT: A 1040 ASP cc_start: 0.8603 (t0) cc_final: 0.8262 (t0)
REVERT: A 1229 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7325 (tmm)
REVERT: A 1302 MET cc_start: 0.5534 (mtt) cc_final: 0.5127 (mmm)
REVERT: B  107 LEU cc_start: 0.7886 (mp) cc_final: 0.7639 (mt)
REVERT: B  305 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7714 (mp)
  outliers start: 22
  outliers final: 13
  residues processed: 95
  average time/residue: 0.1775
  time to fit residues: 25.3082
Evaluate side-chains
  92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1101 ILE
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1178 HIS
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.111990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.099767 restraints weight = 18617.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.102300 restraints weight = 9637.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.103976 restraints weight = 5964.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8780  Z= 0.175
  Angle     :  0.608   9.969  11905  Z= 0.307
  Chirality :  0.045   0.145   1350
  Planarity :  0.004   0.053   1515
  Dihedral  :  4.852  24.600   1173
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.58 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.26), residues: 1067
  helix: -0.31 (0.32), residues: 282
  sheet: -0.15 (0.37), residues: 213
  loop : -2.38 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A1279 
 PHE   0.020   0.001   PHE A 704 
 TYR   0.013   0.001   TYR A 575 
 ARG   0.006   0.000   ARG A 621 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: A  718 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6923 (m-70)
REVERT: A 1040 ASP cc_start: 0.8596 (t0) cc_final: 0.8222 (t0)
REVERT: A 1229 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7311 (tmm)
REVERT: A 1302 MET cc_start: 0.5551 (mtt) cc_final: 0.5172 (mmm)
REVERT: B  107 LEU cc_start: 0.7890 (mp) cc_final: 0.7660 (mt)
  outliers start: 26
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1707
  time to fit residues: 27.6145
Evaluate side-chains
  99 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1178 HIS
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0470
   chunk 40 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 96 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.5684

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1070 ASN
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS
B 350 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.111250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.099832 restraints weight = 18468.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.102219 restraints weight = 9599.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.103804 restraints weight = 5846.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8780  Z= 0.249
  Angle     :  0.647   8.637  11905  Z= 0.328
  Chirality :  0.045   0.153   1350
  Planarity :  0.005   0.053   1515
  Dihedral  :  4.954  23.775   1173
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 21.58 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.26), residues: 1067
  helix: -0.15 (0.32), residues: 272
  sheet: -0.50 (0.36), residues: 226
  loop : -2.32 (0.25), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 900 
 HIS   0.009   0.001   HIS A1178 
 PHE   0.021   0.002   PHE A 704 
 TYR   0.015   0.001   TYR A 575 
 ARG   0.006   0.000   ARG A 621 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A  677 MET cc_start: 0.8250 (mmt) cc_final: 0.7766 (mmt)
REVERT: A  718 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6908 (m-70)
REVERT: A 1040 ASP cc_start: 0.8581 (t0) cc_final: 0.8209 (t0)
REVERT: A 1070 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7856 (p0)
REVERT: A 1229 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7345 (tmm)
REVERT: A 1302 MET cc_start: 0.5633 (mtt) cc_final: 0.5321 (mmm)
REVERT: B  107 LEU cc_start: 0.7890 (mp) cc_final: 0.7635 (mt)
REVERT: B  305 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7718 (mp)
  outliers start: 34
  outliers final: 21
  residues processed: 108
  average time/residue: 0.1618
  time to fit residues: 26.3544
Evaluate side-chains
  106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1070 ASN
Chi-restraints excluded: chain A residue 1101 ILE
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain A residue 1271 CYS
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 0 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   chunk 94 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 104 optimal weight:    0.2980
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1070 ASN
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.112687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.100518 restraints weight = 18676.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.103076 restraints weight = 9630.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.104770 restraints weight = 5928.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8780  Z= 0.156
  Angle     :  0.619  12.555  11905  Z= 0.308
  Chirality :  0.045   0.144   1350
  Planarity :  0.004   0.052   1515
  Dihedral  :  4.785  24.484   1173
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.53 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.26), residues: 1067
  helix: -0.09 (0.33), residues: 270
  sheet: -0.16 (0.37), residues: 215
  loop : -2.33 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 900 
 HIS   0.002   0.001   HIS A 663 
 PHE   0.019   0.001   PHE A 704 
 TYR   0.014   0.001   TYR A 575 
 ARG   0.006   0.000   ARG A 621 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 84
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A  677 MET cc_start: 0.8177 (mmt) cc_final: 0.7652 (mmt)
REVERT: A  718 HIS cc_start: 0.7172 (OUTLIER) cc_final: 0.6881 (m-70)
REVERT: A 1040 ASP cc_start: 0.8566 (t0) cc_final: 0.8177 (t0)
REVERT: A 1229 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7331 (tmm)
REVERT: A 1302 MET cc_start: 0.5527 (mtt) cc_final: 0.5247 (mmm)
REVERT: B  107 LEU cc_start: 0.7886 (mp) cc_final: 0.7659 (mt)
REVERT: B  305 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7718 (mp)
  outliers start: 33
  outliers final: 22
  residues processed: 110
  average time/residue: 0.1711
  time to fit residues: 28.4340
Evaluate side-chains
  105 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1070 ASN
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain A residue 1271 CYS
Chi-restraints excluded: chain B residue  103 HIS
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0670
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.1980
   chunk 10 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.1722

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1070 ASN
A1178 HIS
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.112196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.100604 restraints weight = 18713.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.103042 restraints weight = 9574.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.104649 restraints weight = 5818.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8780  Z= 0.201
  Angle     :  0.625  11.376  11905  Z= 0.313
  Chirality :  0.045   0.148   1350
  Planarity :  0.004   0.051   1515
  Dihedral  :  4.779  23.185   1173
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.63 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.26), residues: 1067
  helix: -0.02 (0.33), residues: 269
  sheet: -0.15 (0.37), residues: 215
  loop : -2.31 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A 663 
 PHE   0.020   0.001   PHE A 704 
 TYR   0.014   0.001   TYR A 575 
 ARG   0.007   0.000   ARG A 621 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 78
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
REVERT: A  677 MET cc_start: 0.8182 (mmt) cc_final: 0.7665 (mmt)
REVERT: A  718 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6867 (m-70)
REVERT: A 1040 ASP cc_start: 0.8578 (t0) cc_final: 0.8193 (t0)
REVERT: A 1229 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7335 (tmm)
REVERT: A 1302 MET cc_start: 0.5514 (mtt) cc_final: 0.5235 (mmm)
REVERT: B  107 LEU cc_start: 0.7864 (mp) cc_final: 0.7643 (mt)
REVERT: B  235 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7186 (mtt)
REVERT: B  305 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7736 (mp)
  outliers start: 35
  outliers final: 25
  residues processed: 105
  average time/residue: 0.1654
  time to fit residues: 26.4582
Evaluate side-chains
  106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1070 ASN
Chi-restraints excluded: chain A residue 1178 HIS
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain A residue 1271 CYS
Chi-restraints excluded: chain B residue  103 HIS
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0970
   chunk 46 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0370
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.106854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.094091 restraints weight = 19259.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.096661 restraints weight = 10095.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.098364 restraints weight = 6210.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8780  Z= 0.139
  Angle     :  0.612  11.215  11905  Z= 0.303
  Chirality :  0.044   0.141   1350
  Planarity :  0.004   0.050   1515
  Dihedral  :  4.625  23.762   1173
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 23.37 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.26), residues: 1067
  helix:  0.00 (0.33), residues: 269
  sheet: -0.12 (0.37), residues: 215
  loop : -2.19 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 900 
 HIS   0.006   0.001   HIS A1178 
 PHE   0.019   0.001   PHE A 704 
 TYR   0.011   0.001   TYR A 575 
 ARG   0.007   0.000   ARG A 621 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A  584 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7450 (mp0)
REVERT: A  718 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.7026 (m-70)
REVERT: A 1040 ASP cc_start: 0.8570 (t0) cc_final: 0.8147 (t0)
REVERT: A 1178 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.7162 (t-90)
REVERT: A 1229 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7247 (tmm)
REVERT: A 1302 MET cc_start: 0.5526 (mtt) cc_final: 0.5232 (mmm)
REVERT: B  107 LEU cc_start: 0.7938 (mp) cc_final: 0.7737 (mt)
REVERT: B  305 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7580 (mp)
  outliers start: 27
  outliers final: 19
  residues processed: 102
  average time/residue: 0.1744
  time to fit residues: 27.1316
Evaluate side-chains
  101 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain A residue  584 GLU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1178 HIS
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain A residue 1271 CYS
Chi-restraints excluded: chain B residue  103 HIS
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0040
   chunk 6 optimal weight:    0.0770
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0870
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.2928

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.116353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.104014 restraints weight = 18563.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.106662 restraints weight = 9631.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.108378 restraints weight = 5895.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8780  Z= 0.132
  Angle     :  0.615  12.061  11905  Z= 0.299
  Chirality :  0.044   0.139   1350
  Planarity :  0.004   0.049   1515
  Dihedral  :  4.416  21.912   1173
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 24.32 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.26), residues: 1067
  helix:  0.22 (0.34), residues: 261
  sheet: -0.13 (0.37), residues: 221
  loop : -2.06 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 900 
 HIS   0.002   0.000   HIS A1279 
 PHE   0.018   0.001   PHE A 704 
 TYR   0.010   0.001   TYR A1145 
 ARG   0.007   0.000   ARG A 621 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
REVERT: A  661 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7317 (tm-30)
REVERT: A  718 HIS cc_start: 0.7020 (OUTLIER) cc_final: 0.6662 (m-70)
REVERT: A 1040 ASP cc_start: 0.8550 (t0) cc_final: 0.8166 (t0)
REVERT: A 1229 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7245 (tmm)
REVERT: A 1302 MET cc_start: 0.5477 (mtt) cc_final: 0.5238 (mmm)
REVERT: B  107 LEU cc_start: 0.7887 (mp) cc_final: 0.7655 (mt)
  outliers start: 22
  outliers final: 15
  residues processed: 104
  average time/residue: 0.1652
  time to fit residues: 26.0537
Evaluate side-chains
  97 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  841 ASP
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1271 CYS
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 100 optimal weight:    0.0020
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 95 optimal weight:    0.4980
   chunk 85 optimal weight:    0.0970
   chunk 101 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0670
   chunk 74 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0170
   overall best weight:    0.0562

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1178 HIS
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.119093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106561 restraints weight = 18550.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.109250 restraints weight = 9670.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.110986 restraints weight = 5944.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8780  Z= 0.131
  Angle     :  0.622  11.452  11905  Z= 0.299
  Chirality :  0.043   0.149   1350
  Planarity :  0.004   0.048   1515
  Dihedral  :  4.282  21.155   1173
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 24.84 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.27), residues: 1067
  helix:  0.38 (0.35), residues: 255
  sheet: -0.00 (0.38), residues: 215
  loop : -1.90 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 900 
 HIS   0.006   0.001   HIS A 781 
 PHE   0.018   0.001   PHE A 704 
 TYR   0.011   0.001   TYR A1145 
 ARG   0.007   0.000   ARG A 621 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2668.99 seconds
wall clock time: 49 minutes 30.03 seconds (2970.03 seconds total)