Starting phenix.real_space_refine
on Thu Mar 13 06:03:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jlu_22380/03_2025/7jlu_22380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jlu_22380/03_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_22380/03_2025/7jlu_22380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jlu_22380/03_2025/7jlu_22380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jlu_22380/03_2025/7jlu_22380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jlu_22380/03_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-5624/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: 7.70, per 1000 atoms: 0.90
  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: 2.40
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.04
  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: 3.24

  Time building geometry restraints manager: 2.85 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:             39.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.750
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   69.830
-------------------------------------------------------------------------------
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  : 1.045 
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: 0.2344
  time to fit residues: 34.7490
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  : 1.026 
-------------------------------------------------------------------------------
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 = 0.113836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.101355 restraints weight = 18585.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.103888 restraints weight = 9820.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.105613 restraints weight = 6140.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
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  31.838   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  : 1.291 
Fit side-chains
REVERT: A  584 GLU cc_start: 0.7445 (mp0) cc_final: 0.7171 (mp0)
REVERT: A  677 MET cc_start: 0.8210 (mmt) cc_final: 0.7845 (mmt)
REVERT: A 1040 ASP cc_start: 0.8571 (t0) cc_final: 0.8369 (t0)
REVERT: B  107 LEU cc_start: 0.7784 (mp) cc_final: 0.7488 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 87
  average time/residue: 0.2430
  time to fit residues: 31.7555
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  : 1.266 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 103 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 = 0.3542 r_free = 0.3542 target = 0.108642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.096480 restraints weight = 18971.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.098972 restraints weight = 9959.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.100610 restraints weight = 6168.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   8780  Z= 0.362
  Angle     :  0.720   7.283  11905  Z= 0.375
  Chirality :  0.049   0.164   1350
  Planarity :  0.005   0.057   1515
  Dihedral  :  5.381  23.385   1173
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.74 %
    Favored  : 78.95 %
  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: -2.13 (0.25), residues: 1067
  helix: -0.50 (0.31), residues: 270
  sheet: -0.19 (0.37), residues: 215
  loop : -2.45 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 582 
 HIS   0.006   0.001   HIS A 663 
 PHE   0.022   0.002   PHE A 704 
 TYR   0.016   0.002   TYR A1186 
 ARG   0.004   0.001   ARG A 621 

*********************** 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  : 0.962 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8250 (mmt) cc_final: 0.7865 (mmt)
REVERT: A  718 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.7034 (m-70)
REVERT: A 1040 ASP cc_start: 0.8621 (t0) cc_final: 0.8354 (t0)
REVERT: A 1070 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7900 (p0)
REVERT: B  107 LEU cc_start: 0.7871 (mp) cc_final: 0.7623 (mt)
REVERT: B  235 MET cc_start: 0.7694 (mtt) cc_final: 0.7322 (mtt)
  outliers start: 22
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1658
  time to fit residues: 23.3548
Evaluate side-chains
  93 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
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 1070 ASN
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:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 100 optimal weight:    0.1980
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.112406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.100138 restraints weight = 18665.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.102723 restraints weight = 9602.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.104419 restraints weight = 5888.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8780  Z= 0.165
  Angle     :  0.616   8.270  11905  Z= 0.313
  Chirality :  0.045   0.144   1350
  Planarity :  0.005   0.053   1515
  Dihedral  :  4.922  25.022   1173
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.16 %
    Favored  : 76.53 %
  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: -0.26 (0.32), residues: 268
  sheet: -0.30 (0.36), residues: 229
  loop : -2.20 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 900 
 HIS   0.004   0.001   HIS A 663 
 PHE   0.020   0.001   PHE A 704 
 TYR   0.014   0.001   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
  108 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8250 (mmt) cc_final: 0.7925 (mmt)
REVERT: A  718 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.6911 (m-70)
REVERT: A 1040 ASP cc_start: 0.8593 (t0) cc_final: 0.8233 (t0)
REVERT: A 1126 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6793 (mp0)
REVERT: A 1229 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7317 (tmm)
REVERT: B  107 LEU cc_start: 0.7865 (mp) cc_final: 0.7634 (mt)
REVERT: B  305 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7682 (mp)
  outliers start: 22
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1687
  time to fit residues: 26.4614
Evaluate side-chains
  92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
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  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1126 GLU
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  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:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0770
   chunk 105 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.0142

-------------------------------------------------------------------------------
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**
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 = 0.3597 r_free = 0.3597 target = 0.112125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.099891 restraints weight = 18644.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.102448 restraints weight = 9666.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.104104 restraints weight = 5947.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2206

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= 0.187
  Angle     :  0.616  10.113  11905  Z= 0.310
  Chirality :  0.045   0.143   1350
  Planarity :  0.004   0.052   1515
  Dihedral  :  4.839  23.681   1173
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 21.26 %
    Favored  : 76.32 %
  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: -1.75 (0.26), residues: 1067
  helix: -0.10 (0.33), residues: 268
  sheet: -0.09 (0.37), residues: 213
  loop : -2.18 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   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   0.006   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
  105 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A  661 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: A  677 MET cc_start: 0.8177 (mmt) cc_final: 0.7717 (mmt)
REVERT: A  718 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.6923 (m-70)
REVERT: A 1040 ASP cc_start: 0.8598 (t0) cc_final: 0.8230 (t0)
REVERT: A 1229 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7330 (tmm)
REVERT: B  107 LEU cc_start: 0.7864 (mp) cc_final: 0.7642 (mt)
REVERT: B  305 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7707 (mp)
  outliers start: 23
  outliers final: 15
  residues processed: 100
  average time/residue: 0.1929
  time to fit residues: 28.7786
Evaluate side-chains
  100 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
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  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  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  147 THR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  388 ILE
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:    0.0570
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   overall best weight:    1.1902

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.111585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.099332 restraints weight = 18487.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.101875 restraints weight = 9588.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.103579 restraints weight = 5894.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2298

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= 0.202
  Angle     :  0.613   8.659  11905  Z= 0.311
  Chirality :  0.045   0.145   1350
  Planarity :  0.004   0.052   1515
  Dihedral  :  4.811  23.621   1173
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.16 %
    Favored  : 75.47 %
  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: -1.81 (0.26), residues: 1067
  helix: -0.09 (0.32), residues: 274
  sheet: -0.11 (0.37), residues: 219
  loop : -2.30 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 900 
 HIS   0.006   0.001   HIS A1178 
 PHE   0.020   0.001   PHE A 704 
 TYR   0.014   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
  113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 1.041 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8184 (mmt) cc_final: 0.7677 (mmt)
REVERT: A  718 HIS cc_start: 0.7212 (OUTLIER) cc_final: 0.6952 (m-70)
REVERT: A 1040 ASP cc_start: 0.8582 (t0) cc_final: 0.8182 (t0)
REVERT: A 1229 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7323 (tmm)
REVERT: B  107 LEU cc_start: 0.7875 (mp) cc_final: 0.7633 (mt)
REVERT: B  305 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7669 (mp)
  outliers start: 32
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1719
  time to fit residues: 27.0521
Evaluate side-chains
  102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
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  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 1101 ILE
Chi-restraints excluded: chain A residue 1177 MET
Chi-restraints excluded: chain A residue 1229 MET
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  305 LEU
Chi-restraints excluded: chain B residue  388 ILE
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:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 38 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0170
   chunk 94 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 104 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7620

-------------------------------------------------------------------------------
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**
A1093 GLN
** 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 = 0.3616 r_free = 0.3616 target = 0.113469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.101209 restraints weight = 18716.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.103820 restraints weight = 9598.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.105512 restraints weight = 5856.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2305

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= 0.159
  Angle     :  0.605  12.022  11905  Z= 0.302
  Chirality :  0.044   0.144   1350
  Planarity :  0.004   0.051   1515
  Dihedral  :  4.660  23.353   1173
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.68 %
    Favored  : 74.95 %
  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: -1.73 (0.26), residues: 1067
  helix:  0.04 (0.33), residues: 269
  sheet: -0.09 (0.37), residues: 219
  loop : -2.25 (0.26), residues: 579

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   0.019   0.001   PHE A 704 
 TYR   0.010   0.001   TYR A1145 
 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
  114 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 82
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: A  718 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6925 (m-70)
REVERT: A 1040 ASP cc_start: 0.8556 (t0) cc_final: 0.8165 (t0)
REVERT: A 1229 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7313 (tmm)
REVERT: B  107 LEU cc_start: 0.7851 (mp) cc_final: 0.7637 (mt)
REVERT: B  305 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7682 (mp)
  outliers start: 32
  outliers final: 21
  residues processed: 108
  average time/residue: 0.1701
  time to fit residues: 27.8574
Evaluate side-chains
  102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
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  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1101 ILE
Chi-restraints excluded: chain A residue 1177 MET
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  388 ILE
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:    0.6980
   chunk 100 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 104 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 ** 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 = 0.3592 r_free = 0.3592 target = 0.111597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.099323 restraints weight = 18842.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.101900 restraints weight = 9745.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.103577 restraints weight = 5974.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2448

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= 0.214
  Angle     :  0.623  10.940  11905  Z= 0.314
  Chirality :  0.045   0.148   1350
  Planarity :  0.004   0.051   1515
  Dihedral  :  4.748  22.707   1173
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.89 %
    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: -1.79 (0.26), residues: 1067
  helix: -0.01 (0.33), residues: 269
  sheet: -0.12 (0.37), residues: 219
  loop : -2.31 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 900 
 HIS   0.003   0.001   HIS A 663 
 PHE   0.020   0.001   PHE A 704 
 TYR   0.012   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
  112 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
REVERT: A  677 MET cc_start: 0.8262 (mmt) cc_final: 0.7768 (mmt)
REVERT: A  718 HIS cc_start: 0.7189 (OUTLIER) cc_final: 0.6902 (m-70)
REVERT: A 1040 ASP cc_start: 0.8565 (t0) cc_final: 0.8187 (t0)
REVERT: A 1229 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7295 (tmm)
REVERT: B  305 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7665 (mp)
  outliers start: 31
  outliers final: 23
  residues processed: 103
  average time/residue: 0.1723
  time to fit residues: 26.7708
Evaluate side-chains
  104 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
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  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 1101 ILE
Chi-restraints excluded: chain A residue 1177 MET
Chi-restraints excluded: chain A residue 1229 MET
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  229 MET
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  388 ILE
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:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 35 optimal weight:    0.4980
   chunk 94 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0970
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.107869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.094994 restraints weight = 19202.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.097576 restraints weight = 10074.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.099316 restraints weight = 6214.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8780  Z= 0.139
  Angle     :  0.604  10.726  11905  Z= 0.298
  Chirality :  0.044   0.140   1350
  Planarity :  0.004   0.050   1515
  Dihedral  :  4.524  22.986   1173
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 23.47 %
    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: -1.62 (0.26), residues: 1067
  helix:  0.03 (0.33), residues: 270
  sheet: -0.05 (0.37), residues: 219
  loop : -2.12 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 900 
 HIS   0.002   0.001   HIS A1279 
 PHE   0.019   0.001   PHE A 704 
 TYR   0.010   0.001   TYR A1145 
 ARG   0.006   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
  106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 1.363 
Fit side-chains
   revert: symmetry clash
REVERT: A  718 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6972 (m-70)
REVERT: A 1040 ASP cc_start: 0.8583 (t0) cc_final: 0.8171 (t0)
REVERT: A 1229 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7237 (tmm)
  outliers start: 24
  outliers final: 18
  residues processed: 102
  average time/residue: 0.1882
  time to fit residues: 28.4991
Evaluate side-chains
  98 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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 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  147 THR
Chi-restraints excluded: chain B residue  388 ILE
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:    1.9990
   chunk 84 optimal weight:    0.0970
   chunk 27 optimal weight:    0.0570
   chunk 41 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0670
   chunk 13 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.2834

-------------------------------------------------------------------------------
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 = 0.3652 r_free = 0.3652 target = 0.115843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.103364 restraints weight = 18540.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.105991 restraints weight = 9630.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.107734 restraints weight = 5935.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8780  Z= 0.132
  Angle     :  0.613  10.886  11905  Z= 0.302
  Chirality :  0.043   0.140   1350
  Planarity :  0.004   0.049   1515
  Dihedral  :  4.426  21.625   1173
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 23.68 %
    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: -1.47 (0.27), residues: 1067
  helix:  0.21 (0.34), residues: 263
  sheet:  0.01 (0.37), residues: 219
  loop : -2.01 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 900 
 HIS   0.006   0.001   HIS A1179 
 PHE   0.018   0.001   PHE A 704 
 TYR   0.013   0.001   TYR A 575 
 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
  111 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  661 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7289 (tm-30)
REVERT: A  718 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.6668 (m-70)
REVERT: A 1040 ASP cc_start: 0.8577 (t0) cc_final: 0.8188 (t0)
REVERT: A 1178 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.7076 (t-90)
REVERT: A 1229 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7274 (tmm)
REVERT: B  305 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7619 (mp)
  outliers start: 25
  outliers final: 18
  residues processed: 107
  average time/residue: 0.1717
  time to fit residues: 27.4013
Evaluate side-chains
  102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
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  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 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  305 LEU
Chi-restraints excluded: chain B residue  388 ILE
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:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   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**
** A1070 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 = 0.3620 r_free = 0.3620 target = 0.113578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.101060 restraints weight = 18767.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.103652 restraints weight = 9793.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.105356 restraints weight = 6072.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2418

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= 0.176
  Angle     :  0.639  10.436  11905  Z= 0.314
  Chirality :  0.044   0.141   1350
  Planarity :  0.004   0.050   1515
  Dihedral  :  4.482  21.570   1173
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 24.21 %
    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: -1.63 (0.27), residues: 1067
  helix:  0.04 (0.33), residues: 275
  sheet: -0.07 (0.37), residues: 221
  loop : -2.15 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A 663 
 PHE   0.019   0.001   PHE A 704 
 TYR   0.012   0.001   TYR A 575 
 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: 3042.64 seconds
wall clock time: 55 minutes 1.12 seconds (3301.12 seconds total)