Starting phenix.real_space_refine
on Thu Jul 24 20:39:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u3r_63825/07_2025/9u3r_63825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u3r_63825/07_2025/9u3r_63825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u3r_63825/07_2025/9u3r_63825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u3r_63825/07_2025/9u3r_63825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u3r_63825/07_2025/9u3r_63825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u3r_63825/07_2025/9u3r_63825.cif"
  }
  resolution = 3.23
  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=   0.002 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4339      2.51       5
     N    1100      2.21       5
     O    1202      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6690
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 847, 6690
          Classifications: {'peptide': 847}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 824}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 4.49, per 1000 atoms: 0.67
  Number of scatterers: 6690
  At special positions: 0
  Unit cell: (63.63, 89.89, 148.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1202      8.00
     N    1100      7.00
     C    4339      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 217 " - pdb=" SG  CYS A 268 " distance=2.03

  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: 2.45
  Conformation dependent library (CDL) restraints added in 993.5 milliseconds
  

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1596

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      68.6% alpha, 15.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 138
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 145 through 165
      removed outlier: 4.036A  pdb=" N   ALA A 149 " --> pdb=" O   MET A 145 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE A 164 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   THR A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 171
      removed outlier: 3.787A  pdb=" N   ALA A 169 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ARG A 170 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 194
      removed outlier: 3.668A  pdb=" N   GLN A 193 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   VAL A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 237
      removed outlier: 3.964A  pdb=" N   SER A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 263
    Processing helix  chain 'A' and resid 279 through 336
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 411 through 434
    Processing helix  chain 'A' and resid 457 through 481
      removed outlier: 3.519A  pdb=" N   LYS A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 523
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.933A  pdb=" N   TYR A 538 " --> pdb=" O   ALA A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 555
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.753A  pdb=" N   LEU A 563 " --> pdb=" O   ALA A 560 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LYS A 564 " --> pdb=" O   ASP A 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 560 through 564'
    Processing helix  chain 'A' and resid 756 through 765
    Processing helix  chain 'A' and resid 765 through 774
    Processing helix  chain 'A' and resid 782 through 810
      removed outlier: 3.533A  pdb=" N   TYR A 809 " --> pdb=" O   CYS A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 843
    Processing helix  chain 'A' and resid 849 through 860
      removed outlier: 3.629A  pdb=" N   LEU A 855 " --> pdb=" O   CYS A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 882
      removed outlier: 3.867A  pdb=" N   ILE A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      Proline residue:  A 876  - end of helix
    Processing helix  chain 'A' and resid 883 through 884
      No H-bonds generated for 'chain 'A' and resid 883 through 884'
    Processing helix  chain 'A' and resid 885 through 889
      removed outlier: 4.384A  pdb=" N   GLU A 889 " --> pdb=" O   SER A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 909
      removed outlier: 3.791A  pdb=" N   ILE A 904 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TYR A 909 " --> pdb=" O   ALA A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 928
    Processing helix  chain 'A' and resid 929 through 937
      removed outlier: 3.683A  pdb=" N   VAL A 937 " --> pdb=" O   LEU A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 1034
    Processing helix  chain 'A' and resid 1037 through 1045
      removed outlier: 3.576A  pdb=" N   ALA A1041 " --> pdb=" O   PRO A1037 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLU A1042 " --> pdb=" O   TYR A1038 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   GLN A1043 " --> pdb=" O   HIS A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1071
    Processing helix  chain 'A' and resid 1081 through 1097
      removed outlier: 3.547A  pdb=" N   LEU A1095 " --> pdb=" O   ASP A1091 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1092 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   SER A1097 " --> pdb=" O   ASP A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1102
      removed outlier: 3.804A  pdb=" N   SER A1102 " --> pdb=" O   PRO A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1132 through 1154
      removed outlier: 3.573A  pdb=" N   ASN A1154 " --> pdb=" O   ASP A1150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1200
      removed outlier: 3.538A  pdb=" N   ASP A1198 " --> pdb=" O   ALA A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1209 through 1220
      removed outlier: 3.976A  pdb=" N   VAL A1215 " --> pdb=" O   GLU A1211 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LYS A1218 " --> pdb=" O   ARG A1214 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   MET A1219 " --> pdb=" O   VAL A1215 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLY A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.607A  pdb=" N   VAL A 401 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE A 438 " --> pdb=" O   TYR A 446 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.607A  pdb=" N   VAL A 401 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS A 528 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR A 492 " --> pdb=" O   SER A 532 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498
      removed outlier: 3.849A  pdb=" N   GLY A 498 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASP A 508 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1104 through 1110
      removed outlier: 4.826A  pdb=" N   LYS A1106 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   ALA A1117 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS A1108 " --> pdb=" O   MET A1115 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   SER A1051 " --> pdb=" O   VAL A1176 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   VAL A1176 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 5.771A  pdb=" N   ASN A1053 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA A1174 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ASP A1055 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   LEU A1172 " --> pdb=" O   ASP A1055 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN A1168 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A1175 " --> pdb=" O   ASP A1185 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP A1185 " --> pdb=" O   GLY A1175 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1104 through 1110
      removed outlier: 4.826A  pdb=" N   LYS A1106 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   ALA A1117 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS A1108 " --> pdb=" O   MET A1115 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   SER A1051 " --> pdb=" O   VAL A1176 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   VAL A1176 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 5.771A  pdb=" N   ASN A1053 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA A1174 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ASP A1055 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   LEU A1172 " --> pdb=" O   ASP A1055 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN A1168 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL A1165 " --> pdb=" O   GLN A1207 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   GLY A1235 " --> pdb=" O   ASN A1230 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   ASN A1230 " --> pdb=" O   GLY A1235 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   MET A1237 " --> pdb=" O   THR A1228 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   THR A1228 " --> pdb=" O   MET A1237 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   THR A1239 " --> pdb=" O   ARG A1226 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG A1226 " --> pdb=" O   THR A1239 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1389 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: 3.25

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2116
        1.34 -     1.46: 1304
        1.46 -     1.58: 3348
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 6840
  Sorted by residual:
  bond pdb=" CB  GLN A 220 "
       pdb=" CG  GLN A 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.50e+00
  bond pdb=" CB  GLN A 303 "
       pdb=" CG  GLN A 303 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.77e-01
  bond pdb=" CG  ARG A 340 "
       pdb=" CD  ARG A 340 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.53e-01
  bond pdb=" CG  GLN A 303 "
       pdb=" CD  GLN A 303 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.19e-01
  bond pdb=" CA  ASN A1053 "
       pdb=" CB  ASN A1053 "
    ideal  model  delta    sigma   weight residual
    1.531  1.546 -0.015 1.58e-02 4.01e+03 8.97e-01
  ... (remaining 6835 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 9113
        1.76 -     3.53: 110
        3.53 -     5.29: 32
        5.29 -     7.06: 10
        7.06 -     8.82: 2
  Bond angle restraints: 9267
  Sorted by residual:
  angle pdb=" CA  LYS A 773 "
        pdb=" CB  LYS A 773 "
        pdb=" CG  LYS A 773 "
      ideal   model   delta    sigma   weight residual
     114.10  121.08   -6.98 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" N   VAL A 337 "
        pdb=" CA  VAL A 337 "
        pdb=" C   VAL A 337 "
      ideal   model   delta    sigma   weight residual
     113.53  110.15    3.38 9.80e-01 1.04e+00 1.19e+01
  angle pdb=" CA  LYS A 808 "
        pdb=" CB  LYS A 808 "
        pdb=" CG  LYS A 808 "
      ideal   model   delta    sigma   weight residual
     114.10  120.22   -6.12 2.00e+00 2.50e-01 9.37e+00
  angle pdb=" N   GLU A1203 "
        pdb=" CA  GLU A1203 "
        pdb=" C   GLU A1203 "
      ideal   model   delta    sigma   weight residual
     109.15  113.31   -4.16 1.44e+00 4.82e-01 8.34e+00
  angle pdb=" CB  GLN A 303 "
        pdb=" CG  GLN A 303 "
        pdb=" CD  GLN A 303 "
      ideal   model   delta    sigma   weight residual
     112.60  117.28   -4.68 1.70e+00 3.46e-01 7.58e+00
  ... (remaining 9262 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.78: 3332
       16.78 -    33.55: 494
       33.55 -    50.33: 147
       50.33 -    67.10: 27
       67.10 -    83.88: 9
  Dihedral angle restraints: 4009
    sinusoidal: 1540
      harmonic: 2469
  Sorted by residual:
  dihedral pdb=" CG  ARG A 487 "
           pdb=" CD  ARG A 487 "
           pdb=" NE  ARG A 487 "
           pdb=" CZ  ARG A 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.93  -44.93     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CA  THR A 236 "
           pdb=" C   THR A 236 "
           pdb=" N   VAL A 237 "
           pdb=" CA  VAL A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.83  -16.17     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CB  GLU A1203 "
           pdb=" CG  GLU A1203 "
           pdb=" CD  GLU A1203 "
           pdb=" OE1 GLU A1203 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.88   83.88     1      3.00e+01 1.11e-03 9.53e+00
  ... (remaining 4006 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 739
       0.031 -    0.061: 233
       0.061 -    0.092: 64
       0.092 -    0.122: 23
       0.122 -    0.153: 3
  Chirality restraints: 1062
  Sorted by residual:
  chirality pdb=" CA  ARG A1205 "
            pdb=" N   ARG A1205 "
            pdb=" C   ARG A1205 "
            pdb=" CB  ARG A1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.85e-01
  chirality pdb=" CA  ILE A 499 "
            pdb=" N   ILE A 499 "
            pdb=" C   ILE A 499 "
            pdb=" CB  ILE A 499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  ILE A 747 "
            pdb=" N   ILE A 747 "
            pdb=" C   ILE A 747 "
            pdb=" CB  ILE A 747 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  ... (remaining 1059 not shown)

  Planarity restraints: 1157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 510 "   -0.022 2.00e-02 2.50e+03   1.64e-02 6.74e+00
        pdb=" CG  TRP A 510 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 510 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 510 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 510 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 510 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 510 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 510 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 510 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 510 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 240 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO A 241 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 241 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 241 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 930 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO A 931 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 931 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 931 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1154 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 197
        2.72 -     3.26: 7045
        3.26 -     3.81: 11260
        3.81 -     4.35: 13786
        4.35 -     4.90: 22710
  Nonbonded interactions: 54998
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A1205 "
            pdb=" O   TYR A1242 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OH  TYR A 809 "
            pdb=" O   HIS A 883 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" ND2 ASN A1066 "
            pdb=" O   ASN A1160 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   LEU A 799 "
            pdb=" OG1 THR A 803 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OE1 GLU A 770 "
            pdb=" OG1 THR A 784 "
     model   vdw
     2.251 3.040
  ... (remaining 54993 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.260
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6293
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      :  0.002   0.037   6841  Z= 0.111
  Angle     :  0.575   8.820   9269  Z= 0.304
  Chirality :  0.035   0.153   1062
  Planarity :  0.004   0.045   1157
  Dihedral  : 17.683  83.880   2410
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 30.65 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.29), residues: 827
  helix:  1.28 (0.22), residues: 511
  sheet: -0.75 (0.69), residues: 58
  loop : -0.23 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 510 
 HIS   0.005   0.001   HIS A 491 
 PHE   0.013   0.001   PHE A 507 
 TYR   0.021   0.001   TYR A 261 
 ARG   0.008   0.001   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23294 (  458)
  hydrogen bonds       : angle       7.92892 ( 1389)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.21053 (    2)
  covalent geometry    : bond        0.00242 ( 6840)
  covalent geometry    : angle       0.57486 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 PHE cc_start: 0.8050 (t80) cc_final: 0.7806 (t80)
REVERT: A  302 SER cc_start: 0.7646 (t) cc_final: 0.7213 (p)
REVERT: A 1002 VAL cc_start: 0.8448 (m) cc_final: 0.8180 (p)
REVERT: A 1004 TYR cc_start: 0.8219 (t80) cc_final: 0.7845 (t80)
REVERT: A 1029 ASP cc_start: 0.7313 (m-30) cc_final: 0.6992 (m-30)
REVERT: A 1033 ARG cc_start: 0.6752 (tpp80) cc_final: 0.6540 (mpp80)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2680
  time to fit residues: 48.4601
Evaluate side-chains
  131 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
A 475 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.184158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.161883 restraints weight = 10060.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.23
r_work: 0.3959 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   6841  Z= 0.187
  Angle     :  0.600   8.383   9269  Z= 0.316
  Chirality :  0.041   0.171   1062
  Planarity :  0.004   0.045   1157
  Dihedral  :  4.071  17.846    910
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 27.46 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.10 (0.29), residues: 827
  helix:  1.56 (0.22), residues: 539
  sheet: -0.52 (0.66), residues: 61
  loop : -0.87 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 510 
 HIS   0.005   0.001   HIS A1009 
 PHE   0.020   0.002   PHE A 897 
 TYR   0.021   0.002   TYR A1050 
 ARG   0.004   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04753 (  458)
  hydrogen bonds       : angle       5.15564 ( 1389)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       0.38181 (    2)
  covalent geometry    : bond        0.00413 ( 6840)
  covalent geometry    : angle       0.60017 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  146 VAL cc_start: 0.7661 (p) cc_final: 0.7354 (m)
REVERT: A  193 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6338 (mp10)
REVERT: A  223 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7778 (p)
REVERT: A  229 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7304 (mt-10)
REVERT: A  395 ILE cc_start: 0.7068 (mt) cc_final: 0.6801 (mp)
REVERT: A  410 LYS cc_start: 0.3353 (mttm) cc_final: 0.2452 (mttm)
REVERT: A 1002 VAL cc_start: 0.8776 (m) cc_final: 0.8466 (p)
  outliers start: 23
  outliers final: 8
  residues processed: 163
  average time/residue: 0.2699
  time to fit residues: 57.4607
Evaluate side-chains
  149 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 1.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 CYS
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1167 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0870
   chunk 73 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 997 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.185283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.162880 restraints weight = 10288.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 2.27
r_work: 0.3960 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6841  Z= 0.143
  Angle     :  0.553  10.095   9269  Z= 0.285
  Chirality :  0.039   0.159   1062
  Planarity :  0.004   0.039   1157
  Dihedral  :  4.047  16.220    910
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 25.94 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.28 (0.29), residues: 827
  helix:  1.76 (0.22), residues: 540
  sheet: -0.66 (0.64), residues: 66
  loop : -0.90 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 510 
 HIS   0.002   0.001   HIS A 866 
 PHE   0.014   0.001   PHE A 780 
 TYR   0.020   0.001   TYR A1050 
 ARG   0.009   0.001   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04184 (  458)
  hydrogen bonds       : angle       4.83473 ( 1389)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       0.31867 (    2)
  covalent geometry    : bond        0.00318 ( 6840)
  covalent geometry    : angle       0.55261 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A  146 VAL cc_start: 0.7626 (p) cc_final: 0.7317 (m)
REVERT: A  223 SER cc_start: 0.8186 (m) cc_final: 0.7816 (p)
REVERT: A  305 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7647 (mtt-85)
REVERT: A  326 GLU cc_start: 0.7024 (tt0) cc_final: 0.6819 (tt0)
REVERT: A  395 ILE cc_start: 0.7059 (mt) cc_final: 0.6818 (mp)
REVERT: A  532 SER cc_start: 0.7122 (t) cc_final: 0.6488 (m)
REVERT: A 1002 VAL cc_start: 0.8732 (m) cc_final: 0.8403 (p)
REVERT: A 1145 MET cc_start: 0.5477 (OUTLIER) cc_final: 0.5002 (ttt)
REVERT: A 1164 ARG cc_start: 0.6754 (mtm180) cc_final: 0.6487 (mtm180)
  outliers start: 32
  outliers final: 17
  residues processed: 167
  average time/residue: 0.2514
  time to fit residues: 54.4452
Evaluate side-chains
  155 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1204 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 65 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 774 ASN
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
A 997 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.184874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.162555 restraints weight = 10244.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 2.23
r_work: 0.3964 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6841  Z= 0.151
  Angle     :  0.561   7.749   9269  Z= 0.290
  Chirality :  0.040   0.164   1062
  Planarity :  0.004   0.040   1157
  Dihedral  :  4.041  16.057    910
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 27.32 %
    Favored  : 68.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.30 (0.29), residues: 827
  helix:  1.79 (0.22), residues: 541
  sheet: -0.47 (0.66), residues: 66
  loop : -1.04 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.012   0.001   PHE A1061 
 TYR   0.017   0.001   TYR A1050 
 ARG   0.006   0.000   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03955 (  458)
  hydrogen bonds       : angle       4.72204 ( 1389)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.36441 (    2)
  covalent geometry    : bond        0.00345 ( 6840)
  covalent geometry    : angle       0.56147 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 1.403 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.3134 (OUTLIER) cc_final: 0.1622 (tp30)
REVERT: A  122 TYR cc_start: 0.8217 (t80) cc_final: 0.6146 (t80)
REVERT: A  146 VAL cc_start: 0.7647 (p) cc_final: 0.7338 (m)
REVERT: A  193 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.5968 (mp10)
REVERT: A  220 GLN cc_start: 0.6738 (tm-30) cc_final: 0.6484 (tm-30)
REVERT: A  223 SER cc_start: 0.8192 (m) cc_final: 0.7839 (p)
REVERT: A  242 LEU cc_start: 0.8330 (tp) cc_final: 0.8125 (tp)
REVERT: A  532 SER cc_start: 0.7127 (t) cc_final: 0.6556 (m)
REVERT: A 1002 VAL cc_start: 0.8732 (m) cc_final: 0.8424 (p)
REVERT: A 1145 MET cc_start: 0.5516 (OUTLIER) cc_final: 0.5023 (ttt)
  outliers start: 29
  outliers final: 16
  residues processed: 163
  average time/residue: 0.4255
  time to fit residues: 90.0645
Evaluate side-chains
  159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0000
   chunk 33 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 774 ASN
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.183833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.161453 restraints weight = 10181.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 2.27
r_work: 0.3943 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6841  Z= 0.156
  Angle     :  0.552   8.148   9269  Z= 0.287
  Chirality :  0.041   0.214   1062
  Planarity :  0.004   0.036   1157
  Dihedral  :  4.066  16.300    910
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 25.94 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.29 (0.29), residues: 827
  helix:  1.78 (0.22), residues: 540
  sheet: -0.27 (0.68), residues: 66
  loop : -1.07 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 510 
 HIS   0.003   0.001   HIS A 866 
 PHE   0.012   0.002   PHE A 780 
 TYR   0.017   0.001   TYR A1050 
 ARG   0.006   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  458)
  hydrogen bonds       : angle       4.66915 ( 1389)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.37269 (    2)
  covalent geometry    : bond        0.00352 ( 6840)
  covalent geometry    : angle       0.55219 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.2957 (OUTLIER) cc_final: 0.1446 (tp30)
REVERT: A  146 VAL cc_start: 0.7598 (p) cc_final: 0.7301 (m)
REVERT: A  193 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.5931 (mp10)
REVERT: A  220 GLN cc_start: 0.6726 (tm-30) cc_final: 0.6433 (tm-30)
REVERT: A  223 SER cc_start: 0.8176 (m) cc_final: 0.7868 (p)
REVERT: A  246 LEU cc_start: 0.8163 (tp) cc_final: 0.7925 (tt)
REVERT: A  487 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7190 (ttp-110)
REVERT: A  532 SER cc_start: 0.7179 (t) cc_final: 0.6585 (m)
REVERT: A  566 LEU cc_start: 0.7732 (tp) cc_final: 0.7518 (tt)
REVERT: A  840 ARG cc_start: 0.7471 (mmm-85) cc_final: 0.7193 (ttt-90)
REVERT: A  849 MET cc_start: 0.7458 (pmm) cc_final: 0.7172 (pmm)
REVERT: A 1002 VAL cc_start: 0.8755 (m) cc_final: 0.8414 (p)
REVERT: A 1145 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.5128 (ttt)
  outliers start: 37
  outliers final: 23
  residues processed: 168
  average time/residue: 0.3278
  time to fit residues: 71.8520
Evaluate side-chains
  166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1204 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0770
   chunk 43 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 80 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0970
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.184713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.162689 restraints weight = 10162.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 2.26
r_work: 0.3959 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6841  Z= 0.128
  Angle     :  0.558   8.832   9269  Z= 0.281
  Chirality :  0.040   0.309   1062
  Planarity :  0.004   0.040   1157
  Dihedral  :  3.989  17.172    910
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 28.99 %
    Favored  : 66.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.25 (0.29), residues: 827
  helix:  1.80 (0.22), residues: 544
  sheet: -0.03 (0.76), residues: 54
  loop : -1.36 (0.38), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 510 
 HIS   0.003   0.001   HIS A 866 
 PHE   0.011   0.001   PHE A 152 
 TYR   0.012   0.001   TYR A1050 
 ARG   0.007   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  458)
  hydrogen bonds       : angle       4.55391 ( 1389)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.27104 (    2)
  covalent geometry    : bond        0.00293 ( 6840)
  covalent geometry    : angle       0.55853 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 1.691 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.3051 (OUTLIER) cc_final: 0.1565 (tp30)
REVERT: A  146 VAL cc_start: 0.7556 (p) cc_final: 0.7268 (m)
REVERT: A  193 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.5853 (mp10)
REVERT: A  220 GLN cc_start: 0.6611 (tm-30) cc_final: 0.6359 (tm-30)
REVERT: A  223 SER cc_start: 0.8137 (m) cc_final: 0.7794 (p)
REVERT: A  246 LEU cc_start: 0.8166 (tp) cc_final: 0.7941 (tt)
REVERT: A  301 MET cc_start: 0.7939 (tpp) cc_final: 0.7730 (mmm)
REVERT: A  326 GLU cc_start: 0.6953 (tt0) cc_final: 0.6224 (mt-10)
REVERT: A  487 ARG cc_start: 0.7757 (mtp-110) cc_final: 0.7501 (mtp-110)
REVERT: A  532 SER cc_start: 0.7082 (t) cc_final: 0.6422 (m)
REVERT: A  840 ARG cc_start: 0.7336 (mmm-85) cc_final: 0.7111 (ttt-90)
REVERT: A  849 MET cc_start: 0.7482 (pmm) cc_final: 0.7199 (pmm)
REVERT: A 1002 VAL cc_start: 0.8711 (m) cc_final: 0.8383 (p)
REVERT: A 1024 MET cc_start: 0.7457 (tpp) cc_final: 0.7159 (mmt)
REVERT: A 1145 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.5080 (ttt)
REVERT: A 1205 ARG cc_start: 0.5252 (mmm160) cc_final: 0.4647 (mmm160)
  outliers start: 31
  outliers final: 20
  residues processed: 166
  average time/residue: 0.4559
  time to fit residues: 100.2419
Evaluate side-chains
  162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 70 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0470
   chunk 10 optimal weight:    0.2980
   chunk 20 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.3678

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.181933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.158939 restraints weight = 10051.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 2.26
r_work: 0.3971 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6841  Z= 0.123
  Angle     :  0.565  10.988   9269  Z= 0.278
  Chirality :  0.040   0.289   1062
  Planarity :  0.003   0.037   1157
  Dihedral  :  3.901  17.136    910
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 29.68 %
    Favored  : 66.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.30), residues: 827
  helix:  1.90 (0.22), residues: 541
  sheet: -0.40 (0.64), residues: 72
  loop : -1.25 (0.42), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 866 
 PHE   0.010   0.001   PHE A 152 
 TYR   0.012   0.001   TYR A1114 
 ARG   0.006   0.001   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  458)
  hydrogen bonds       : angle       4.47640 ( 1389)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.19713 (    2)
  covalent geometry    : bond        0.00279 ( 6840)
  covalent geometry    : angle       0.56483 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.3071 (OUTLIER) cc_final: 0.1603 (tp30)
REVERT: A  146 VAL cc_start: 0.7527 (p) cc_final: 0.7255 (m)
REVERT: A  193 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.5824 (mp10)
REVERT: A  223 SER cc_start: 0.8106 (m) cc_final: 0.7870 (p)
REVERT: A  246 LEU cc_start: 0.8215 (tp) cc_final: 0.8002 (tt)
REVERT: A  301 MET cc_start: 0.7885 (tpp) cc_final: 0.7656 (mmm)
REVERT: A  326 GLU cc_start: 0.6969 (tt0) cc_final: 0.6255 (mt-10)
REVERT: A  487 ARG cc_start: 0.7757 (mtp-110) cc_final: 0.7543 (mtp-110)
REVERT: A  532 SER cc_start: 0.7220 (t) cc_final: 0.6610 (m)
REVERT: A  849 MET cc_start: 0.7484 (pmm) cc_final: 0.7250 (pmm)
REVERT: A  922 SER cc_start: 0.8149 (m) cc_final: 0.7810 (m)
REVERT: A 1002 VAL cc_start: 0.8716 (m) cc_final: 0.8397 (p)
REVERT: A 1024 MET cc_start: 0.7315 (tpp) cc_final: 0.7064 (mmt)
REVERT: A 1145 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5104 (ttt)
REVERT: A 1205 ARG cc_start: 0.5126 (mmm160) cc_final: 0.4444 (mmm160)
  outliers start: 31
  outliers final: 22
  residues processed: 167
  average time/residue: 0.2841
  time to fit residues: 61.3009
Evaluate side-chains
  172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1204 CYS
Chi-restraints excluded: chain A residue 1208 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0050
   chunk 33 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 82 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.8596

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

Flipped N/Q/H residues before XYZ refinement:
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.179402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.156084 restraints weight = 9995.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 2.27
r_work: 0.3942 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6841  Z= 0.173
  Angle     :  0.625  10.075   9269  Z= 0.313
  Chirality :  0.042   0.283   1062
  Planarity :  0.004   0.055   1157
  Dihedral  :  4.050  17.107    910
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 29.96 %
    Favored  : 65.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.21 (0.29), residues: 827
  helix:  1.79 (0.22), residues: 540
  sheet: -0.23 (0.73), residues: 59
  loop : -1.35 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 510 
 HIS   0.006   0.001   HIS A1009 
 PHE   0.012   0.001   PHE A 505 
 TYR   0.020   0.002   TYR A 118 
 ARG   0.006   0.001   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  458)
  hydrogen bonds       : angle       4.59575 ( 1389)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.26414 (    2)
  covalent geometry    : bond        0.00399 ( 6840)
  covalent geometry    : angle       0.62541 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.3091 (OUTLIER) cc_final: 0.1507 (tp30)
REVERT: A  146 VAL cc_start: 0.7550 (p) cc_final: 0.7277 (m)
REVERT: A  164 PHE cc_start: 0.7566 (m-80) cc_final: 0.7266 (m-80)
REVERT: A  193 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5807 (mp10)
REVERT: A  220 GLN cc_start: 0.6481 (tm-30) cc_final: 0.6132 (tm-30)
REVERT: A  223 SER cc_start: 0.8209 (m) cc_final: 0.7918 (p)
REVERT: A  301 MET cc_start: 0.7972 (tpp) cc_final: 0.7748 (mmm)
REVERT: A  487 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7583 (mtm110)
REVERT: A  532 SER cc_start: 0.7140 (t) cc_final: 0.6569 (m)
REVERT: A  874 SER cc_start: 0.7889 (t) cc_final: 0.7689 (p)
REVERT: A 1002 VAL cc_start: 0.8777 (m) cc_final: 0.8436 (p)
REVERT: A 1145 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5076 (mtp)
  outliers start: 31
  outliers final: 23
  residues processed: 168
  average time/residue: 0.4620
  time to fit residues: 104.7526
Evaluate side-chains
  166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 2.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1120 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1204 CYS
Chi-restraints excluded: chain A residue 1208 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    0.0970
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 78 optimal weight:    0.4980
   chunk 48 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.180531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.157239 restraints weight = 10113.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 2.29
r_work: 0.3954 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6841  Z= 0.141
  Angle     :  0.622   9.867   9269  Z= 0.307
  Chirality :  0.041   0.263   1062
  Planarity :  0.004   0.045   1157
  Dihedral  :  4.041  19.161    910
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 29.82 %
    Favored  : 65.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.31 (0.30), residues: 827
  helix:  1.87 (0.22), residues: 541
  sheet: -0.46 (0.65), residues: 71
  loop : -1.25 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 510 
 HIS   0.005   0.001   HIS A1009 
 PHE   0.016   0.001   PHE A 780 
 TYR   0.016   0.001   TYR A 118 
 ARG   0.006   0.001   ARG A 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (  458)
  hydrogen bonds       : angle       4.54747 ( 1389)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.29956 (    2)
  covalent geometry    : bond        0.00325 ( 6840)
  covalent geometry    : angle       0.62205 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.3021 (OUTLIER) cc_final: 0.2275 (mm-30)
REVERT: A  146 VAL cc_start: 0.7507 (p) cc_final: 0.7253 (m)
REVERT: A  164 PHE cc_start: 0.7554 (m-80) cc_final: 0.7253 (m-80)
REVERT: A  193 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.5767 (mp10)
REVERT: A  220 GLN cc_start: 0.6501 (tm-30) cc_final: 0.6098 (tm-30)
REVERT: A  223 SER cc_start: 0.8151 (m) cc_final: 0.7841 (p)
REVERT: A  246 LEU cc_start: 0.8220 (tp) cc_final: 0.8017 (tt)
REVERT: A  326 GLU cc_start: 0.7025 (tt0) cc_final: 0.6360 (tt0)
REVERT: A  532 SER cc_start: 0.7083 (t) cc_final: 0.6504 (m)
REVERT: A  760 GLU cc_start: 0.7485 (tp30) cc_final: 0.7083 (tm-30)
REVERT: A  773 LYS cc_start: 0.8376 (mmtm) cc_final: 0.7922 (mmtm)
REVERT: A  874 SER cc_start: 0.7858 (t) cc_final: 0.7655 (p)
REVERT: A 1002 VAL cc_start: 0.8735 (m) cc_final: 0.8406 (p)
REVERT: A 1009 HIS cc_start: 0.7770 (t-90) cc_final: 0.7510 (t-170)
REVERT: A 1145 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5335 (ttm)
  outliers start: 31
  outliers final: 25
  residues processed: 164
  average time/residue: 0.2280
  time to fit residues: 47.8901
Evaluate side-chains
  172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  998 ARG
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1204 CYS
Chi-restraints excluded: chain A residue 1208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0770
   chunk 50 optimal weight:    0.0670
   chunk 81 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 41 optimal weight:    0.3980
   chunk 34 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.3276

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 315 GLN
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.181752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.158696 restraints weight = 10270.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.4090 rms_B_bonded: 2.28
r_work: 0.3973 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6841  Z= 0.127
  Angle     :  0.623   9.714   9269  Z= 0.304
  Chirality :  0.040   0.260   1062
  Planarity :  0.004   0.035   1157
  Dihedral  :  3.927  16.066    910
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 29.82 %
    Favored  : 66.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.35 (0.30), residues: 827
  helix:  1.92 (0.22), residues: 540
  sheet: -0.57 (0.64), residues: 73
  loop : -1.23 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 335 
 PHE   0.013   0.001   PHE A 403 
 TYR   0.014   0.001   TYR A 118 
 ARG   0.007   0.001   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  458)
  hydrogen bonds       : angle       4.47596 ( 1389)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       0.43712 (    2)
  covalent geometry    : bond        0.00295 ( 6840)
  covalent geometry    : angle       0.62282 ( 9267)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.3066 (OUTLIER) cc_final: 0.2330 (mm-30)
REVERT: A  146 VAL cc_start: 0.7471 (p) cc_final: 0.7229 (m)
REVERT: A  164 PHE cc_start: 0.7556 (m-80) cc_final: 0.7266 (m-80)
REVERT: A  193 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.5801 (mp10)
REVERT: A  220 GLN cc_start: 0.6451 (tm-30) cc_final: 0.6122 (tm-30)
REVERT: A  223 SER cc_start: 0.8107 (m) cc_final: 0.7827 (p)
REVERT: A  254 VAL cc_start: 0.8230 (p) cc_final: 0.7956 (m)
REVERT: A  326 GLU cc_start: 0.6975 (tt0) cc_final: 0.6324 (tt0)
REVERT: A  433 THR cc_start: 0.5066 (OUTLIER) cc_final: 0.4604 (m)
REVERT: A  532 SER cc_start: 0.7157 (t) cc_final: 0.6573 (m)
REVERT: A  760 GLU cc_start: 0.7486 (tp30) cc_final: 0.7118 (tm-30)
REVERT: A  773 LYS cc_start: 0.8290 (mmtm) cc_final: 0.7892 (mmtm)
REVERT: A  922 SER cc_start: 0.8145 (m) cc_final: 0.7843 (m)
REVERT: A 1002 VAL cc_start: 0.8712 (m) cc_final: 0.8369 (p)
REVERT: A 1061 PHE cc_start: 0.7230 (m-80) cc_final: 0.6789 (m-80)
REVERT: A 1145 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.5342 (ttm)
  outliers start: 30
  outliers final: 22
  residues processed: 170
  average time/residue: 0.2194
  time to fit residues: 47.6596
Evaluate side-chains
  172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  324 GLU
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1145 MET
Chi-restraints excluded: chain A residue 1161 PHE
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1173 THR
Chi-restraints excluded: chain A residue 1208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0020
   chunk 77 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.180432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.157314 restraints weight = 10240.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 2.28
r_work: 0.3958 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6841  Z= 0.141
  Angle     :  0.648   9.764   9269  Z= 0.312
  Chirality :  0.040   0.264   1062
  Planarity :  0.004   0.055   1157
  Dihedral  :  3.947  15.391    910
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 30.79 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.29 (0.30), residues: 827
  helix:  1.91 (0.22), residues: 540
  sheet: -0.49 (0.72), residues: 61
  loop : -1.37 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.015   0.001   PHE A 780 
 TYR   0.015   0.001   TYR A 118 
 ARG   0.013   0.001   ARG A1083 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03621 (  458)
  hydrogen bonds       : angle       4.47655 ( 1389)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       0.21012 (    2)
  covalent geometry    : bond        0.00328 ( 6840)
  covalent geometry    : angle       0.64779 ( 9267)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4352.05 seconds
wall clock time: 82 minutes 19.39 seconds (4939.39 seconds total)