Starting phenix.real_space_refine
on Wed Mar 12 06:53:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p6w_20265/03_2025/6p6w_20265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p6w_20265/03_2025/6p6w_20265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p6w_20265/03_2025/6p6w_20265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p6w_20265/03_2025/6p6w_20265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p6w_20265/03_2025/6p6w_20265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p6w_20265/03_2025/6p6w_20265.cif"
  }
  resolution = 4.0
  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
-------------------------------------------------------------------------------
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=   0.011 sd=   0.279
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      52      5.16       5
     C    5084      2.51       5
     N    1108      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7468
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1867
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
    Chain: "B"
      Number of atoms: 1867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1867
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
    Chain: "C"
      Number of atoms: 1867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1867
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
    Chain: "D"
      Number of atoms: 1867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1867
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
  Time building chain proxies: 4.95, per 1000 atoms: 0.66
  Number of scatterers: 7468
  At special positions: 0
  Unit cell: (102.432, 102.432, 74.976, 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      52     16.00
     O    1224      8.00
     N    1108      7.00
     C    5084      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1094 " - pdb=" SG  CYS B1150 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1150 " - pdb=" SG  CYS D1094 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1094 " - pdb=" SG  CYS C1150 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1094 " - pdb=" SG  CYS D1150 " 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: 1.73
  Conformation dependent library (CDL) restraints added in 964.7 milliseconds
  

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      83.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1001 through 1010
      removed outlier: 4.055A  pdb=" N   GLU A1010 " --> pdb=" O   THR A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1032
    Processing helix  chain 'A' and resid 1034 through 1041
    Processing helix  chain 'A' and resid 1041 through 1067
    Processing helix  chain 'A' and resid 1074 through 1087
      removed outlier: 3.539A  pdb=" N   SER A1087 " --> pdb=" O   VAL A1083 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1109
      removed outlier: 4.129A  pdb=" N   ILE A1097 " --> pdb=" O   CYS A1094 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A1098 " --> pdb=" O   PHE A1095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1115 through 1126
      removed outlier: 4.207A  pdb=" N   ILE A1119 " --> pdb=" O   GLN A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1152
      removed outlier: 4.705A  pdb=" N   SER A1132 " --> pdb=" O   PRO A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1162 through 1175
      removed outlier: 3.724A  pdb=" N   SER A1166 " --> pdb=" O   THR A1162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1183 through 1188
      removed outlier: 3.530A  pdb=" N   LEU A1187 " --> pdb=" O   ILE A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1226
      removed outlier: 3.670A  pdb=" N   PHE A1198 " --> pdb=" O   ALA A1194 " (cutoff:3.500A)
      Proline residue:  A1200  - end of helix
      removed outlier: 3.557A  pdb=" N   PHE A1203 " --> pdb=" O   ILE A1199 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   THR A1206 " --> pdb=" O   ILE A1202 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL A1213 " --> pdb=" O   MET A1209 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE A1223 " --> pdb=" O   ASP A1219 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   LEU A1224 " --> pdb=" O   ALA A1220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1227 through 1229
      No H-bonds generated for 'chain 'A' and resid 1227 through 1229'
    Processing helix  chain 'B' and resid 1002 through 1010
      removed outlier: 4.047A  pdb=" N   GLU B1010 " --> pdb=" O   THR B1006 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1011 through 1032
    Processing helix  chain 'B' and resid 1034 through 1041
    Processing helix  chain 'B' and resid 1041 through 1067
    Processing helix  chain 'B' and resid 1074 through 1087
      removed outlier: 3.559A  pdb=" N   SER B1087 " --> pdb=" O   VAL B1083 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1094 through 1109
      removed outlier: 4.292A  pdb=" N   ILE B1097 " --> pdb=" O   CYS B1094 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU B1098 " --> pdb=" O   PHE B1095 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1115 through 1126
      removed outlier: 4.215A  pdb=" N   ILE B1119 " --> pdb=" O   GLN B1115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1126 through 1152
      removed outlier: 4.681A  pdb=" N   SER B1132 " --> pdb=" O   PRO B1128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1162 through 1175
      removed outlier: 3.733A  pdb=" N   SER B1166 " --> pdb=" O   THR B1162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1183 through 1188
      removed outlier: 3.517A  pdb=" N   LEU B1187 " --> pdb=" O   ILE B1183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1194 through 1226
      removed outlier: 3.830A  pdb=" N   PHE B1198 " --> pdb=" O   ALA B1194 " (cutoff:3.500A)
      Proline residue:  B1200  - end of helix
      removed outlier: 3.581A  pdb=" N   PHE B1203 " --> pdb=" O   ILE B1199 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   THR B1206 " --> pdb=" O   ILE B1202 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL B1213 " --> pdb=" O   MET B1209 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE B1223 " --> pdb=" O   ASP B1219 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   LEU B1224 " --> pdb=" O   ALA B1220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1227 through 1229
      No H-bonds generated for 'chain 'B' and resid 1227 through 1229'
    Processing helix  chain 'C' and resid 1002 through 1010
      removed outlier: 4.047A  pdb=" N   GLU C1010 " --> pdb=" O   THR C1006 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1011 through 1032
    Processing helix  chain 'C' and resid 1034 through 1041
    Processing helix  chain 'C' and resid 1041 through 1067
    Processing helix  chain 'C' and resid 1074 through 1087
      removed outlier: 3.574A  pdb=" N   SER C1087 " --> pdb=" O   VAL C1083 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1094 through 1109
      removed outlier: 4.298A  pdb=" N   ILE C1097 " --> pdb=" O   CYS C1094 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU C1098 " --> pdb=" O   PHE C1095 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1115 through 1126
      removed outlier: 4.242A  pdb=" N   ILE C1119 " --> pdb=" O   GLN C1115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1126 through 1152
      removed outlier: 4.719A  pdb=" N   SER C1132 " --> pdb=" O   PRO C1128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1162 through 1175
      removed outlier: 3.753A  pdb=" N   SER C1166 " --> pdb=" O   THR C1162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1183 through 1188
      removed outlier: 3.520A  pdb=" N   LEU C1187 " --> pdb=" O   ILE C1183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1194 through 1226
      removed outlier: 3.671A  pdb=" N   PHE C1198 " --> pdb=" O   ALA C1194 " (cutoff:3.500A)
      Proline residue:  C1200  - end of helix
      removed outlier: 3.555A  pdb=" N   PHE C1203 " --> pdb=" O   ILE C1199 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR C1206 " --> pdb=" O   ILE C1202 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL C1213 " --> pdb=" O   MET C1209 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE C1223 " --> pdb=" O   ASP C1219 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LEU C1224 " --> pdb=" O   ALA C1220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1227 through 1229
      No H-bonds generated for 'chain 'C' and resid 1227 through 1229'
    Processing helix  chain 'D' and resid 1002 through 1010
      removed outlier: 4.040A  pdb=" N   GLU D1010 " --> pdb=" O   THR D1006 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1011 through 1033
      removed outlier: 4.132A  pdb=" N   THR D1033 " --> pdb=" O   MET D1029 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1034 through 1041
    Processing helix  chain 'D' and resid 1041 through 1067
    Processing helix  chain 'D' and resid 1074 through 1087
      removed outlier: 3.596A  pdb=" N   SER D1087 " --> pdb=" O   VAL D1083 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1094 through 1109
      removed outlier: 4.248A  pdb=" N   ILE D1097 " --> pdb=" O   CYS D1094 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU D1098 " --> pdb=" O   PHE D1095 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1115 through 1126
      removed outlier: 4.206A  pdb=" N   ILE D1119 " --> pdb=" O   GLN D1115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1126 through 1152
      removed outlier: 4.711A  pdb=" N   SER D1132 " --> pdb=" O   PRO D1128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1162 through 1175
      removed outlier: 3.722A  pdb=" N   SER D1166 " --> pdb=" O   THR D1162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1183 through 1188
    Processing helix  chain 'D' and resid 1194 through 1226
      removed outlier: 3.881A  pdb=" N   PHE D1198 " --> pdb=" O   ALA D1194 " (cutoff:3.500A)
      Proline residue:  D1200  - end of helix
      removed outlier: 3.649A  pdb=" N   PHE D1203 " --> pdb=" O   ILE D1199 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR D1206 " --> pdb=" O   ILE D1202 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL D1213 " --> pdb=" O   MET D1209 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ILE D1223 " --> pdb=" O   ASP D1219 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LEU D1224 " --> pdb=" O   ALA D1220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1227 through 1229
      No H-bonds generated for 'chain 'D' and resid 1227 through 1229'

    514 hydrogen bonds defined for protein.
    1410 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: 1.85

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2097
        1.34 -     1.47: 2167
        1.47 -     1.60: 3312
        1.60 -     1.73: 0
        1.73 -     1.86: 96
  Bond restraints: 7672
  Sorted by residual:
  bond pdb=" N   CYS A1094 "
       pdb=" CA  CYS A1094 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.020 1.29e-02 6.01e+03 2.41e+00
  bond pdb=" CB  CYS A1094 "
       pdb=" SG  CYS A1094 "
    ideal  model  delta    sigma   weight residual
    1.808  1.858 -0.050 3.30e-02 9.18e+02 2.29e+00
  bond pdb=" N   CYS C1094 "
       pdb=" CA  CYS C1094 "
    ideal  model  delta    sigma   weight residual
    1.459  1.476 -0.017 1.15e-02 7.56e+03 2.29e+00
  bond pdb=" CB  THR C1028 "
       pdb=" CG2 THR C1028 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.90e+00
  bond pdb=" CB  TRP B1179 "
       pdb=" CG  TRP B1179 "
    ideal  model  delta    sigma   weight residual
    1.498  1.456  0.042 3.10e-02 1.04e+03 1.82e+00
  ... (remaining 7667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 9836
        1.94 -     3.89: 503
        3.89 -     5.83: 64
        5.83 -     7.78: 28
        7.78 -     9.72: 5
  Bond angle restraints: 10436
  Sorted by residual:
  angle pdb=" CA  CYS A1094 "
        pdb=" CB  CYS A1094 "
        pdb=" SG  CYS A1094 "
      ideal   model   delta    sigma   weight residual
     114.40  124.12   -9.72 2.30e+00 1.89e-01 1.79e+01
  angle pdb=" N   VAL C1113 "
        pdb=" CA  VAL C1113 "
        pdb=" C   VAL C1113 "
      ideal   model   delta    sigma   weight residual
     108.88  116.37   -7.49 2.16e+00 2.14e-01 1.20e+01
  angle pdb=" N   VAL A1113 "
        pdb=" CA  VAL A1113 "
        pdb=" C   VAL A1113 "
      ideal   model   delta    sigma   weight residual
     108.88  116.17   -7.29 2.16e+00 2.14e-01 1.14e+01
  angle pdb=" N   VAL B1113 "
        pdb=" CA  VAL B1113 "
        pdb=" C   VAL B1113 "
      ideal   model   delta    sigma   weight residual
     108.88  116.12   -7.24 2.16e+00 2.14e-01 1.12e+01
  angle pdb=" C   HIS A1067 "
        pdb=" N   ARG A1068 "
        pdb=" CA  ARG A1068 "
      ideal   model   delta    sigma   weight residual
     121.54  127.84   -6.30 1.91e+00 2.74e-01 1.09e+01
  ... (remaining 10431 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 3853
       17.01 -    34.01: 486
       34.01 -    51.02: 99
       51.02 -    68.02: 5
       68.02 -    85.03: 9
  Dihedral angle restraints: 4452
    sinusoidal: 1740
      harmonic: 2712
  Sorted by residual:
  dihedral pdb=" CB  CYS A1150 "
           pdb=" SG  CYS A1150 "
           pdb=" SG  CYS D1094 "
           pdb=" CB  CYS D1094 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.03   85.03     1      1.00e+01 1.00e-02 8.77e+01
  dihedral pdb=" CB  CYS B1094 "
           pdb=" SG  CYS B1094 "
           pdb=" SG  CYS C1150 "
           pdb=" CB  CYS C1150 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -170.13   84.13     1      1.00e+01 1.00e-02 8.62e+01
  dihedral pdb=" CB  CYS C1094 "
           pdb=" SG  CYS C1094 "
           pdb=" SG  CYS D1150 "
           pdb=" CB  CYS D1150 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -169.67   83.67     1      1.00e+01 1.00e-02 8.54e+01
  ... (remaining 4449 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 725
       0.041 -    0.082: 363
       0.082 -    0.123: 117
       0.123 -    0.164: 49
       0.164 -    0.205: 10
  Chirality restraints: 1264
  Sorted by residual:
  chirality pdb=" CA  VAL C1113 "
            pdb=" N   VAL C1113 "
            pdb=" C   VAL C1113 "
            pdb=" CB  VAL C1113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.24    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  VAL D1103 "
            pdb=" CA  VAL D1103 "
            pdb=" CG1 VAL D1103 "
            pdb=" CG2 VAL D1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.08e-01
  chirality pdb=" CB  VAL D1126 "
            pdb=" CA  VAL D1126 "
            pdb=" CG1 VAL D1126 "
            pdb=" CG2 VAL D1126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.43e-01
  ... (remaining 1261 not shown)

  Planarity restraints: 1232
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D1185 "   -0.045 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO D1186 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO D1186 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D1186 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C1185 "   -0.044 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO C1186 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C1186 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C1186 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1185 "   -0.044 5.00e-02 4.00e+02   6.62e-02 7.01e+00
        pdb=" N   PRO A1186 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A1186 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A1186 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1229 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2040
        2.79 -     3.32: 7607
        3.32 -     3.85: 12230
        3.85 -     4.37: 13209
        4.37 -     4.90: 22125
  Nonbonded interactions: 57211
  Sorted by model distance:
  nonbonded pdb=" O   VAL B1083 "
            pdb=" OG  SER B1087 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   PHE B1041 "
            pdb=" OG1 THR B1045 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   ARG D1108 "
            pdb=" OG1 THR D1111 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   PHE C1041 "
            pdb=" OG1 THR C1045 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG  SER B1125 "
            pdb=" OD1 ASP B1219 "
     model   vdw
     2.308 3.040
  ... (remaining 57206 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.850
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
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      :  0.005   0.050   7672  Z= 0.349
  Angle     :  0.998   9.722  10436  Z= 0.562
  Chirality :  0.057   0.205   1264
  Planarity :  0.008   0.067   1232
  Dihedral  : 15.271  81.545   2672
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 10.53 %
    Favored  : 88.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.12 (0.20), residues: 908
  helix: -2.78 (0.14), residues: 756
  sheet:  None (None), residues: 0
  loop : -5.33 (0.32), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D1195 
 HIS   0.001   0.000   HIS C1067 
 PHE   0.025   0.002   PHE B1095 
 TYR   0.015   0.003   TYR C1142 
 ARG   0.005   0.000   ARG A1099 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 280
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1079 PHE cc_start: 0.9102 (t80) cc_final: 0.8730 (m-80)
REVERT: A 1080 ASP cc_start: 0.8779 (p0) cc_final: 0.8508 (p0)
REVERT: A 1102 ARG cc_start: 0.9019 (tpt-90) cc_final: 0.8655 (tpp-160)
REVERT: A 1117 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8769 (tpp80)
REVERT: A 1174 MET cc_start: 0.8475 (tmm) cc_final: 0.8201 (tmm)
REVERT: B 1079 PHE cc_start: 0.9082 (t80) cc_final: 0.8704 (m-10)
REVERT: B 1080 ASP cc_start: 0.8817 (p0) cc_final: 0.8566 (p0)
REVERT: B 1102 ARG cc_start: 0.8976 (tpt-90) cc_final: 0.8579 (tpp-160)
REVERT: B 1117 ARG cc_start: 0.8922 (ttt90) cc_final: 0.8668 (tpp80)
REVERT: B 1147 MET cc_start: 0.8711 (tpp) cc_final: 0.8488 (tpp)
REVERT: B 1174 MET cc_start: 0.8606 (tmm) cc_final: 0.8136 (tmm)
REVERT: C 1016 LYS cc_start: 0.6841 (tptt) cc_final: 0.6353 (mmtt)
REVERT: C 1079 PHE cc_start: 0.9036 (t80) cc_final: 0.8464 (m-10)
REVERT: C 1174 MET cc_start: 0.8621 (tmm) cc_final: 0.8326 (tmm)
REVERT: C 1192 PRO cc_start: 0.9055 (Cg_endo) cc_final: 0.8808 (Cg_exo)
REVERT: D 1016 LYS cc_start: 0.6857 (tptt) cc_final: 0.6570 (mmtt)
REVERT: D 1025 ASN cc_start: 0.8912 (t0) cc_final: 0.8652 (t0)
REVERT: D 1079 PHE cc_start: 0.9083 (t80) cc_final: 0.8587 (m-10)
REVERT: D 1174 MET cc_start: 0.8564 (tmm) cc_final: 0.8085 (tmm)
REVERT: D 1192 PRO cc_start: 0.9026 (Cg_endo) cc_final: 0.8799 (Cg_exo)
  outliers start: 5
  outliers final: 3
  residues processed: 285
  average time/residue: 0.2195
  time to fit residues: 80.3547
Evaluate side-chains
  217 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 214
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1196 VAL
Chi-restraints excluded: chain C residue 1196 VAL
Chi-restraints excluded: chain D residue 1196 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    0.2980
   chunk 22 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A1007 ASN
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 HIS
B1007 ASN
B1050 GLN
B1067 HIS
C1007 ASN
C1050 GLN
D1007 ASN
D1050 GLN
D1067 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.136117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.117969 restraints weight = 22107.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.120680 restraints weight = 13670.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.122176 restraints weight = 9627.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7672  Z= 0.245
  Angle     :  0.729   6.920  10436  Z= 0.390
  Chirality :  0.044   0.167   1264
  Planarity :  0.005   0.035   1232
  Dihedral  :  5.909  26.436    983
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 17.82 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.25), residues: 908
  helix: -1.33 (0.17), residues: 764
  sheet:  None (None), residues: 0
  loop : -4.82 (0.38), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C1179 
 HIS   0.001   0.000   HIS C1067 
 PHE   0.030   0.002   PHE C1056 
 TYR   0.039   0.002   TYR B1020 
 ARG   0.004   0.000   ARG C1063 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 237
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.7037 (tptt) cc_final: 0.6583 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8551 (t0) cc_final: 0.8081 (t0)
REVERT: A 1071 PHE cc_start: 0.8497 (t80) cc_final: 0.8129 (t80)
REVERT: A 1074 ASP cc_start: 0.8700 (t0) cc_final: 0.8424 (t0)
REVERT: A 1079 PHE cc_start: 0.9174 (t80) cc_final: 0.8726 (m-80)
REVERT: A 1102 ARG cc_start: 0.9099 (tpt-90) cc_final: 0.8791 (tpp-160)
REVERT: A 1117 ARG cc_start: 0.9118 (ttt90) cc_final: 0.8813 (tpp80)
REVERT: A 1168 TYR cc_start: 0.8319 (t80) cc_final: 0.8068 (t80)
REVERT: A 1172 GLN cc_start: 0.9307 (tm-30) cc_final: 0.8585 (tp40)
REVERT: A 1174 MET cc_start: 0.8620 (tmm) cc_final: 0.8088 (tmm)
REVERT: A 1179 TRP cc_start: 0.7897 (p-90) cc_final: 0.7669 (p-90)
REVERT: A 1209 MET cc_start: 0.6015 (ttt) cc_final: 0.5732 (tmm)
REVERT: B 1049 LYS cc_start: 0.9300 (mttt) cc_final: 0.8830 (mttp)
REVERT: B 1050 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8516 (mm-40)
REVERT: B 1073 LYS cc_start: 0.7673 (tptp) cc_final: 0.7464 (tptp)
REVERT: B 1074 ASP cc_start: 0.8567 (t0) cc_final: 0.8220 (t0)
REVERT: B 1079 PHE cc_start: 0.9157 (t80) cc_final: 0.8749 (m-80)
REVERT: B 1102 ARG cc_start: 0.9128 (tpt-90) cc_final: 0.8756 (tpp-160)
REVERT: B 1117 ARG cc_start: 0.9084 (ttt90) cc_final: 0.8819 (tpp80)
REVERT: B 1172 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8605 (tp40)
REVERT: B 1174 MET cc_start: 0.8731 (tmm) cc_final: 0.8159 (tmm)
REVERT: B 1179 TRP cc_start: 0.7908 (p-90) cc_final: 0.7559 (p-90)
REVERT: C 1016 LYS cc_start: 0.6906 (tptt) cc_final: 0.6578 (mmtt)
REVERT: C 1074 ASP cc_start: 0.8747 (t0) cc_final: 0.8498 (t0)
REVERT: C 1079 PHE cc_start: 0.9136 (t80) cc_final: 0.8618 (m-80)
REVERT: C 1174 MET cc_start: 0.8705 (tmm) cc_final: 0.8136 (tmm)
REVERT: C 1179 TRP cc_start: 0.7912 (p-90) cc_final: 0.7598 (p-90)
REVERT: D 1016 LYS cc_start: 0.6871 (tptt) cc_final: 0.6528 (mmtt)
REVERT: D 1025 ASN cc_start: 0.9090 (t0) cc_final: 0.8745 (t0)
REVERT: D 1079 PHE cc_start: 0.9180 (t80) cc_final: 0.8711 (m-80)
REVERT: D 1102 ARG cc_start: 0.9099 (tpp-160) cc_final: 0.8790 (tpp80)
REVERT: D 1174 MET cc_start: 0.8705 (tmm) cc_final: 0.8098 (tmm)
  outliers start: 40
  outliers final: 24
  residues processed: 257
  average time/residue: 0.2131
  time to fit residues: 70.2969
Evaluate side-chains
  240 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 216
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1067 HIS
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1067 HIS
Chi-restraints excluded: chain B residue 1101 LEU
Chi-restraints excluded: chain B residue 1138 THR
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1170 LEU
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1138 THR
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1170 LEU
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1067 HIS
Chi-restraints excluded: chain D residue 1101 LEU
Chi-restraints excluded: chain D residue 1138 THR
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1170 LEU
Chi-restraints excluded: chain D residue 1187 LEU
Chi-restraints excluded: chain D residue 1196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 86 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 84 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1007 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 = 0.4046 r_free = 0.4046 target = 0.134695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.116964 restraints weight = 22692.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.119497 restraints weight = 13766.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.121495 restraints weight = 9565.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7672  Z= 0.225
  Angle     :  0.718   7.023  10436  Z= 0.380
  Chirality :  0.044   0.172   1264
  Planarity :  0.005   0.045   1232
  Dihedral  :  5.551  23.644    981
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 19.74 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.26), residues: 908
  helix: -0.71 (0.18), residues: 764
  sheet:  None (None), residues: 0
  loop : -4.60 (0.40), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP D1179 
 HIS   0.002   0.001   HIS A1067 
 PHE   0.048   0.002   PHE D1048 
 TYR   0.056   0.002   TYR B1020 
 ARG   0.006   0.001   ARG C1185 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 243
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.7079 (tptt) cc_final: 0.6563 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8518 (t0) cc_final: 0.8044 (t0)
REVERT: A 1079 PHE cc_start: 0.9167 (t80) cc_final: 0.8870 (m-80)
REVERT: A 1102 ARG cc_start: 0.9136 (tpt-90) cc_final: 0.8758 (tpp-160)
REVERT: A 1174 MET cc_start: 0.8609 (tmm) cc_final: 0.8104 (tmm)
REVERT: B 1050 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8548 (mm-40)
REVERT: B 1073 LYS cc_start: 0.7757 (tptp) cc_final: 0.7478 (tptp)
REVERT: B 1074 ASP cc_start: 0.8611 (t0) cc_final: 0.8232 (t0)
REVERT: B 1079 PHE cc_start: 0.9157 (t80) cc_final: 0.8799 (m-80)
REVERT: B 1102 ARG cc_start: 0.9157 (tpt-90) cc_final: 0.8749 (tpp80)
REVERT: B 1117 ARG cc_start: 0.9073 (ttt90) cc_final: 0.8826 (tpp80)
REVERT: B 1174 MET cc_start: 0.8626 (tmm) cc_final: 0.8127 (tmm)
REVERT: C 1016 LYS cc_start: 0.6884 (tptt) cc_final: 0.6518 (mmtt)
REVERT: C 1073 LYS cc_start: 0.7514 (tptp) cc_final: 0.7310 (tptp)
REVERT: C 1074 ASP cc_start: 0.8735 (t0) cc_final: 0.8496 (t0)
REVERT: C 1079 PHE cc_start: 0.9164 (t80) cc_final: 0.8676 (m-80)
REVERT: C 1174 MET cc_start: 0.8646 (tmm) cc_final: 0.8053 (tmm)
REVERT: D 1016 LYS cc_start: 0.6865 (tptt) cc_final: 0.6491 (mmtt)
REVERT: D 1025 ASN cc_start: 0.9016 (t0) cc_final: 0.8713 (t0)
REVERT: D 1074 ASP cc_start: 0.8683 (t0) cc_final: 0.8373 (t0)
REVERT: D 1079 PHE cc_start: 0.9153 (t80) cc_final: 0.8723 (m-80)
REVERT: D 1174 MET cc_start: 0.8611 (tmm) cc_final: 0.8072 (tmm)
  outliers start: 43
  outliers final: 25
  residues processed: 266
  average time/residue: 0.2103
  time to fit residues: 72.3434
Evaluate side-chains
  244 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 219
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1198 PHE
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1071 PHE
Chi-restraints excluded: chain B residue 1101 LEU
Chi-restraints excluded: chain B residue 1138 THR
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1176 LEU
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1170 LEU
Chi-restraints excluded: chain C residue 1176 LEU
Chi-restraints excluded: chain C residue 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1078 LEU
Chi-restraints excluded: chain D residue 1101 LEU
Chi-restraints excluded: chain D residue 1138 THR
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1170 LEU
Chi-restraints excluded: chain D residue 1176 LEU
Chi-restraints excluded: chain D residue 1196 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 82 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1067 HIS
** D1025 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 = 0.4069 r_free = 0.4069 target = 0.135745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.117508 restraints weight = 22315.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.120114 restraints weight = 13486.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.121952 restraints weight = 9398.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7672  Z= 0.206
  Angle     :  0.715   6.801  10436  Z= 0.373
  Chirality :  0.044   0.165   1264
  Planarity :  0.004   0.030   1232
  Dihedral  :  5.325  22.673    981
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 19.50 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.27), residues: 908
  helix: -0.36 (0.18), residues: 768
  sheet:  None (None), residues: 0
  loop : -4.34 (0.42), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP C1179 
 HIS   0.001   0.000   HIS C1067 
 PHE   0.051   0.002   PHE C1048 
 TYR   0.047   0.002   TYR B1020 
 ARG   0.006   0.000   ARG C1117 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 226
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.7034 (tptt) cc_final: 0.6716 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8464 (t0) cc_final: 0.8121 (t0)
REVERT: A 1063 ARG cc_start: 0.8618 (ptp-170) cc_final: 0.8270 (ptm160)
REVERT: A 1074 ASP cc_start: 0.8798 (t0) cc_final: 0.8492 (t0)
REVERT: A 1079 PHE cc_start: 0.9161 (t80) cc_final: 0.8836 (m-80)
REVERT: A 1102 ARG cc_start: 0.8991 (tpt-90) cc_final: 0.8448 (tpp80)
REVERT: A 1174 MET cc_start: 0.8587 (tmm) cc_final: 0.8112 (tmm)
REVERT: B 1032 GLU cc_start: 0.7555 (tt0) cc_final: 0.7280 (mm-30)
REVERT: B 1050 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8556 (mm-40)
REVERT: B 1073 LYS cc_start: 0.7843 (tptp) cc_final: 0.7553 (tptp)
REVERT: B 1074 ASP cc_start: 0.8627 (t0) cc_final: 0.8215 (t0)
REVERT: B 1079 PHE cc_start: 0.9162 (t80) cc_final: 0.8851 (m-80)
REVERT: B 1102 ARG cc_start: 0.9119 (tpt-90) cc_final: 0.8663 (tpp80)
REVERT: B 1172 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8624 (tp40)
REVERT: B 1174 MET cc_start: 0.8665 (tmm) cc_final: 0.8125 (tmm)
REVERT: C 1016 LYS cc_start: 0.6881 (tptt) cc_final: 0.6506 (mmtt)
REVERT: C 1050 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8405 (mm-40)
REVERT: C 1073 LYS cc_start: 0.7585 (tptp) cc_final: 0.7309 (tptp)
REVERT: C 1074 ASP cc_start: 0.8748 (t0) cc_final: 0.8458 (t0)
REVERT: C 1079 PHE cc_start: 0.9171 (t80) cc_final: 0.8803 (m-80)
REVERT: C 1174 MET cc_start: 0.8681 (tmm) cc_final: 0.8095 (tmm)
REVERT: D 1016 LYS cc_start: 0.6849 (tptt) cc_final: 0.6490 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9184 (t80) cc_final: 0.8805 (m-80)
REVERT: D 1174 MET cc_start: 0.8643 (tmm) cc_final: 0.8098 (tmm)
  outliers start: 46
  outliers final: 31
  residues processed: 254
  average time/residue: 0.2138
  time to fit residues: 69.7523
Evaluate side-chains
  250 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 219
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LYS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1198 PHE
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1057 THR
Chi-restraints excluded: chain B residue 1067 HIS
Chi-restraints excluded: chain B residue 1071 PHE
Chi-restraints excluded: chain B residue 1078 LEU
Chi-restraints excluded: chain B residue 1101 LEU
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1170 LEU
Chi-restraints excluded: chain B residue 1176 LEU
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1056 PHE
Chi-restraints excluded: chain C residue 1078 LEU
Chi-restraints excluded: chain C residue 1101 LEU
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1176 LEU
Chi-restraints excluded: chain C residue 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1056 PHE
Chi-restraints excluded: chain D residue 1078 LEU
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1176 LEU
Chi-restraints excluded: chain D residue 1196 VAL
Chi-restraints excluded: chain D residue 1208 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 77 optimal weight:    0.0980
   chunk 49 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 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 = 0.4067 r_free = 0.4067 target = 0.135372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.117486 restraints weight = 22270.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.120005 restraints weight = 13576.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.122079 restraints weight = 9485.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7672  Z= 0.207
  Angle     :  0.729   7.261  10436  Z= 0.377
  Chirality :  0.044   0.140   1264
  Planarity :  0.004   0.030   1232
  Dihedral  :  5.250  22.187    981
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 23.21 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.28), residues: 908
  helix: -0.13 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop : -4.08 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A1179 
 HIS   0.004   0.001   HIS B1067 
 PHE   0.055   0.002   PHE D1048 
 TYR   0.043   0.002   TYR B1020 
 ARG   0.006   0.001   ARG A1117 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 225
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.7019 (tptt) cc_final: 0.6692 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8491 (t0) cc_final: 0.7947 (t0)
REVERT: A 1063 ARG cc_start: 0.8632 (ptp-170) cc_final: 0.8322 (ptm160)
REVERT: A 1079 PHE cc_start: 0.9144 (t80) cc_final: 0.8863 (m-80)
REVERT: A 1102 ARG cc_start: 0.8947 (tpt-90) cc_final: 0.8517 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8530 (mmm-85)
REVERT: A 1174 MET cc_start: 0.8557 (tmm) cc_final: 0.8060 (tmm)
REVERT: B 1032 GLU cc_start: 0.7585 (tt0) cc_final: 0.7317 (mm-30)
REVERT: B 1073 LYS cc_start: 0.7830 (tptp) cc_final: 0.7540 (tptp)
REVERT: B 1074 ASP cc_start: 0.8740 (t0) cc_final: 0.8337 (t0)
REVERT: B 1079 PHE cc_start: 0.9096 (t80) cc_final: 0.8849 (m-80)
REVERT: B 1102 ARG cc_start: 0.9105 (tpt-90) cc_final: 0.8571 (tpp80)
REVERT: B 1174 MET cc_start: 0.8630 (tmm) cc_final: 0.8090 (tmm)
REVERT: C 1016 LYS cc_start: 0.6864 (tptt) cc_final: 0.6497 (mmtt)
REVERT: C 1050 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8423 (mm-40)
REVERT: C 1073 LYS cc_start: 0.7547 (tptp) cc_final: 0.7265 (tptp)
REVERT: C 1074 ASP cc_start: 0.8796 (t0) cc_final: 0.8494 (t0)
REVERT: C 1079 PHE cc_start: 0.9138 (t80) cc_final: 0.8852 (m-80)
REVERT: C 1174 MET cc_start: 0.8650 (tmm) cc_final: 0.8071 (tmm)
REVERT: D 1016 LYS cc_start: 0.6932 (tptt) cc_final: 0.6561 (mmtt)
REVERT: D 1073 LYS cc_start: 0.7553 (tptp) cc_final: 0.7332 (tptp)
REVERT: D 1079 PHE cc_start: 0.9260 (t80) cc_final: 0.8918 (m-80)
REVERT: D 1172 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8710 (tp40)
REVERT: D 1174 MET cc_start: 0.8605 (tmm) cc_final: 0.8048 (tmm)
  outliers start: 47
  outliers final: 34
  residues processed: 254
  average time/residue: 0.2308
  time to fit residues: 75.9863
Evaluate side-chains
  255 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 221
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LYS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1198 PHE
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1057 THR
Chi-restraints excluded: chain B residue 1078 LEU
Chi-restraints excluded: chain B residue 1101 LEU
Chi-restraints excluded: chain B residue 1138 THR
Chi-restraints excluded: chain B residue 1143 ILE
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1176 LEU
Chi-restraints excluded: chain B residue 1198 PHE
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1067 HIS
Chi-restraints excluded: chain C residue 1078 LEU
Chi-restraints excluded: chain C residue 1151 LEU
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1176 LEU
Chi-restraints excluded: chain C residue 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1056 PHE
Chi-restraints excluded: chain D residue 1067 HIS
Chi-restraints excluded: chain D residue 1078 LEU
Chi-restraints excluded: chain D residue 1151 LEU
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1176 LEU
Chi-restraints excluded: chain D residue 1196 VAL
Chi-restraints excluded: chain D residue 1208 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0010
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 86 optimal weight:    0.4980
   chunk 76 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 HIS
C1211 ASN
** D1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1211 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.134822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.116775 restraints weight = 22359.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.119374 restraints weight = 13617.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.121371 restraints weight = 9488.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7672  Z= 0.200
  Angle     :  0.726   7.116  10436  Z= 0.375
  Chirality :  0.044   0.173   1264
  Planarity :  0.004   0.031   1232
  Dihedral  :  5.159  21.607    981
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 25.00 %
    Favored  : 69.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.28), residues: 908
  helix:  0.02 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop : -3.79 (0.47), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A1179 
 HIS   0.005   0.001   HIS A1067 
 PHE   0.057   0.002   PHE D1048 
 TYR   0.041   0.002   TYR B1020 
 ARG   0.006   0.001   ARG D1117 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 234
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.7022 (tptt) cc_final: 0.6680 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8483 (t0) cc_final: 0.8115 (t0)
REVERT: A 1063 ARG cc_start: 0.8644 (ptp-170) cc_final: 0.8288 (ptm160)
REVERT: A 1074 ASP cc_start: 0.8777 (t0) cc_final: 0.8521 (t0)
REVERT: A 1077 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7944 (p)
REVERT: A 1079 PHE cc_start: 0.9121 (t80) cc_final: 0.8890 (m-80)
REVERT: A 1102 ARG cc_start: 0.8927 (tpt-90) cc_final: 0.8564 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8613 (mmm-85)
REVERT: A 1174 MET cc_start: 0.8519 (tmm) cc_final: 0.8035 (tmm)
REVERT: B 1029 MET cc_start: 0.8496 (mmp) cc_final: 0.8166 (mmp)
REVERT: B 1032 GLU cc_start: 0.7520 (tt0) cc_final: 0.7020 (mt-10)
REVERT: B 1073 LYS cc_start: 0.7798 (tptp) cc_final: 0.7562 (tptp)
REVERT: B 1074 ASP cc_start: 0.8813 (t0) cc_final: 0.8389 (t0)
REVERT: B 1102 ARG cc_start: 0.9114 (tpt-90) cc_final: 0.8760 (tpp80)
REVERT: B 1147 MET cc_start: 0.8667 (tpp) cc_final: 0.8436 (tpp)
REVERT: B 1174 MET cc_start: 0.8587 (tmm) cc_final: 0.8018 (tmm)
REVERT: C 1016 LYS cc_start: 0.6805 (tptt) cc_final: 0.6411 (mmtt)
REVERT: C 1050 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8424 (mm-40)
REVERT: C 1073 LYS cc_start: 0.7548 (tptp) cc_final: 0.7343 (tptp)
REVERT: C 1074 ASP cc_start: 0.8802 (t0) cc_final: 0.8495 (t0)
REVERT: C 1079 PHE cc_start: 0.9226 (t80) cc_final: 0.8923 (m-80)
REVERT: C 1101 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: C 1174 MET cc_start: 0.8593 (tmm) cc_final: 0.7980 (tmm)
REVERT: D 1016 LYS cc_start: 0.6884 (tptt) cc_final: 0.6497 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9185 (t80) cc_final: 0.8904 (m-80)
REVERT: D 1172 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8747 (tp40)
REVERT: D 1174 MET cc_start: 0.8551 (tmm) cc_final: 0.7958 (tmm)
  outliers start: 45
  outliers final: 37
  residues processed: 256
  average time/residue: 0.2220
  time to fit residues: 72.6476
Evaluate side-chains
  256 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 217
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LYS
Chi-restraints excluded: chain A residue 1067 HIS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1077 SER
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1198 PHE
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1057 THR
Chi-restraints excluded: chain B residue 1071 PHE
Chi-restraints excluded: chain B residue 1078 LEU
Chi-restraints excluded: chain B residue 1138 THR
Chi-restraints excluded: chain B residue 1143 ILE
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1176 LEU
Chi-restraints excluded: chain B residue 1198 PHE
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1067 HIS
Chi-restraints excluded: chain C residue 1078 LEU
Chi-restraints excluded: chain C residue 1097 ILE
Chi-restraints excluded: chain C residue 1101 LEU
Chi-restraints excluded: chain C residue 1151 LEU
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1176 LEU
Chi-restraints excluded: chain C residue 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1035 LYS
Chi-restraints excluded: chain D residue 1056 PHE
Chi-restraints excluded: chain D residue 1067 HIS
Chi-restraints excluded: chain D residue 1078 LEU
Chi-restraints excluded: chain D residue 1138 THR
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1176 LEU
Chi-restraints excluded: chain D residue 1198 PHE
Chi-restraints excluded: chain D residue 1208 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 HIS
A1211 ASN
** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1025 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 = 0.4031 r_free = 0.4031 target = 0.132828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.114933 restraints weight = 22572.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.117477 restraints weight = 13531.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.119404 restraints weight = 9392.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7672  Z= 0.241
  Angle     :  0.767   7.238  10436  Z= 0.399
  Chirality :  0.046   0.179   1264
  Planarity :  0.004   0.032   1232
  Dihedral  :  5.162  19.310    980
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 25.48 %
    Favored  : 68.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.28), residues: 908
  helix:  0.06 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop : -3.70 (0.48), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A1179 
 HIS   0.009   0.002   HIS A1067 
 PHE   0.055   0.002   PHE C1048 
 TYR   0.039   0.002   TYR B1020 
 ARG   0.005   0.001   ARG A1117 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 233
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.6947 (tptt) cc_final: 0.6655 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8582 (t0) cc_final: 0.8228 (t0)
REVERT: A 1063 ARG cc_start: 0.8712 (ptp-170) cc_final: 0.8445 (ptm160)
REVERT: A 1079 PHE cc_start: 0.9141 (t80) cc_final: 0.8892 (m-80)
REVERT: A 1102 ARG cc_start: 0.8948 (tpt-90) cc_final: 0.8522 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8634 (mmm-85)
REVERT: A 1174 MET cc_start: 0.8559 (tmm) cc_final: 0.8122 (tmm)
REVERT: B 1073 LYS cc_start: 0.7858 (tptp) cc_final: 0.7657 (tptp)
REVERT: B 1074 ASP cc_start: 0.8677 (t0) cc_final: 0.8200 (t0)
REVERT: B 1079 PHE cc_start: 0.7092 (m-80) cc_final: 0.6819 (m-80)
REVERT: B 1102 ARG cc_start: 0.9055 (tpt-90) cc_final: 0.8596 (tpp80)
REVERT: B 1174 MET cc_start: 0.8577 (tmm) cc_final: 0.7966 (tmm)
REVERT: C 1016 LYS cc_start: 0.6922 (tptt) cc_final: 0.6561 (mmtt)
REVERT: C 1025 ASN cc_start: 0.8950 (t0) cc_final: 0.8722 (t0)
REVERT: C 1074 ASP cc_start: 0.8774 (t0) cc_final: 0.8449 (t0)
REVERT: C 1079 PHE cc_start: 0.9240 (t80) cc_final: 0.8937 (m-80)
REVERT: C 1099 ARG cc_start: 0.8589 (ptt90) cc_final: 0.8225 (pmt-80)
REVERT: C 1174 MET cc_start: 0.8603 (tmm) cc_final: 0.8063 (tmm)
REVERT: D 1016 LYS cc_start: 0.6942 (tptt) cc_final: 0.6571 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9188 (t80) cc_final: 0.8920 (m-80)
REVERT: D 1172 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8706 (tp40)
REVERT: D 1174 MET cc_start: 0.8559 (tmm) cc_final: 0.8048 (tmm)
  outliers start: 52
  outliers final: 44
  residues processed: 259
  average time/residue: 0.2177
  time to fit residues: 72.4535
Evaluate side-chains
  264 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 220
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LYS
Chi-restraints excluded: chain A residue 1067 HIS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1198 PHE
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1035 LYS
Chi-restraints excluded: chain B residue 1057 THR
Chi-restraints excluded: chain B residue 1071 PHE
Chi-restraints excluded: chain B residue 1101 LEU
Chi-restraints excluded: chain B residue 1138 THR
Chi-restraints excluded: chain B residue 1143 ILE
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1176 LEU
Chi-restraints excluded: chain B residue 1196 VAL
Chi-restraints excluded: chain B residue 1198 PHE
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1035 LYS
Chi-restraints excluded: chain C residue 1056 PHE
Chi-restraints excluded: chain C residue 1067 HIS
Chi-restraints excluded: chain C residue 1078 LEU
Chi-restraints excluded: chain C residue 1138 THR
Chi-restraints excluded: chain C residue 1151 LEU
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1176 LEU
Chi-restraints excluded: chain C residue 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1035 LYS
Chi-restraints excluded: chain D residue 1056 PHE
Chi-restraints excluded: chain D residue 1067 HIS
Chi-restraints excluded: chain D residue 1078 LEU
Chi-restraints excluded: chain D residue 1138 THR
Chi-restraints excluded: chain D residue 1143 ILE
Chi-restraints excluded: chain D residue 1151 LEU
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1176 LEU
Chi-restraints excluded: chain D residue 1196 VAL
Chi-restraints excluded: chain D residue 1198 PHE
Chi-restraints excluded: chain D residue 1208 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    0.0070
   chunk 56 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1067 HIS
** D1025 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 = 0.4051 r_free = 0.4051 target = 0.133738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.115456 restraints weight = 22830.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.118182 restraints weight = 14106.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.120160 restraints weight = 9804.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7672  Z= 0.225
  Angle     :  0.810   9.571  10436  Z= 0.417
  Chirality :  0.048   0.230   1264
  Planarity :  0.004   0.031   1232
  Dihedral  :  5.223  21.484    980
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 26.56 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.28), residues: 908
  helix:  0.07 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop : -3.41 (0.53), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP D1179 
 HIS   0.010   0.002   HIS A1067 
 PHE   0.057   0.002   PHE D1048 
 TYR   0.042   0.002   TYR B1020 
 ARG   0.008   0.001   ARG D1117 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 242
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.6971 (tptt) cc_final: 0.6675 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8439 (t0) cc_final: 0.8061 (t0)
REVERT: A 1063 ARG cc_start: 0.8706 (ptp-170) cc_final: 0.8349 (ptm160)
REVERT: A 1079 PHE cc_start: 0.9152 (t80) cc_final: 0.8916 (m-80)
REVERT: A 1102 ARG cc_start: 0.8901 (tpt-90) cc_final: 0.8576 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8684 (mmm-85)
REVERT: A 1172 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8626 (tp40)
REVERT: B 1074 ASP cc_start: 0.8671 (t0) cc_final: 0.8183 (t0)
REVERT: B 1079 PHE cc_start: 0.7028 (m-80) cc_final: 0.6737 (m-80)
REVERT: B 1102 ARG cc_start: 0.9027 (tpt-90) cc_final: 0.8552 (tpp80)
REVERT: B 1147 MET cc_start: 0.8708 (tpp) cc_final: 0.8354 (tpp)
REVERT: B 1174 MET cc_start: 0.8568 (tmm) cc_final: 0.8100 (tmm)
REVERT: C 1016 LYS cc_start: 0.6896 (tptt) cc_final: 0.6520 (mmtt)
REVERT: C 1025 ASN cc_start: 0.8867 (t0) cc_final: 0.8575 (t0)
REVERT: C 1079 PHE cc_start: 0.9191 (t80) cc_final: 0.8956 (m-80)
REVERT: C 1099 ARG cc_start: 0.8495 (ptt90) cc_final: 0.8186 (pmt-80)
REVERT: C 1172 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8580 (tp40)
REVERT: D 1016 LYS cc_start: 0.6914 (tptt) cc_final: 0.6533 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9155 (t80) cc_final: 0.8907 (m-80)
REVERT: D 1172 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8511 (tp40)
  outliers start: 55
  outliers final: 46
  residues processed: 269
  average time/residue: 0.2145
  time to fit residues: 74.2893
Evaluate side-chains
  268 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 222
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LYS
Chi-restraints excluded: chain A residue 1067 HIS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1198 PHE
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1035 LYS
Chi-restraints excluded: chain B residue 1057 THR
Chi-restraints excluded: chain B residue 1071 PHE
Chi-restraints excluded: chain B residue 1138 THR
Chi-restraints excluded: chain B residue 1143 ILE
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1176 LEU
Chi-restraints excluded: chain B residue 1196 VAL
Chi-restraints excluded: chain B residue 1198 PHE
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1035 LYS
Chi-restraints excluded: chain C residue 1056 PHE
Chi-restraints excluded: chain C residue 1067 HIS
Chi-restraints excluded: chain C residue 1078 LEU
Chi-restraints excluded: chain C residue 1098 LEU
Chi-restraints excluded: chain C residue 1151 LEU
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1170 LEU
Chi-restraints excluded: chain C residue 1176 LEU
Chi-restraints excluded: chain C residue 1196 VAL
Chi-restraints excluded: chain C residue 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1035 LYS
Chi-restraints excluded: chain D residue 1056 PHE
Chi-restraints excluded: chain D residue 1067 HIS
Chi-restraints excluded: chain D residue 1078 LEU
Chi-restraints excluded: chain D residue 1138 THR
Chi-restraints excluded: chain D residue 1143 ILE
Chi-restraints excluded: chain D residue 1151 LEU
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1196 VAL
Chi-restraints excluded: chain D residue 1198 PHE
Chi-restraints excluded: chain D residue 1208 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 82 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0060
   chunk 45 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1025 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 = 0.4059 r_free = 0.4059 target = 0.134331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.116213 restraints weight = 23102.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.118983 restraints weight = 14040.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.120922 restraints weight = 9736.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7672  Z= 0.227
  Angle     :  0.873  13.356  10436  Z= 0.440
  Chirality :  0.049   0.246   1264
  Planarity :  0.005   0.030   1232
  Dihedral  :  5.282  24.373    980
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 18.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 28.83 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.28), residues: 908
  helix:  0.12 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop : -3.46 (0.51), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP B1179 
 HIS   0.010   0.002   HIS C1067 
 PHE   0.062   0.002   PHE C1048 
 TYR   0.044   0.002   TYR B1020 
 ARG   0.007   0.001   ARG C1117 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 229
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.6964 (tptt) cc_final: 0.6656 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8488 (t0) cc_final: 0.8130 (t0)
REVERT: A 1063 ARG cc_start: 0.8711 (ptp-170) cc_final: 0.8413 (ptm160)
REVERT: A 1076 TRP cc_start: 0.8808 (m100) cc_final: 0.8177 (m-90)
REVERT: A 1102 ARG cc_start: 0.8870 (tpt-90) cc_final: 0.8534 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8710 (mmm-85)
REVERT: A 1172 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8593 (tp40)
REVERT: A 1174 MET cc_start: 0.7846 (tmm) cc_final: 0.7623 (tmm)
REVERT: A 1179 TRP cc_start: 0.7869 (p-90) cc_final: 0.7182 (p-90)
REVERT: B 1074 ASP cc_start: 0.8711 (t0) cc_final: 0.8428 (t0)
REVERT: B 1077 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7731 (p)
REVERT: B 1079 PHE cc_start: 0.6954 (m-80) cc_final: 0.6664 (m-80)
REVERT: B 1097 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9020 (mm)
REVERT: B 1102 ARG cc_start: 0.9018 (tpt-90) cc_final: 0.8575 (tpp80)
REVERT: B 1147 MET cc_start: 0.8720 (tpp) cc_final: 0.8274 (tpp)
REVERT: B 1172 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8617 (tp40)
REVERT: C 1016 LYS cc_start: 0.6915 (tptt) cc_final: 0.6535 (mmtt)
REVERT: C 1025 ASN cc_start: 0.8758 (t0) cc_final: 0.8433 (t0)
REVERT: C 1079 PHE cc_start: 0.9161 (t80) cc_final: 0.8957 (m-80)
REVERT: C 1099 ARG cc_start: 0.8457 (ptt90) cc_final: 0.8092 (pmt-80)
REVERT: C 1172 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8626 (tp40)
REVERT: C 1174 MET cc_start: 0.8122 (tmm) cc_final: 0.7837 (tmm)
REVERT: D 1016 LYS cc_start: 0.6940 (tptt) cc_final: 0.6541 (mmtt)
REVERT: D 1073 LYS cc_start: 0.7580 (tptp) cc_final: 0.7335 (tptp)
REVERT: D 1079 PHE cc_start: 0.9105 (t80) cc_final: 0.8886 (m-80)
REVERT: D 1099 ARG cc_start: 0.8567 (ptm-80) cc_final: 0.8365 (ptt90)
REVERT: D 1172 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8592 (tp40)
REVERT: D 1174 MET cc_start: 0.7657 (tmm) cc_final: 0.7412 (tmm)
  outliers start: 45
  outliers final: 41
  residues processed: 253
  average time/residue: 0.2261
  time to fit residues: 73.3571
Evaluate side-chains
  262 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 219
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LYS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1196 VAL
Chi-restraints excluded: chain A residue 1198 PHE
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1035 LYS
Chi-restraints excluded: chain B residue 1057 THR
Chi-restraints excluded: chain B residue 1071 PHE
Chi-restraints excluded: chain B residue 1077 SER
Chi-restraints excluded: chain B residue 1097 ILE
Chi-restraints excluded: chain B residue 1138 THR
Chi-restraints excluded: chain B residue 1143 ILE
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1176 LEU
Chi-restraints excluded: chain B residue 1196 VAL
Chi-restraints excluded: chain B residue 1198 PHE
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1035 LYS
Chi-restraints excluded: chain C residue 1056 PHE
Chi-restraints excluded: chain C residue 1078 LEU
Chi-restraints excluded: chain C residue 1098 LEU
Chi-restraints excluded: chain C residue 1151 LEU
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1170 LEU
Chi-restraints excluded: chain C residue 1196 VAL
Chi-restraints excluded: chain C residue 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1035 LYS
Chi-restraints excluded: chain D residue 1056 PHE
Chi-restraints excluded: chain D residue 1067 HIS
Chi-restraints excluded: chain D residue 1078 LEU
Chi-restraints excluded: chain D residue 1138 THR
Chi-restraints excluded: chain D residue 1143 ILE
Chi-restraints excluded: chain D residue 1151 LEU
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1196 VAL
Chi-restraints excluded: chain D residue 1208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 81 optimal weight:    0.3980
   chunk 69 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1067 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1067 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.133807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.115655 restraints weight = 23237.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.118281 restraints weight = 14032.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.120294 restraints weight = 9823.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7672  Z= 0.239
  Angle     :  0.909  14.734  10436  Z= 0.458
  Chirality :  0.050   0.225   1264
  Planarity :  0.005   0.032   1232
  Dihedral  :  5.338  23.920    980
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 30.62 %
    Favored  : 64.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.28), residues: 908
  helix:  0.15 (0.19), residues: 764
  sheet:  None (None), residues: 0
  loop : -3.55 (0.49), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP C1179 
 HIS   0.008   0.002   HIS A1067 
 PHE   0.062   0.002   PHE C1048 
 TYR   0.045   0.002   TYR B1020 
 ARG   0.007   0.001   ARG D1117 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 240
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.6976 (tptt) cc_final: 0.6671 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8396 (t0) cc_final: 0.8105 (t0)
REVERT: A 1063 ARG cc_start: 0.8650 (ptp-170) cc_final: 0.8332 (ptm160)
REVERT: A 1079 PHE cc_start: 0.7221 (m-80) cc_final: 0.6967 (m-80)
REVERT: A 1117 ARG cc_start: 0.8955 (mmm-85) cc_final: 0.8727 (mmm-85)
REVERT: A 1172 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8619 (tp40)
REVERT: A 1179 TRP cc_start: 0.7896 (p-90) cc_final: 0.7257 (p-90)
REVERT: B 1074 ASP cc_start: 0.8640 (t0) cc_final: 0.8354 (t0)
REVERT: B 1077 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.7757 (p)
REVERT: B 1079 PHE cc_start: 0.7004 (m-80) cc_final: 0.6712 (m-80)
REVERT: B 1102 ARG cc_start: 0.8971 (tpt-90) cc_final: 0.8606 (tpp80)
REVERT: B 1147 MET cc_start: 0.8736 (tpp) cc_final: 0.8298 (tpp)
REVERT: B 1172 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8669 (tp40)
REVERT: C 1016 LYS cc_start: 0.6903 (tptt) cc_final: 0.6513 (mmtt)
REVERT: C 1025 ASN cc_start: 0.8662 (t0) cc_final: 0.8458 (t0)
REVERT: C 1172 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8664 (tp40)
REVERT: C 1174 MET cc_start: 0.7938 (tmm) cc_final: 0.7669 (tmm)
REVERT: D 1016 LYS cc_start: 0.6820 (tptt) cc_final: 0.6471 (mmtt)
REVERT: D 1073 LYS cc_start: 0.7611 (tptp) cc_final: 0.7395 (tptp)
REVERT: D 1172 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8632 (tp40)
  outliers start: 42
  outliers final: 40
  residues processed: 263
  average time/residue: 0.2501
  time to fit residues: 86.2720
Evaluate side-chains
  273 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 232
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1035 LYS
Chi-restraints excluded: chain A residue 1071 PHE
Chi-restraints excluded: chain A residue 1138 THR
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1196 VAL
Chi-restraints excluded: chain A residue 1198 PHE
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1035 LYS
Chi-restraints excluded: chain B residue 1057 THR
Chi-restraints excluded: chain B residue 1071 PHE
Chi-restraints excluded: chain B residue 1077 SER
Chi-restraints excluded: chain B residue 1097 ILE
Chi-restraints excluded: chain B residue 1138 THR
Chi-restraints excluded: chain B residue 1143 ILE
Chi-restraints excluded: chain B residue 1167 PHE
Chi-restraints excluded: chain B residue 1196 VAL
Chi-restraints excluded: chain B residue 1198 PHE
Chi-restraints excluded: chain C residue 1024 LEU
Chi-restraints excluded: chain C residue 1035 LYS
Chi-restraints excluded: chain C residue 1056 PHE
Chi-restraints excluded: chain C residue 1078 LEU
Chi-restraints excluded: chain C residue 1098 LEU
Chi-restraints excluded: chain C residue 1138 THR
Chi-restraints excluded: chain C residue 1151 LEU
Chi-restraints excluded: chain C residue 1167 PHE
Chi-restraints excluded: chain C residue 1170 LEU
Chi-restraints excluded: chain C residue 1196 VAL
Chi-restraints excluded: chain C residue 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1035 LYS
Chi-restraints excluded: chain D residue 1056 PHE
Chi-restraints excluded: chain D residue 1067 HIS
Chi-restraints excluded: chain D residue 1078 LEU
Chi-restraints excluded: chain D residue 1138 THR
Chi-restraints excluded: chain D residue 1143 ILE
Chi-restraints excluded: chain D residue 1151 LEU
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1196 VAL
Chi-restraints excluded: chain D residue 1208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0670
   chunk 40 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1067 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1025 ASN
B1211 ASN
** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1025 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 = 0.4083 r_free = 0.4083 target = 0.135586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.117502 restraints weight = 22596.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.120175 restraints weight = 13727.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.122103 restraints weight = 9581.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.4320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7672  Z= 0.243
  Angle     :  0.922  14.187  10436  Z= 0.468
  Chirality :  0.050   0.230   1264
  Planarity :  0.005   0.039   1232
  Dihedral  :  5.331  24.944    980
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 18.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 32.06 %
    Favored  : 63.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.28), residues: 908
  helix:  0.13 (0.19), residues: 764
  sheet:  None (None), residues: 0
  loop : -3.48 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP B1179 
 HIS   0.010   0.003   HIS D1067 
 PHE   0.060   0.002   PHE C1048 
 TYR   0.046   0.002   TYR B1020 
 ARG   0.007   0.001   ARG D1117 

===============================================================================
Job complete
usr+sys time: 2546.21 seconds
wall clock time: 45 minutes 8.72 seconds (2708.72 seconds total)