Starting phenix.real_space_refine
on Tue Mar  3 17:13:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p6w_20265/03_2026/6p6w_20265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p6w_20265/03_2026/6p6w_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_2026/6p6w_20265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p6w_20265/03_2026/6p6w_20265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p6w_20265/03_2026/6p6w_20265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p6w_20265/03_2026/6p6w_20265.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.65, per 1000 atoms: 0.22
  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: 0.64
  Conformation dependent library (CDL) restraints added in 282.4 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: 0.15
  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: 0.94

  Time building geometry restraints manager: 0.84 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: 0.01
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:             2.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.690
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.850
-------------------------------------------------------------------------------
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   7676  Z= 0.261
  Angle     :  1.001   9.722  10444  Z= 0.563
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.005   0.000   ARG A1099 
 TYR   0.015   0.003   TYR C1142 
 PHE   0.025   0.002   PHE B1095 
 TRP   0.018   0.002   TRP D1195 
 HIS   0.001   0.000   HIS C1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 7672)
  covalent geometry    : angle       0.99751 (10436)
  SS BOND              : bond        0.00491 (    4)
  SS BOND              : angle       3.17263 (    8)
  hydrogen bonds       : bond        0.09374 (  514)
  hydrogen bonds       : angle       6.01824 ( 1410)

*********************** 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  : 0.314 
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: 0.8703 (m-10)
REVERT: B 1102 ARG cc_start: 0.8976 (tpt-90) cc_final: 0.8577 (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: 0.6352 (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: 0.8325 (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: 0.0884
  time to fit residues: 32.9666
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  : 0.289 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.136596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.117994 restraints weight = 22773.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.120880 restraints weight = 14040.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.122412 restraints weight = 9859.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.124193 restraints weight = 7761.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.125201 restraints weight = 6258.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7676  Z= 0.167
  Angle     :  0.740   7.008  10444  Z= 0.395
  Chirality :  0.045   0.173   1264
  Planarity :  0.005   0.035   1232
  Dihedral  :  5.977  26.346    983
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 18.18 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.09 (0.25), residues: 908
  helix: -1.38 (0.17), residues: 764
  sheet:  None (None), residues: 0
  loop : -4.84 (0.38), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D1063 
 TYR   0.039   0.002   TYR B1020 
 PHE   0.028   0.002   PHE C1056 
 TRP   0.026   0.002   TRP B1179 
 HIS   0.001   0.001   HIS C1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 7672)
  covalent geometry    : angle       0.73752 (10436)
  SS BOND              : bond        0.00384 (    4)
  SS BOND              : angle       2.17172 (    8)
  hydrogen bonds       : bond        0.04419 (  514)
  hydrogen bonds       : angle       4.75552 ( 1410)

*********************** 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
  279 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 240
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1016 LYS cc_start: 0.7068 (tptt) cc_final: 0.6605 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8573 (t0) cc_final: 0.8106 (t0)
REVERT: A 1071 PHE cc_start: 0.8502 (t80) cc_final: 0.8139 (t80)
REVERT: A 1074 ASP cc_start: 0.8711 (t0) cc_final: 0.8425 (t0)
REVERT: A 1079 PHE cc_start: 0.9176 (t80) cc_final: 0.8760 (m-80)
REVERT: A 1102 ARG cc_start: 0.9143 (tpt-90) cc_final: 0.8850 (tpp-160)
REVERT: A 1117 ARG cc_start: 0.9135 (ttt90) cc_final: 0.8827 (tpp80)
REVERT: A 1168 TYR cc_start: 0.8275 (t80) cc_final: 0.8020 (t80)
REVERT: A 1172 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8521 (tp40)
REVERT: A 1174 MET cc_start: 0.8580 (tmm) cc_final: 0.8063 (tmm)
REVERT: A 1209 MET cc_start: 0.5994 (ttt) cc_final: 0.5751 (tmm)
REVERT: B 1050 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8527 (mm-40)
REVERT: B 1074 ASP cc_start: 0.8617 (t0) cc_final: 0.8311 (t0)
REVERT: B 1079 PHE cc_start: 0.9145 (t80) cc_final: 0.8724 (m-80)
REVERT: B 1102 ARG cc_start: 0.9084 (tpt-90) cc_final: 0.8707 (tpp-160)
REVERT: B 1117 ARG cc_start: 0.9112 (ttt90) cc_final: 0.8848 (tpp80)
REVERT: B 1172 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8480 (tp40)
REVERT: B 1174 MET cc_start: 0.8700 (tmm) cc_final: 0.8134 (tmm)
REVERT: B 1179 TRP cc_start: 0.7947 (p-90) cc_final: 0.7530 (p-90)
REVERT: C 1016 LYS cc_start: 0.6941 (tptt) cc_final: 0.6212 (mmtt)
REVERT: C 1020 TYR cc_start: 0.8505 (m-80) cc_final: 0.8275 (m-80)
REVERT: C 1050 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8469 (mm-40)
REVERT: C 1074 ASP cc_start: 0.8764 (t0) cc_final: 0.8480 (t0)
REVERT: C 1079 PHE cc_start: 0.9117 (t80) cc_final: 0.8623 (m-10)
REVERT: C 1174 MET cc_start: 0.8669 (tmm) cc_final: 0.8093 (tmm)
REVERT: C 1179 TRP cc_start: 0.7966 (p-90) cc_final: 0.7566 (p-90)
REVERT: D 1016 LYS cc_start: 0.6925 (tptt) cc_final: 0.6578 (mmtt)
REVERT: D 1025 ASN cc_start: 0.9076 (t0) cc_final: 0.8731 (t0)
REVERT: D 1079 PHE cc_start: 0.9174 (t80) cc_final: 0.8713 (m-80)
REVERT: D 1174 MET cc_start: 0.8674 (tmm) cc_final: 0.8076 (tmm)
  outliers start: 39
  outliers final: 23
  residues processed: 260
  average time/residue: 0.0938
  time to fit residues: 31.7742
Evaluate side-chains
  241 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 218
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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 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 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0070
   chunk 48 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.4798

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.135805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.117710 restraints weight = 22105.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.120186 restraints weight = 13733.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.122056 restraints weight = 9760.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.123505 restraints weight = 7729.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.124239 restraints weight = 6190.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7676  Z= 0.141
  Angle     :  0.716   6.984  10444  Z= 0.377
  Chirality :  0.043   0.152   1264
  Planarity :  0.005   0.054   1232
  Dihedral  :  5.549  23.603    981
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 20.10 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.11 (0.27), residues: 908
  helix: -0.70 (0.18), residues: 764
  sheet:  None (None), residues: 0
  loop : -4.59 (0.40), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C1117 
 TYR   0.057   0.002   TYR B1020 
 PHE   0.049   0.002   PHE C1048 
 TRP   0.027   0.001   TRP D1179 
 HIS   0.006   0.002   HIS A1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7672)
  covalent geometry    : angle       0.71323 (10436)
  SS BOND              : bond        0.00293 (    4)
  SS BOND              : angle       2.29895 (    8)
  hydrogen bonds       : bond        0.04152 (  514)
  hydrogen bonds       : angle       4.54507 ( 1410)

*********************** 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
  285 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 246
  time to evaluate  : 0.227 
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: A 1016 LYS cc_start: 0.7065 (tptt) cc_final: 0.6762 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8530 (t0) cc_final: 0.8251 (t0)
REVERT: A 1073 LYS cc_start: 0.7420 (tptp) cc_final: 0.7174 (tptp)
REVERT: A 1074 ASP cc_start: 0.8784 (t0) cc_final: 0.8426 (t0)
REVERT: A 1079 PHE cc_start: 0.9148 (t80) cc_final: 0.8874 (m-80)
REVERT: A 1080 ASP cc_start: 0.8974 (p0) cc_final: 0.8755 (p0)
REVERT: A 1102 ARG cc_start: 0.9160 (tpt-90) cc_final: 0.8752 (tpp-160)
REVERT: A 1174 MET cc_start: 0.8571 (tmm) cc_final: 0.8066 (tmm)
REVERT: A 1209 MET cc_start: 0.5982 (ttt) cc_final: 0.5767 (tmm)
REVERT: B 1050 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8556 (mm-40)
REVERT: B 1073 LYS cc_start: 0.7690 (tptp) cc_final: 0.7465 (tptp)
REVERT: B 1074 ASP cc_start: 0.8694 (t0) cc_final: 0.8354 (t0)
REVERT: B 1079 PHE cc_start: 0.9132 (t80) cc_final: 0.8765 (m-80)
REVERT: B 1102 ARG cc_start: 0.9071 (tpt-90) cc_final: 0.8690 (tpp80)
REVERT: B 1174 MET cc_start: 0.8600 (tmm) cc_final: 0.8065 (tmm)
REVERT: C 1016 LYS cc_start: 0.6905 (tptt) cc_final: 0.6544 (mmtt)
REVERT: C 1073 LYS cc_start: 0.7431 (tptp) cc_final: 0.7216 (tptp)
REVERT: C 1074 ASP cc_start: 0.8736 (t0) cc_final: 0.8476 (t0)
REVERT: C 1079 PHE cc_start: 0.9180 (t80) cc_final: 0.8682 (m-80)
REVERT: C 1102 ARG cc_start: 0.9038 (tpp80) cc_final: 0.8713 (tpp80)
REVERT: C 1174 MET cc_start: 0.8636 (tmm) cc_final: 0.8079 (tmm)
REVERT: D 1016 LYS cc_start: 0.6894 (tptt) cc_final: 0.6517 (mmtt)
REVERT: D 1025 ASN cc_start: 0.9003 (t0) cc_final: 0.8708 (t0)
REVERT: D 1063 ARG cc_start: 0.8547 (mtp85) cc_final: 0.8346 (mtp180)
REVERT: D 1074 ASP cc_start: 0.8669 (t0) cc_final: 0.8331 (t0)
REVERT: D 1079 PHE cc_start: 0.9183 (t80) cc_final: 0.8729 (m-80)
REVERT: D 1172 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8587 (tp40)
REVERT: D 1174 MET cc_start: 0.8586 (tmm) cc_final: 0.8005 (tmm)
  outliers start: 39
  outliers final: 22
  residues processed: 270
  average time/residue: 0.0913
  time to fit residues: 32.1327
Evaluate side-chains
  247 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 225
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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 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 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 C residue 1212 LEU
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 1143 ILE
Chi-restraints excluded: chain D residue 1167 PHE
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 37 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**
B1067 HIS
** 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 = 0.4077 r_free = 0.4077 target = 0.136019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.118186 restraints weight = 22856.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.120721 restraints weight = 13774.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.122756 restraints weight = 9700.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.123739 restraints weight = 7369.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.124843 restraints weight = 6197.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7676  Z= 0.142
  Angle     :  0.713   6.784  10444  Z= 0.373
  Chirality :  0.044   0.150   1264
  Planarity :  0.004   0.028   1232
  Dihedral  :  5.332  22.633    981
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 20.22 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.27), residues: 908
  helix: -0.37 (0.18), residues: 768
  sheet:  None (None), residues: 0
  loop : -4.32 (0.42), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C1117 
 TYR   0.047   0.002   TYR B1020 
 PHE   0.049   0.002   PHE D1048 
 TRP   0.029   0.002   TRP C1179 
 HIS   0.001   0.001   HIS D1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7672)
  covalent geometry    : angle       0.71131 (10436)
  SS BOND              : bond        0.00333 (    4)
  SS BOND              : angle       2.01997 (    8)
  hydrogen bonds       : bond        0.03959 (  514)
  hydrogen bonds       : angle       4.45498 ( 1410)

*********************** 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: 44
    poor density    : 228
  time to evaluate  : 0.287 
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: A 1016 LYS cc_start: 0.7069 (tptt) cc_final: 0.6747 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8488 (t0) cc_final: 0.7973 (t0)
REVERT: A 1063 ARG cc_start: 0.8504 (ptp-170) cc_final: 0.7883 (ptm160)
REVERT: A 1079 PHE cc_start: 0.9123 (t80) cc_final: 0.8866 (m-80)
REVERT: A 1102 ARG cc_start: 0.9074 (tpt-90) cc_final: 0.8602 (tpp80)
REVERT: A 1172 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8566 (tp40)
REVERT: A 1174 MET cc_start: 0.8545 (tmm) cc_final: 0.8005 (tmm)
REVERT: B 1032 GLU cc_start: 0.7557 (tt0) cc_final: 0.7339 (mm-30)
REVERT: B 1050 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8551 (mm-40)
REVERT: B 1073 LYS cc_start: 0.7734 (tptp) cc_final: 0.7466 (tptp)
REVERT: B 1074 ASP cc_start: 0.8747 (t0) cc_final: 0.8313 (t0)
REVERT: B 1079 PHE cc_start: 0.9117 (t80) cc_final: 0.8786 (m-80)
REVERT: B 1102 ARG cc_start: 0.9048 (tpt-90) cc_final: 0.8645 (tpp80)
REVERT: B 1172 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8588 (tp40)
REVERT: B 1174 MET cc_start: 0.8617 (tmm) cc_final: 0.8095 (tmm)
REVERT: C 1016 LYS cc_start: 0.6886 (tptt) cc_final: 0.6516 (mmtt)
REVERT: C 1073 LYS cc_start: 0.7511 (tptp) cc_final: 0.7249 (tptp)
REVERT: C 1074 ASP cc_start: 0.8779 (t0) cc_final: 0.8447 (t0)
REVERT: C 1079 PHE cc_start: 0.9150 (t80) cc_final: 0.8782 (m-80)
REVERT: C 1174 MET cc_start: 0.8624 (tmm) cc_final: 0.8054 (tmm)
REVERT: D 1016 LYS cc_start: 0.6881 (tptt) cc_final: 0.6488 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9167 (t80) cc_final: 0.8806 (m-80)
REVERT: D 1117 ARG cc_start: 0.8961 (mmm-85) cc_final: 0.8756 (mmm-85)
REVERT: D 1172 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8555 (tp40)
REVERT: D 1174 MET cc_start: 0.8605 (tmm) cc_final: 0.8056 (tmm)
  outliers start: 44
  outliers final: 30
  residues processed: 254
  average time/residue: 0.0885
  time to fit residues: 29.3002
Evaluate side-chains
  250 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 220
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1024 LEU
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 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 B residue 1176 LEU
Chi-restraints excluded: chain C residue 1024 LEU
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 1138 THR
Chi-restraints excluded: chain D residue 1143 ILE
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1176 LEU
Chi-restraints excluded: chain D residue 1196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0040
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.135710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.117906 restraints weight = 22454.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.120507 restraints weight = 13363.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.122457 restraints weight = 9244.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.123416 restraints weight = 7085.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.124511 restraints weight = 5975.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7676  Z= 0.137
  Angle     :  0.722   7.243  10444  Z= 0.374
  Chirality :  0.044   0.182   1264
  Planarity :  0.004   0.049   1232
  Dihedral  :  5.241  22.070    981
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 23.68 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.28), residues: 908
  helix: -0.13 (0.19), residues: 768
  sheet:  None (None), residues: 0
  loop : -4.06 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1117 
 TYR   0.043   0.002   TYR B1020 
 PHE   0.048   0.002   PHE A1048 
 TRP   0.018   0.001   TRP B1179 
 HIS   0.011   0.002   HIS B1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7672)
  covalent geometry    : angle       0.71980 (10436)
  SS BOND              : bond        0.00557 (    4)
  SS BOND              : angle       2.17531 (    8)
  hydrogen bonds       : bond        0.03901 (  514)
  hydrogen bonds       : angle       4.40414 ( 1410)

*********************** 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
  275 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 228
  time to evaluate  : 0.306 
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: 0.7023 (tptt) cc_final: 0.6694 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8567 (t0) cc_final: 0.8175 (t0)
REVERT: A 1056 PHE cc_start: 0.8102 (t80) cc_final: 0.7856 (t80)
REVERT: A 1063 ARG cc_start: 0.8548 (ptp-170) cc_final: 0.7946 (ptm160)
REVERT: A 1074 ASP cc_start: 0.8852 (t0) cc_final: 0.8550 (t0)
REVERT: A 1079 PHE cc_start: 0.9122 (t80) cc_final: 0.8893 (m-80)
REVERT: A 1102 ARG cc_start: 0.9090 (tpt-90) cc_final: 0.8565 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8546 (mmm-85)
REVERT: A 1174 MET cc_start: 0.8510 (tmm) cc_final: 0.8034 (tmm)
REVERT: B 1050 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8549 (mm-40)
REVERT: B 1073 LYS cc_start: 0.7766 (tptp) cc_final: 0.7424 (tptp)
REVERT: B 1074 ASP cc_start: 0.8776 (t0) cc_final: 0.8297 (t0)
REVERT: B 1077 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7704 (p)
REVERT: B 1079 PHE cc_start: 0.9109 (t80) cc_final: 0.8777 (m-80)
REVERT: B 1102 ARG cc_start: 0.9043 (tpt-90) cc_final: 0.8549 (tpp80)
REVERT: B 1174 MET cc_start: 0.8582 (tmm) cc_final: 0.8039 (tmm)
REVERT: C 1016 LYS cc_start: 0.6884 (tptt) cc_final: 0.6512 (mmtt)
REVERT: C 1073 LYS cc_start: 0.7542 (tptp) cc_final: 0.7261 (tptp)
REVERT: C 1074 ASP cc_start: 0.8807 (t0) cc_final: 0.8500 (t0)
REVERT: C 1079 PHE cc_start: 0.9162 (t80) cc_final: 0.8881 (m-80)
REVERT: C 1174 MET cc_start: 0.8576 (tmm) cc_final: 0.7991 (tmm)
REVERT: D 1016 LYS cc_start: 0.6941 (tptt) cc_final: 0.6579 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9210 (t80) cc_final: 0.8892 (m-80)
REVERT: D 1172 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8509 (tp40)
REVERT: D 1174 MET cc_start: 0.8565 (tmm) cc_final: 0.7985 (tmm)
  outliers start: 47
  outliers final: 33
  residues processed: 258
  average time/residue: 0.0950
  time to fit residues: 31.8696
Evaluate side-chains
  252 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 218
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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 1071 PHE
Chi-restraints excluded: chain B residue 1077 SER
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 1056 PHE
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 C residue 1212 LEU
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 1143 ILE
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1176 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   chunk 84 optimal weight:    0.0980
   chunk 21 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0020
   chunk 86 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3388

-------------------------------------------------------------------------------
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
** C1025 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 = 0.4073 r_free = 0.4073 target = 0.135992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.118005 restraints weight = 22220.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.120263 restraints weight = 13415.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.122448 restraints weight = 9491.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.123684 restraints weight = 7264.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.124683 restraints weight = 6031.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7676  Z= 0.133
  Angle     :  0.732   7.748  10444  Z= 0.376
  Chirality :  0.044   0.139   1264
  Planarity :  0.004   0.033   1232
  Dihedral  :  5.063  19.239    980
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 24.52 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.29), residues: 908
  helix:  0.56 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop : -2.32 (0.48), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1117 
 TYR   0.042   0.002   TYR B1020 
 PHE   0.053   0.002   PHE C1048 
 TRP   0.015   0.001   TRP B1179 
 HIS   0.007   0.002   HIS A1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7672)
  covalent geometry    : angle       0.73027 (10436)
  SS BOND              : bond        0.00289 (    4)
  SS BOND              : angle       1.91932 (    8)
  hydrogen bonds       : bond        0.03835 (  514)
  hydrogen bonds       : angle       4.34772 ( 1410)

*********************** 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
  285 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 240
  time to evaluate  : 0.242 
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: 0.7054 (tptt) cc_final: 0.6711 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8544 (t0) cc_final: 0.8130 (t0)
REVERT: A 1056 PHE cc_start: 0.8123 (t80) cc_final: 0.7900 (t80)
REVERT: A 1063 ARG cc_start: 0.8618 (ptp-170) cc_final: 0.8070 (ptm160)
REVERT: A 1074 ASP cc_start: 0.8831 (t0) cc_final: 0.8610 (t0)
REVERT: A 1102 ARG cc_start: 0.9115 (tpt-90) cc_final: 0.8641 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8601 (mmm-85)
REVERT: A 1172 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8541 (tp40)
REVERT: A 1174 MET cc_start: 0.8436 (tmm) cc_final: 0.7928 (tmm)
REVERT: B 1010 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8529 (mp0)
REVERT: B 1029 MET cc_start: 0.8774 (mmp) cc_final: 0.8465 (mmp)
REVERT: B 1074 ASP cc_start: 0.8797 (t0) cc_final: 0.8582 (t0)
REVERT: B 1077 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7812 (p)
REVERT: B 1079 PHE cc_start: 0.9095 (t80) cc_final: 0.8823 (m-80)
REVERT: B 1102 ARG cc_start: 0.9050 (tpt-90) cc_final: 0.8661 (tpp80)
REVERT: B 1147 MET cc_start: 0.8749 (tpp) cc_final: 0.8458 (tpp)
REVERT: B 1172 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8591 (tp40)
REVERT: B 1174 MET cc_start: 0.8507 (tmm) cc_final: 0.7989 (tmm)
REVERT: C 1016 LYS cc_start: 0.6885 (tptt) cc_final: 0.6503 (mmtt)
REVERT: C 1025 ASN cc_start: 0.8921 (t0) cc_final: 0.8713 (t0)
REVERT: C 1073 LYS cc_start: 0.7497 (tptp) cc_final: 0.7260 (tptp)
REVERT: C 1074 ASP cc_start: 0.8759 (t0) cc_final: 0.8446 (t0)
REVERT: C 1079 PHE cc_start: 0.9207 (t80) cc_final: 0.8917 (m-80)
REVERT: C 1172 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8545 (tp40)
REVERT: C 1174 MET cc_start: 0.8532 (tmm) cc_final: 0.7964 (tmm)
REVERT: D 1016 LYS cc_start: 0.6872 (tptt) cc_final: 0.6477 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9156 (t80) cc_final: 0.8918 (m-80)
REVERT: D 1172 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8541 (tp40)
REVERT: D 1174 MET cc_start: 0.8536 (tmm) cc_final: 0.7971 (tmm)
  outliers start: 45
  outliers final: 33
  residues processed: 266
  average time/residue: 0.0974
  time to fit residues: 33.5111
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  : 0.281 
-------------------------------------------------------------------------------
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 1151 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 1035 LYS
Chi-restraints excluded: chain B residue 1057 THR
Chi-restraints excluded: chain B residue 1077 SER
Chi-restraints excluded: chain B residue 1078 LEU
Chi-restraints excluded: chain B residue 1101 LEU
Chi-restraints excluded: chain B residue 1143 ILE
Chi-restraints excluded: chain B residue 1167 PHE
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 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 C residue 1212 LEU
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 1143 ILE
Chi-restraints excluded: chain D residue 1167 PHE
Chi-restraints excluded: chain D residue 1176 LEU
Chi-restraints excluded: chain D residue 1212 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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
B1211 ASN
** C1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1211 ASN
D1211 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.134380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.116473 restraints weight = 22674.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.119040 restraints weight = 13642.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.121029 restraints weight = 9530.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.122326 restraints weight = 7282.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.123078 restraints weight = 5963.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7676  Z= 0.153
  Angle     :  0.782   9.288  10444  Z= 0.404
  Chirality :  0.046   0.191   1264
  Planarity :  0.004   0.036   1232
  Dihedral  :  5.092  17.363    980
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 25.12 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.28), residues: 908
  helix:  0.17 (0.19), residues: 764
  sheet:  None (None), residues: 0
  loop : -3.69 (0.49), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C1117 
 TYR   0.041   0.002   TYR B1020 
 PHE   0.057   0.002   PHE D1048 
 TRP   0.014   0.001   TRP A1076 
 HIS   0.012   0.002   HIS A1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7672)
  covalent geometry    : angle       0.78032 (10436)
  SS BOND              : bond        0.00315 (    4)
  SS BOND              : angle       2.00728 (    8)
  hydrogen bonds       : bond        0.03990 (  514)
  hydrogen bonds       : angle       4.43994 ( 1410)

*********************** 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
  281 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 230
  time to evaluate  : 0.250 
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: 0.6972 (tptt) cc_final: 0.6682 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8491 (t0) cc_final: 0.8174 (t0)
REVERT: A 1056 PHE cc_start: 0.8072 (t80) cc_final: 0.7848 (t80)
REVERT: A 1063 ARG cc_start: 0.8585 (ptp-170) cc_final: 0.8156 (ptm160)
REVERT: A 1074 ASP cc_start: 0.8672 (t0) cc_final: 0.8389 (t0)
REVERT: A 1102 ARG cc_start: 0.8946 (tpt-90) cc_final: 0.8590 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8903 (mmm-85) cc_final: 0.8673 (mmm-85)
REVERT: A 1174 MET cc_start: 0.8509 (tmm) cc_final: 0.7977 (tmm)
REVERT: B 1049 LYS cc_start: 0.9198 (mttt) cc_final: 0.8823 (mttp)
REVERT: B 1050 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8570 (mm-40)
REVERT: B 1074 ASP cc_start: 0.8904 (t0) cc_final: 0.8484 (t0)
REVERT: B 1077 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7770 (p)
REVERT: B 1079 PHE cc_start: 0.9088 (t80) cc_final: 0.8810 (m-80)
REVERT: B 1102 ARG cc_start: 0.8995 (tpt-90) cc_final: 0.8615 (tpp80)
REVERT: B 1174 MET cc_start: 0.8542 (tmm) cc_final: 0.7973 (tmm)
REVERT: C 1016 LYS cc_start: 0.6914 (tptt) cc_final: 0.6530 (mmtt)
REVERT: C 1025 ASN cc_start: 0.8892 (t0) cc_final: 0.8521 (t0)
REVERT: C 1073 LYS cc_start: 0.7549 (tptp) cc_final: 0.7342 (tptp)
REVERT: C 1074 ASP cc_start: 0.8725 (t0) cc_final: 0.8399 (t0)
REVERT: C 1079 PHE cc_start: 0.9225 (t80) cc_final: 0.8928 (m-80)
REVERT: C 1174 MET cc_start: 0.8568 (tmm) cc_final: 0.7951 (tmm)
REVERT: D 1016 LYS cc_start: 0.6901 (tptt) cc_final: 0.6509 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9133 (t80) cc_final: 0.8892 (m-80)
REVERT: D 1102 ARG cc_start: 0.8755 (tpt170) cc_final: 0.8530 (tpp80)
REVERT: D 1174 MET cc_start: 0.8514 (tmm) cc_final: 0.7998 (tmm)
  outliers start: 51
  outliers final: 38
  residues processed: 258
  average time/residue: 0.0936
  time to fit residues: 31.3043
Evaluate side-chains
  261 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 222
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
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 1151 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 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 1078 LEU
Chi-restraints excluded: chain B residue 1101 LEU
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 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 1176 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 84 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0980
   chunk 32 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   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**
** 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 = 0.4072 r_free = 0.4072 target = 0.134872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.116948 restraints weight = 22839.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.119531 restraints weight = 13948.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.121269 restraints weight = 9747.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.122725 restraints weight = 7685.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.123692 restraints weight = 6183.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7676  Z= 0.153
  Angle     :  0.829   9.309  10444  Z= 0.425
  Chirality :  0.047   0.251   1264
  Planarity :  0.004   0.031   1232
  Dihedral  :  5.108  17.987    980
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 28.47 %
    Favored  : 66.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.29), residues: 908
  helix:  0.34 (0.19), residues: 740
  sheet:  None (None), residues: 0
  loop : -2.84 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C1117 
 TYR   0.039   0.002   TYR B1020 
 PHE   0.057   0.002   PHE D1048 
 TRP   0.043   0.003   TRP A1179 
 HIS   0.004   0.001   HIS A1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7672)
  covalent geometry    : angle       0.82668 (10436)
  SS BOND              : bond        0.00266 (    4)
  SS BOND              : angle       2.26284 (    8)
  hydrogen bonds       : bond        0.04074 (  514)
  hydrogen bonds       : angle       4.51867 ( 1410)

*********************** 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
  284 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 239
  time to evaluate  : 0.284 
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: A 1016 LYS cc_start: 0.6970 (tptt) cc_final: 0.6660 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8465 (t0) cc_final: 0.8132 (t0)
REVERT: A 1056 PHE cc_start: 0.8062 (t80) cc_final: 0.7836 (t80)
REVERT: A 1063 ARG cc_start: 0.8543 (ptp-170) cc_final: 0.8118 (ptm160)
REVERT: A 1074 ASP cc_start: 0.8729 (t0) cc_final: 0.8438 (t0)
REVERT: A 1077 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7666 (p)
REVERT: A 1102 ARG cc_start: 0.8934 (tpt-90) cc_final: 0.8611 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8697 (mmm-85)
REVERT: A 1172 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8632 (tp40)
REVERT: A 1174 MET cc_start: 0.8489 (tmm) cc_final: 0.8034 (tmm)
REVERT: B 1049 LYS cc_start: 0.9227 (mttt) cc_final: 0.8759 (mttm)
REVERT: B 1050 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8572 (mm-40)
REVERT: B 1079 PHE cc_start: 0.9120 (t80) cc_final: 0.8885 (m-80)
REVERT: B 1102 ARG cc_start: 0.8943 (tpt-90) cc_final: 0.8694 (tpp80)
REVERT: B 1147 MET cc_start: 0.8699 (tpp) cc_final: 0.8316 (tpp)
REVERT: B 1172 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8622 (tp40)
REVERT: B 1174 MET cc_start: 0.8530 (tmm) cc_final: 0.8010 (tmm)
REVERT: C 1016 LYS cc_start: 0.6924 (tptt) cc_final: 0.6534 (mmtt)
REVERT: C 1050 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8409 (mm-40)
REVERT: C 1073 LYS cc_start: 0.7486 (tptp) cc_final: 0.7270 (tptp)
REVERT: C 1074 ASP cc_start: 0.8759 (t0) cc_final: 0.8413 (t0)
REVERT: C 1079 PHE cc_start: 0.9179 (t80) cc_final: 0.8914 (m-80)
REVERT: C 1172 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8535 (tp40)
REVERT: C 1174 MET cc_start: 0.8552 (tmm) cc_final: 0.7943 (tmm)
REVERT: D 1016 LYS cc_start: 0.6955 (tptt) cc_final: 0.6556 (mmtt)
REVERT: D 1079 PHE cc_start: 0.9123 (t80) cc_final: 0.8886 (m-80)
REVERT: D 1102 ARG cc_start: 0.8802 (tpt170) cc_final: 0.8514 (tpp80)
REVERT: D 1172 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8653 (tp40)
  outliers start: 45
  outliers final: 34
  residues processed: 263
  average time/residue: 0.0944
  time to fit residues: 32.2756
Evaluate side-chains
  263 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 228
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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 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 1078 LEU
Chi-restraints excluded: chain B residue 1097 ILE
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 1035 LYS
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 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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0270
   chunk 85 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0470
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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**
** B1025 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 = 0.4089 r_free = 0.4089 target = 0.136099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.118216 restraints weight = 22565.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.120968 restraints weight = 13679.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.122904 restraints weight = 9403.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.124227 restraints weight = 7130.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.124969 restraints weight = 5818.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7676  Z= 0.149
  Angle     :  0.891  14.765  10444  Z= 0.447
  Chirality :  0.049   0.251   1264
  Planarity :  0.005   0.053   1232
  Dihedral  :  5.083  20.613    980
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 30.14 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.29), residues: 908
  helix:  0.32 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -2.74 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B1117 
 TYR   0.041   0.002   TYR B1020 
 PHE   0.059   0.002   PHE C1048 
 TRP   0.041   0.003   TRP A1179 
 HIS   0.001   0.000   HIS C1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7672)
  covalent geometry    : angle       0.88961 (10436)
  SS BOND              : bond        0.00270 (    4)
  SS BOND              : angle       2.17827 (    8)
  hydrogen bonds       : bond        0.04146 (  514)
  hydrogen bonds       : angle       4.60049 ( 1410)

*********************** 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
  282 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 241
  time to evaluate  : 0.295 
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: 0.6941 (tptt) cc_final: 0.6620 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8413 (t0) cc_final: 0.8091 (t0)
REVERT: A 1056 PHE cc_start: 0.8056 (t80) cc_final: 0.7849 (t80)
REVERT: A 1063 ARG cc_start: 0.8511 (ptp-170) cc_final: 0.8112 (ptm160)
REVERT: A 1074 ASP cc_start: 0.8773 (t0) cc_final: 0.8359 (t0)
REVERT: A 1077 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7550 (p)
REVERT: A 1102 ARG cc_start: 0.8927 (tpt-90) cc_final: 0.8621 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8703 (mmm-85)
REVERT: A 1172 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8588 (tp40)
REVERT: B 1049 LYS cc_start: 0.9199 (mttt) cc_final: 0.8946 (mttp)
REVERT: B 1076 TRP cc_start: 0.8730 (m100) cc_final: 0.8290 (m-90)
REVERT: B 1079 PHE cc_start: 0.9110 (t80) cc_final: 0.8885 (m-80)
REVERT: B 1102 ARG cc_start: 0.8886 (tpt-90) cc_final: 0.8331 (tpp80)
REVERT: B 1147 MET cc_start: 0.8760 (tpp) cc_final: 0.8273 (tpp)
REVERT: B 1174 MET cc_start: 0.8489 (tmm) cc_final: 0.8005 (tmm)
REVERT: C 1016 LYS cc_start: 0.6928 (tptt) cc_final: 0.6522 (mmtt)
REVERT: C 1073 LYS cc_start: 0.7514 (tptp) cc_final: 0.7284 (tptp)
REVERT: C 1079 PHE cc_start: 0.9161 (t80) cc_final: 0.8914 (m-80)
REVERT: C 1102 ARG cc_start: 0.9069 (tpp80) cc_final: 0.8852 (tpt90)
REVERT: C 1172 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8601 (tp40)
REVERT: C 1174 MET cc_start: 0.8467 (tmm) cc_final: 0.7965 (tmm)
REVERT: D 1016 LYS cc_start: 0.6820 (tptt) cc_final: 0.6454 (mmtt)
REVERT: D 1172 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8619 (tp40)
  outliers start: 41
  outliers final: 32
  residues processed: 266
  average time/residue: 0.0960
  time to fit residues: 33.4313
Evaluate side-chains
  259 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 226
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
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 1077 SER
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 1078 LEU
Chi-restraints excluded: chain B residue 1097 ILE
Chi-restraints excluded: chain B residue 1098 LEU
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 1035 LYS
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 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 1097 ILE
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 1208 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 63 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 ** 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 = 0.4089 r_free = 0.4089 target = 0.135742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.117832 restraints weight = 22826.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.120552 restraints weight = 13869.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.122559 restraints weight = 9620.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.123877 restraints weight = 7306.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.124773 restraints weight = 5978.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7676  Z= 0.160
  Angle     :  0.940  16.343  10444  Z= 0.468
  Chirality :  0.050   0.229   1264
  Planarity :  0.004   0.032   1232
  Dihedral  :  5.171  23.418    980
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 19.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 31.46 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.28), residues: 908
  helix:  0.26 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -2.80 (0.49), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B1117 
 TYR   0.044   0.002   TYR B1020 
 PHE   0.062   0.002   PHE C1048 
 TRP   0.040   0.003   TRP C1179 
 HIS   0.007   0.001   HIS A1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7672)
  covalent geometry    : angle       0.93804 (10436)
  SS BOND              : bond        0.00319 (    4)
  SS BOND              : angle       2.15329 (    8)
  hydrogen bonds       : bond        0.04269 (  514)
  hydrogen bonds       : angle       4.71619 ( 1410)

********************** 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
  266 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 234
  time to evaluate  : 0.287 
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: 0.7050 (tptt) cc_final: 0.6741 (mmtt)
REVERT: A 1025 ASN cc_start: 0.8504 (t0) cc_final: 0.8291 (t0)
REVERT: A 1056 PHE cc_start: 0.8027 (t80) cc_final: 0.7708 (t80)
REVERT: A 1074 ASP cc_start: 0.8800 (t0) cc_final: 0.8444 (t0)
REVERT: A 1077 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7543 (p)
REVERT: A 1079 PHE cc_start: 0.6924 (m-80) cc_final: 0.6661 (m-80)
REVERT: A 1102 ARG cc_start: 0.8899 (tpt-90) cc_final: 0.8454 (tpp80)
REVERT: A 1117 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.8712 (mmm-85)
REVERT: A 1172 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8588 (tp40)
REVERT: B 1076 TRP cc_start: 0.8737 (m100) cc_final: 0.8225 (m-90)
REVERT: B 1079 PHE cc_start: 0.9103 (t80) cc_final: 0.8868 (m-80)
REVERT: B 1102 ARG cc_start: 0.8793 (tpt-90) cc_final: 0.8277 (tpp80)
REVERT: B 1147 MET cc_start: 0.8679 (tpp) cc_final: 0.8230 (tpp)
REVERT: B 1172 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8524 (tp40)
REVERT: C 1016 LYS cc_start: 0.6820 (tptt) cc_final: 0.6482 (mmtt)
REVERT: C 1050 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8420 (mm-40)
REVERT: C 1073 LYS cc_start: 0.7506 (tptp) cc_final: 0.7281 (tptp)
REVERT: C 1079 PHE cc_start: 0.9132 (t80) cc_final: 0.8904 (m-80)
REVERT: C 1102 ARG cc_start: 0.9118 (tpp80) cc_final: 0.8877 (tpt90)
REVERT: C 1172 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8575 (tp40)
REVERT: C 1174 MET cc_start: 0.8386 (tmm) cc_final: 0.8168 (tmm)
REVERT: D 1016 LYS cc_start: 0.6835 (tptt) cc_final: 0.6463 (mmtt)
REVERT: D 1172 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8574 (tp40)
  outliers start: 32
  outliers final: 29
  residues processed: 250
  average time/residue: 0.0949
  time to fit residues: 30.8911
Evaluate side-chains
  258 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 228
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
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 1077 SER
Chi-restraints excluded: chain A residue 1098 LEU
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1167 PHE
Chi-restraints excluded: chain A residue 1209 MET
Chi-restraints excluded: chain B residue 1024 LEU
Chi-restraints excluded: chain B residue 1035 LYS
Chi-restraints excluded: chain B residue 1071 PHE
Chi-restraints excluded: chain B residue 1078 LEU
Chi-restraints excluded: chain B residue 1097 ILE
Chi-restraints excluded: chain B residue 1098 LEU
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 1035 LYS
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 1198 PHE
Chi-restraints excluded: chain D residue 1024 LEU
Chi-restraints excluded: chain D residue 1035 LYS
Chi-restraints excluded: chain D residue 1067 HIS
Chi-restraints excluded: chain D residue 1097 ILE
Chi-restraints excluded: chain D residue 1151 LEU
Chi-restraints excluded: chain D residue 1167 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 73 optimal weight:    0.3980
   chunk 70 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0050
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.5394

-------------------------------------------------------------------------------
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 ** 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 = 0.4086 r_free = 0.4086 target = 0.135635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.117826 restraints weight = 22630.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.120593 restraints weight = 13575.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.122532 restraints weight = 9387.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.123698 restraints weight = 7148.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.124603 restraints weight = 5947.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7676  Z= 0.161
  Angle     :  0.942  15.680  10444  Z= 0.469
  Chirality :  0.050   0.225   1264
  Planarity :  0.004   0.032   1232
  Dihedral  :  5.202  23.092    980
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 19.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 32.66 %
    Favored  : 63.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.29), residues: 908
  helix:  0.21 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -2.76 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C1117 
 TYR   0.045   0.002   TYR B1020 
 PHE   0.060   0.002   PHE C1048 
 TRP   0.039   0.003   TRP C1179 
 HIS   0.008   0.002   HIS A1067 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7672)
  covalent geometry    : angle       0.94032 (10436)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       2.15714 (    8)
  hydrogen bonds       : bond        0.04277 (  514)
  hydrogen bonds       : angle       4.79050 ( 1410)

===============================================================================
Job complete
usr+sys time: 1353.02 seconds
wall clock time: 23 minutes 58.52 seconds (1438.52 seconds total)