Starting phenix.real_space_refine
on Fri Jun  6 06:48:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tuy_26135/06_2025/7tuy_26135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tuy_26135/06_2025/7tuy_26135.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tuy_26135/06_2025/7tuy_26135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tuy_26135/06_2025/7tuy_26135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tuy_26135/06_2025/7tuy_26135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tuy_26135/06_2025/7tuy_26135.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     Cl      3      4.86       5
     C    4575      2.51       5
     N    1201      2.21       5
     O    1342      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7157
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 1682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1682
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "K"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 921
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "L"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1624
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 10, 'TRANS': 201}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "R"
      Number of atoms: 2899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2899
          Classifications: {'peptide': 371}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 11, 'TRANS': 359}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "R"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'KKF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.64, per 1000 atoms: 0.65
  Number of scatterers: 7157
  At special positions: 0
  Unit cell: (64.74, 100.43, 141.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      3     17.00
     S      36     16.00
     O    1342      8.00
     N    1201      7.00
     C    4575      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 154 " - pdb=" SG  CYS H 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 104 " - pdb=" SG  CYS R 181 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 974.9 milliseconds
  

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1742

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 15 sheets defined
      37.3% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.685A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 107 through 112
    Processing helix  chain 'H' and resid 201 through 206
      removed outlier: 4.010A  pdb=" N   GLN H 206 " --> pdb=" O   LEU H 203 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 214 through 218
    Processing helix  chain 'L' and resid 123 through 128
    Processing helix  chain 'L' and resid 185 through 189
      removed outlier: 3.514A  pdb=" N   GLU L 189 " --> pdb=" O   LYS L 185 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 185 through 189'
    Processing helix  chain 'R' and resid 26 through 59
      removed outlier: 3.901A  pdb=" N   ILE R  32 " --> pdb=" O   SER R  28 " (cutoff:3.500A)
      Proline residue:  R  35  - end of helix
    Processing helix  chain 'R' and resid 66 through 83
    Processing helix  chain 'R' and resid 101 through 133
      removed outlier: 4.031A  pdb=" N   ALA R 117 " --> pdb=" O   ILE R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 135 through 143
    Processing helix  chain 'R' and resid 144 through 164
      removed outlier: 3.679A  pdb=" N   ALA R 148 " --> pdb=" O   ARG R 144 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU R 164 " --> pdb=" O   PHE R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 168
      removed outlier: 4.248A  pdb=" N   ILE R 168 " --> pdb=" O   PRO R 165 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 165 through 168'
    Processing helix  chain 'R' and resid 195 through 205
      removed outlier: 4.160A  pdb=" N   GLY R 199 " --> pdb=" O   TRP R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 205 through 225
    Processing helix  chain 'R' and resid 1002 through 1025
    Processing helix  chain 'R' and resid 1030 through 1046
      removed outlier: 3.620A  pdb=" N   LYS R1037 " --> pdb=" O   ASP R1033 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASP R1044 " --> pdb=" O   ALA R1040 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1062 through 1087
      removed outlier: 3.547A  pdb=" N   GLY R1069 " --> pdb=" O   ASP R1065 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE R1070 " --> pdb=" O   PHE R1066 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU R1083 " --> pdb=" O   ASP R1079 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1090 through 1092
      No H-bonds generated for 'chain 'R' and resid 1090 through 1092'
    Processing helix  chain 'R' and resid 1094 through 1107
      removed outlier: 4.051A  pdb=" N   GLN R1098 " --> pdb=" O   ALA R1094 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   LEU R1099 " --> pdb=" O   ALA R1095 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   LYS R1100 " --> pdb=" O   ALA R1096 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   THR R1101 " --> pdb=" O   GLU R1097 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1107 through 1117
      removed outlier: 4.081A  pdb=" N   GLU R1112 " --> pdb=" O   GLN R1108 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   ARG R1113 " --> pdb=" O   LYS R1109 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 227 through 247
    Processing helix  chain 'R' and resid 247 through 260
      removed outlier: 3.546A  pdb=" N   HIS R 251 " --> pdb=" O   PHE R 247 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 276 through 301
      removed outlier: 4.963A  pdb=" N   CYS R 291 " --> pdb=" O   MET R 287 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   CYS R 292 " --> pdb=" O   ASN R 288 " (cutoff:3.500A)
      Proline residue:  R 295  - end of helix
      removed outlier: 3.527A  pdb=" N   TYR R 298 " --> pdb=" O   ASP R 294 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE R 300 " --> pdb=" O   PHE R 296 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 310
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 8
      removed outlier: 3.610A  pdb=" N   THR H  81 " --> pdb=" O   ASP H  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15
    Processing sheet with id=AA3, first strand: chain 'H' and resid 62 through 63
      removed outlier: 3.570A  pdb=" N   SER H  62 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 63
      removed outlier: 3.570A  pdb=" N   SER H  62 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 138
      removed outlier: 3.798A  pdb=" N   LYS H 157 " --> pdb=" O   SER H 134 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY H 153 " --> pdb=" O   LEU H 138 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL H 198 " --> pdb=" O   ALA H 150 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 134 through 138
      removed outlier: 3.798A  pdb=" N   LYS H 157 " --> pdb=" O   SER H 134 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY H 153 " --> pdb=" O   LEU H 138 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL H 198 " --> pdb=" O   ALA H 150 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 165 through 168
      removed outlier: 3.908A  pdb=" N   THR H 165 " --> pdb=" O   ASN H 213 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN H 213 " --> pdb=" O   THR H 165 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS H 223 " --> pdb=" O   CYS H 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 3 through 7
      removed outlier: 3.843A  pdb=" N   GLN K   3 " --> pdb=" O   SER K  25 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   SER K  21 " --> pdb=" O   SER K   7 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL K  79 " --> pdb=" O   CYS K  22 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TYR K  80 " --> pdb=" O   SER K  71 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 58 through 60
      removed outlier: 5.187A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA K  49 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   TYR K 110 " --> pdb=" O   ILE K  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 92 through 93
    Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14
    Processing sheet with id=AB4, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.435A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 120
      removed outlier: 3.556A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 147 through 152

    360 hydrogen bonds defined for protein.
    1008 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: 2.05

  Time building geometry restraints manager: 1.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2242
        1.34 -     1.46: 1464
        1.46 -     1.58: 3557
        1.58 -     1.69: 1
        1.69 -     1.81: 51
  Bond restraints: 7315
  Sorted by residual:
  bond pdb=" C17 KKF R1301 "
       pdb=" N07 KKF R1301 "
    ideal  model  delta    sigma   weight residual
    1.352  1.425 -0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C22 KKF R1301 "
       pdb=" C26 KKF R1301 "
    ideal  model  delta    sigma   weight residual
    1.460  1.524 -0.064 2.00e-02 2.50e+03 1.04e+01
  bond pdb=" C13 KKF R1301 "
       pdb=" N07 KKF R1301 "
    ideal  model  delta    sigma   weight residual
    1.459  1.514 -0.055 2.00e-02 2.50e+03 7.61e+00
  bond pdb=" C15 KKF R1301 "
       pdb=" O05 KKF R1301 "
    ideal  model  delta    sigma   weight residual
    1.207  1.257 -0.050 2.00e-02 2.50e+03 6.17e+00
  bond pdb=" C16 KKF R1301 "
       pdb=" N08 KKF R1301 "
    ideal  model  delta    sigma   weight residual
    1.438  1.487 -0.049 2.00e-02 2.50e+03 5.92e+00
  ... (remaining 7310 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 9691
        2.41 -     4.82: 198
        4.82 -     7.23: 41
        7.23 -     9.65: 7
        9.65 -    12.06: 2
  Bond angle restraints: 9939
  Sorted by residual:
  angle pdb=" N   VAL R 206 "
        pdb=" CA  VAL R 206 "
        pdb=" C   VAL R 206 "
      ideal   model   delta    sigma   weight residual
     110.42  117.64   -7.22 9.60e-01 1.09e+00 5.65e+01
  angle pdb=" C   GLU R 183 "
        pdb=" N   TYR R 184 "
        pdb=" CA  TYR R 184 "
      ideal   model   delta    sigma   weight residual
     120.44  126.13   -5.69 1.30e+00 5.92e-01 1.91e+01
  angle pdb=" N   TYR R 205 "
        pdb=" CA  TYR R 205 "
        pdb=" C   TYR R 205 "
      ideal   model   delta    sigma   weight residual
     112.72  118.18   -5.46 1.28e+00 6.10e-01 1.82e+01
  angle pdb=" CA  LEU R 207 "
        pdb=" C   LEU R 207 "
        pdb=" N   PRO R 208 "
      ideal   model   delta    sigma   weight residual
     120.93  116.62    4.31 1.06e+00 8.90e-01 1.65e+01
  angle pdb=" C17 KKF R1301 "
        pdb=" C19 KKF R1301 "
        pdb=" C22 KKF R1301 "
      ideal   model   delta    sigma   weight residual
     120.00  132.06  -12.06 3.00e+00 1.11e-01 1.62e+01
  ... (remaining 9934 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 4009
       17.80 -    35.59: 296
       35.59 -    53.39: 45
       53.39 -    71.19: 4
       71.19 -    88.99: 6
  Dihedral angle restraints: 4360
    sinusoidal: 1657
      harmonic: 2703
  Sorted by residual:
  dihedral pdb=" CB  CYS K  22 "
           pdb=" SG  CYS K  22 "
           pdb=" SG  CYS K  96 "
           pdb=" CB  CYS K  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   28.93   64.07     1      1.00e+01 1.00e-02 5.40e+01
  dihedral pdb=" CB  CYS R 104 "
           pdb=" SG  CYS R 104 "
           pdb=" SG  CYS R 181 "
           pdb=" CB  CYS R 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.60  -45.60     1      1.00e+01 1.00e-02 2.88e+01
  dihedral pdb=" CA  GLU K  44 "
           pdb=" C   GLU K  44 "
           pdb=" N   ARG K  45 "
           pdb=" CA  ARG K  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.97   25.03     0      5.00e+00 4.00e-02 2.51e+01
  ... (remaining 4357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 724
       0.041 -    0.082: 286
       0.082 -    0.122: 102
       0.122 -    0.163: 15
       0.163 -    0.204: 8
  Chirality restraints: 1135
  Sorted by residual:
  chirality pdb=" CA  TYR R 205 "
            pdb=" N   TYR R 205 "
            pdb=" C   TYR R 205 "
            pdb=" CB  TYR R 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  ILE R 210 "
            pdb=" N   ILE R 210 "
            pdb=" C   ILE R 210 "
            pdb=" CB  ILE R 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  TYR L 142 "
            pdb=" N   TYR L 142 "
            pdb=" C   TYR L 142 "
            pdb=" CB  TYR L 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.94e-01
  ... (remaining 1132 not shown)

  Planarity restraints: 1250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 108 "   -0.039 5.00e-02 4.00e+02   5.78e-02 5.35e+00
        pdb=" N   PRO H 109 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO H 109 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO H 109 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 294 "   -0.036 5.00e-02 4.00e+02   5.46e-02 4.77e+00
        pdb=" N   PRO R 295 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO R 295 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO R 295 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 164 "   -0.034 5.00e-02 4.00e+02   5.15e-02 4.25e+00
        pdb=" N   PRO R 165 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO R 165 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 165 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1247 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 695
        2.74 -     3.28: 7168
        3.28 -     3.82: 11624
        3.82 -     4.36: 13933
        4.36 -     4.90: 23820
  Nonbonded interactions: 57240
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R  38 "
            pdb=" OD1 ASN R 288 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OE1 GLU L 107 "
            pdb=" OH  TYR L 175 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR R 205 "
            pdb=" OG1 THR R 248 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" NH2 ARG H  70 "
            pdb=" OD2 ASP H  93 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" OE2 GLU K   6 "
            pdb=" N   GLY K 114 "
     model   vdw
     2.307 3.120
  ... (remaining 57235 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.820
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
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   0.073   7321  Z= 0.237
  Angle     :  0.869  12.057   9951  Z= 0.452
  Chirality :  0.051   0.204   1135
  Planarity :  0.006   0.058   1250
  Dihedral  : 12.817  88.986   2600
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.24 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.24), residues: 904
  helix: -1.93 (0.24), residues: 316
  sheet: -2.09 (0.31), residues: 238
  loop : -3.08 (0.28), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.008   0.001   HIS R 251 
 PHE   0.013   0.002   PHE H 114 
 TYR   0.018   0.001   TYR H  53 
 ARG   0.002   0.000   ARG R1039 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17095 (  344)
  hydrogen bonds       : angle       7.63128 ( 1008)
  SS BOND              : bond        0.00396 (    6)
  SS BOND              : angle       1.01102 (   12)
  covalent geometry    : bond        0.00513 ( 7315)
  covalent geometry    : angle       0.86848 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 147
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   76 ASP cc_start: 0.7819 (t0) cc_final: 0.7489 (t0)
REVERT: H   92 GLU cc_start: 0.8639 (pm20) cc_final: 0.8316 (pm20)
REVERT: H  185 GLN cc_start: 0.8579 (tt0) cc_final: 0.8193 (mt0)
REVERT: H  209 ILE cc_start: 0.8768 (pt) cc_final: 0.8443 (pp)
REVERT: H  226 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8478 (mt-10)
REVERT: K   30 SER cc_start: 0.8593 (p) cc_final: 0.8287 (m)
REVERT: K   34 MET cc_start: 0.7706 (mmt) cc_final: 0.7419 (mmt)
REVERT: K   46 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7350 (mp0)
REVERT: K   98 ILE cc_start: 0.8458 (tp) cc_final: 0.8052 (tp)
REVERT: K  101 ASP cc_start: 0.8694 (t0) cc_final: 0.8341 (t0)
REVERT: L  124 ASP cc_start: 0.9072 (p0) cc_final: 0.8817 (m-30)
REVERT: L  128 LYS cc_start: 0.9215 (mptt) cc_final: 0.9007 (mmtm)
REVERT: L  167 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8083 (tp30)
REVERT: L  192 LYS cc_start: 0.8498 (pttp) cc_final: 0.8170 (mmtt)
REVERT: R   37 HIS cc_start: 0.7186 (t70) cc_final: 0.6812 (t-170)
REVERT: R  156 TRP cc_start: 0.8127 (t-100) cc_final: 0.7871 (m100)
REVERT: R  202 PHE cc_start: 0.7816 (t80) cc_final: 0.7364 (m-80)
REVERT: R 1091 GLU cc_start: 0.8037 (mp0) cc_final: 0.7706 (mp0)
REVERT: R  288 ASN cc_start: 0.7678 (m110) cc_final: 0.7220 (m110)
  outliers start: 2
  outliers final: 0
  residues processed: 147
  average time/residue: 1.0848
  time to fit residues: 169.0473
Evaluate side-chains
  105 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0870
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0050
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 83 optimal weight:    7.9990
   overall best weight:    0.4372

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

Flipped N/Q/H residues before XYZ refinement:
K  39 GLN
L 126 GLN
** R  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R1030 GLN
R1104 ASN
R1108 GLN
R 234 ASN
R 251 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.136835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.091533 restraints weight = 12802.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 3.33
r_work: 0.3268 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7321  Z= 0.126
  Angle     :  0.666  12.628   9951  Z= 0.337
  Chirality :  0.044   0.194   1135
  Planarity :  0.005   0.047   1250
  Dihedral  :  5.619  52.441   1030
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.18 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.26), residues: 904
  helix: -0.64 (0.27), residues: 314
  sheet: -1.84 (0.30), residues: 251
  loop : -2.49 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K 111 
 HIS   0.006   0.001   HIS R 281 
 PHE   0.008   0.001   PHE R 289 
 TYR   0.025   0.001   TYR R 298 
 ARG   0.007   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03691 (  344)
  hydrogen bonds       : angle       5.35120 ( 1008)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       0.86603 (   12)
  covalent geometry    : bond        0.00269 ( 7315)
  covalent geometry    : angle       0.66602 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   76 ASP cc_start: 0.8045 (t0) cc_final: 0.7469 (OUTLIER)
REVERT: H   79 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8552 (mtpt)
REVERT: H   92 GLU cc_start: 0.8840 (pm20) cc_final: 0.8525 (pm20)
REVERT: H  119 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8702 (pt0)
REVERT: H  185 GLN cc_start: 0.8864 (tt0) cc_final: 0.8569 (mt0)
REVERT: H  209 ILE cc_start: 0.8759 (pt) cc_final: 0.8496 (pp)
REVERT: H  226 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8533 (mt-10)
REVERT: K   31 ARG cc_start: 0.8305 (ptm160) cc_final: 0.7920 (ttp-170)
REVERT: K   34 MET cc_start: 0.8229 (mmt) cc_final: 0.7979 (mmt)
REVERT: K   46 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7780 (mp0)
REVERT: K   74 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7796 (m-30)
REVERT: K   87 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7836 (mtmm)
REVERT: K   98 ILE cc_start: 0.8624 (tp) cc_final: 0.8321 (tp)
REVERT: K  101 ASP cc_start: 0.8755 (t0) cc_final: 0.8230 (t0)
REVERT: L  107 GLU cc_start: 0.8423 (pt0) cc_final: 0.7888 (pt0)
REVERT: L  124 ASP cc_start: 0.9069 (p0) cc_final: 0.8845 (OUTLIER)
REVERT: L  128 LYS cc_start: 0.9229 (mptt) cc_final: 0.8952 (mmtm)
REVERT: L  192 LYS cc_start: 0.8668 (pttp) cc_final: 0.8276 (mmtt)
REVERT: L  213 ARG cc_start: 0.7112 (tpt90) cc_final: 0.6845 (tpt90)
REVERT: R   34 MET cc_start: 0.3458 (ttt) cc_final: 0.3213 (ttt)
REVERT: R  198 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6113 (mt)
REVERT: R  202 PHE cc_start: 0.7983 (t80) cc_final: 0.7355 (m-10)
REVERT: R 1091 GLU cc_start: 0.8261 (mp0) cc_final: 0.7816 (mp0)
REVERT: R  288 ASN cc_start: 0.8107 (m110) cc_final: 0.7238 (m110)
  outliers start: 18
  outliers final: 7
  residues processed: 126
  average time/residue: 1.6238
  time to fit residues: 217.8652
Evaluate side-chains
  113 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue  119 GLN
Chi-restraints excluded: chain K residue   74 ASP
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain K residue  109 ASP
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue  284 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 0 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** R  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R1018 ASN
R 234 ASN
R 288 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.134679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.088378 restraints weight = 13027.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 3.38
r_work: 0.3216 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7321  Z= 0.166
  Angle     :  0.678   9.239   9951  Z= 0.344
  Chirality :  0.045   0.153   1135
  Planarity :  0.004   0.047   1250
  Dihedral  :  5.580  55.452   1030
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.54 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.27), residues: 904
  helix: -0.28 (0.28), residues: 314
  sheet: -1.58 (0.31), residues: 251
  loop : -2.23 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  50 
 HIS   0.003   0.001   HIS R 281 
 PHE   0.008   0.001   PHE L 141 
 TYR   0.018   0.001   TYR R  69 
 ARG   0.004   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03654 (  344)
  hydrogen bonds       : angle       5.04555 ( 1008)
  SS BOND              : bond        0.00330 (    6)
  SS BOND              : angle       1.22913 (   12)
  covalent geometry    : bond        0.00384 ( 7315)
  covalent geometry    : angle       0.67744 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   76 ASP cc_start: 0.7972 (t0) cc_final: 0.7292 (t0)
REVERT: H   79 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8411 (mtpt)
REVERT: H   92 GLU cc_start: 0.8863 (pm20) cc_final: 0.8522 (pm20)
REVERT: H  119 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8714 (pt0)
REVERT: H  185 GLN cc_start: 0.8831 (tt0) cc_final: 0.8499 (mt0)
REVERT: H  209 ILE cc_start: 0.8750 (pt) cc_final: 0.8485 (pp)
REVERT: H  226 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8457 (mt-10)
REVERT: K   31 ARG cc_start: 0.8454 (ptm160) cc_final: 0.8075 (ttm170)
REVERT: K   34 MET cc_start: 0.8123 (mmt) cc_final: 0.7892 (mmt)
REVERT: K   46 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7727 (mp0)
REVERT: K   87 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7836 (mtmm)
REVERT: K   98 ILE cc_start: 0.8702 (tp) cc_final: 0.8280 (tp)
REVERT: K  101 ASP cc_start: 0.8773 (t0) cc_final: 0.8154 (t0)
REVERT: L  107 GLU cc_start: 0.8441 (pt0) cc_final: 0.7887 (pt0)
REVERT: L  124 ASP cc_start: 0.9106 (p0) cc_final: 0.8812 (m-30)
REVERT: L  128 LYS cc_start: 0.9231 (mptt) cc_final: 0.8986 (mmtm)
REVERT: L  192 LYS cc_start: 0.8438 (pttp) cc_final: 0.8113 (mmtt)
REVERT: R   34 MET cc_start: 0.3950 (ttt) cc_final: 0.3250 (ttt)
REVERT: R  156 TRP cc_start: 0.8164 (t-100) cc_final: 0.7881 (m100)
REVERT: R  198 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.6051 (mt)
REVERT: R  202 PHE cc_start: 0.8056 (t80) cc_final: 0.7435 (m-10)
REVERT: R 1091 GLU cc_start: 0.8352 (mp0) cc_final: 0.7862 (mp0)
REVERT: R  287 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7789 (ttm)
REVERT: R  288 ASN cc_start: 0.8144 (m-40) cc_final: 0.7501 (m110)
REVERT: R  294 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.7036 (t70)
  outliers start: 23
  outliers final: 8
  residues processed: 117
  average time/residue: 1.1042
  time to fit residues: 137.2725
Evaluate side-chains
  110 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue  119 GLN
Chi-restraints excluded: chain K residue   22 CYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue  239 ILE
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  287 MET
Chi-restraints excluded: chain R residue  294 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
R  37 HIS
R 135 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.130460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.083528 restraints weight = 12979.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 3.36
r_work: 0.3135 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.089   7321  Z= 0.330
  Angle     :  0.777   8.580   9951  Z= 0.399
  Chirality :  0.049   0.164   1135
  Planarity :  0.005   0.052   1250
  Dihedral  :  6.048  59.742   1030
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 17.49 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.27), residues: 904
  helix: -0.34 (0.29), residues: 311
  sheet: -1.55 (0.31), residues: 254
  loop : -2.22 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  50 
 HIS   0.006   0.001   HIS R  37 
 PHE   0.013   0.002   PHE R 296 
 TYR   0.021   0.002   TYR R  69 
 ARG   0.003   0.001   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04211 (  344)
  hydrogen bonds       : angle       5.25754 ( 1008)
  SS BOND              : bond        0.00343 (    6)
  SS BOND              : angle       1.42563 (   12)
  covalent geometry    : bond        0.00775 ( 7315)
  covalent geometry    : angle       0.77611 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: H   76 ASP cc_start: 0.8044 (t0) cc_final: 0.7343 (t0)
REVERT: H   79 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8345 (mtpt)
REVERT: H   92 GLU cc_start: 0.8950 (pm20) cc_final: 0.8627 (pm20)
REVERT: H  185 GLN cc_start: 0.8808 (tt0) cc_final: 0.8525 (mt0)
REVERT: H  209 ILE cc_start: 0.8757 (pt) cc_final: 0.8499 (OUTLIER)
REVERT: H  226 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8397 (mt-10)
REVERT: K   46 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7885 (mm-30)
REVERT: K   74 ASP cc_start: 0.8230 (m-30) cc_final: 0.7983 (m-30)
REVERT: K   87 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7890 (mtmm)
REVERT: K  101 ASP cc_start: 0.8771 (t0) cc_final: 0.8281 (t0)
REVERT: L  192 LYS cc_start: 0.8271 (pttp) cc_final: 0.7958 (mmtt)
REVERT: R  144 ARG cc_start: 0.8158 (pmm-80) cc_final: 0.7883 (pmm-80)
REVERT: R  156 TRP cc_start: 0.8229 (t-100) cc_final: 0.7971 (m100)
REVERT: R  202 PHE cc_start: 0.8136 (t80) cc_final: 0.7498 (m-10)
REVERT: R 1009 GLU cc_start: 0.8893 (tp30) cc_final: 0.8689 (tp30)
REVERT: R 1091 GLU cc_start: 0.8479 (mp0) cc_final: 0.8018 (mp0)
REVERT: R  243 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6088 (t80)
REVERT: R  288 ASN cc_start: 0.8438 (m-40) cc_final: 0.7700 (m110)
  outliers start: 29
  outliers final: 15
  residues processed: 119
  average time/residue: 1.4548
  time to fit residues: 183.6518
Evaluate side-chains
  105 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain K residue   22 CYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain L residue  135 VAL
Chi-restraints excluded: chain L residue  191 HIS
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain L residue  199 THR
Chi-restraints excluded: chain R residue  125 LEU
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue  239 ILE
Chi-restraints excluded: chain R residue  243 PHE
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  284 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 24 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R 281 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.135107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.088907 restraints weight = 12800.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.37
r_work: 0.3225 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7321  Z= 0.138
  Angle     :  0.690  11.189   9951  Z= 0.344
  Chirality :  0.044   0.163   1135
  Planarity :  0.004   0.056   1250
  Dihedral  :  5.878  53.733   1030
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.08 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.28), residues: 904
  helix:  0.02 (0.29), residues: 313
  sheet: -1.32 (0.31), residues: 247
  loop : -1.90 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP K 111 
 HIS   0.004   0.001   HIS R 281 
 PHE   0.009   0.001   PHE L 141 
 TYR   0.014   0.001   TYR R  69 
 ARG   0.010   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  344)
  hydrogen bonds       : angle       4.81387 ( 1008)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       0.95359 (   12)
  covalent geometry    : bond        0.00306 ( 7315)
  covalent geometry    : angle       0.69004 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   76 ASP cc_start: 0.7931 (t0) cc_final: 0.7197 (t0)
REVERT: H   79 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8444 (mtpt)
REVERT: H   92 GLU cc_start: 0.8885 (pm20) cc_final: 0.8549 (pm20)
REVERT: H  185 GLN cc_start: 0.8765 (tt0) cc_final: 0.8494 (mt0)
REVERT: H  209 ILE cc_start: 0.8809 (pt) cc_final: 0.8541 (pp)
REVERT: H  226 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8399 (mt-10)
REVERT: K   18 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7462 (mp)
REVERT: K   31 ARG cc_start: 0.8380 (ptm160) cc_final: 0.7844 (ttp-170)
REVERT: K   46 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7755 (mp0)
REVERT: K   87 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7738 (mtmm)
REVERT: K  101 ASP cc_start: 0.8748 (t0) cc_final: 0.8115 (t0)
REVERT: L  107 GLU cc_start: 0.8445 (pt0) cc_final: 0.7929 (pt0)
REVERT: L  189 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7816 (mm-30)
REVERT: L  192 LYS cc_start: 0.8340 (pttp) cc_final: 0.8000 (mmtt)
REVERT: L  213 ARG cc_start: 0.7153 (tpt90) cc_final: 0.6902 (tpt90)
REVERT: R  156 TRP cc_start: 0.8138 (t-100) cc_final: 0.7905 (m100)
REVERT: R  184 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5848 (m-80)
REVERT: R  198 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.6120 (mt)
REVERT: R  202 PHE cc_start: 0.8108 (t80) cc_final: 0.7490 (m-10)
REVERT: R 1091 GLU cc_start: 0.8397 (mp0) cc_final: 0.7840 (mp0)
REVERT: R  243 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.5750 (t80)
REVERT: R  281 HIS cc_start: 0.7272 (t-90) cc_final: 0.6490 (t70)
REVERT: R  285 CYS cc_start: 0.8284 (m) cc_final: 0.7668 (m)
REVERT: R  288 ASN cc_start: 0.8197 (m-40) cc_final: 0.7316 (m110)
  outliers start: 24
  outliers final: 8
  residues processed: 119
  average time/residue: 1.3332
  time to fit residues: 166.7821
Evaluate side-chains
  102 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain K residue   18 LEU
Chi-restraints excluded: chain K residue   22 CYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain R residue  147 HIS
Chi-restraints excluded: chain R residue  184 TYR
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue  243 PHE
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  284 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 84 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 88 optimal weight:    8.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
R 281 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.132687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.086000 restraints weight = 12801.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 3.36
r_work: 0.3171 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   7321  Z= 0.224
  Angle     :  0.731  10.425   9951  Z= 0.368
  Chirality :  0.045   0.180   1135
  Planarity :  0.004   0.054   1250
  Dihedral  :  5.683  45.117   1030
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.21 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.28), residues: 904
  helix: -0.00 (0.29), residues: 310
  sheet: -1.28 (0.32), residues: 246
  loop : -1.75 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP K 111 
 HIS   0.004   0.001   HIS R 281 
 PHE   0.010   0.001   PHE L 141 
 TYR   0.021   0.001   TYR L 142 
 ARG   0.008   0.001   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03580 (  344)
  hydrogen bonds       : angle       4.92041 ( 1008)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       1.12223 (   12)
  covalent geometry    : bond        0.00530 ( 7315)
  covalent geometry    : angle       0.73036 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 87
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: H   76 ASP cc_start: 0.7986 (t0) cc_final: 0.7246 (t0)
REVERT: H   79 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8404 (mtpt)
REVERT: H   92 GLU cc_start: 0.8923 (pm20) cc_final: 0.8587 (pm20)
REVERT: H  185 GLN cc_start: 0.8747 (tt0) cc_final: 0.8456 (mt0)
REVERT: H  209 ILE cc_start: 0.8809 (pt) cc_final: 0.8527 (pp)
REVERT: H  226 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8369 (mt-10)
REVERT: K   18 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7462 (mp)
REVERT: K   46 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7825 (mm-30)
REVERT: K   87 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7828 (mtmm)
REVERT: K  101 ASP cc_start: 0.8763 (t0) cc_final: 0.8140 (t0)
REVERT: L  107 GLU cc_start: 0.8447 (pt0) cc_final: 0.7913 (pt0)
REVERT: L  192 LYS cc_start: 0.8351 (pttp) cc_final: 0.7936 (mmtm)
REVERT: R  156 TRP cc_start: 0.8204 (t-100) cc_final: 0.7969 (m100)
REVERT: R  198 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.6078 (mt)
REVERT: R  202 PHE cc_start: 0.8119 (t80) cc_final: 0.7510 (m-10)
REVERT: R 1009 GLU cc_start: 0.8906 (tp30) cc_final: 0.8661 (tp30)
REVERT: R 1091 GLU cc_start: 0.8446 (mp0) cc_final: 0.7907 (mp0)
REVERT: R  285 CYS cc_start: 0.8305 (m) cc_final: 0.7694 (m)
REVERT: R  288 ASN cc_start: 0.8385 (m-40) cc_final: 0.7553 (m110)
  outliers start: 29
  outliers final: 12
  residues processed: 109
  average time/residue: 0.9835
  time to fit residues: 114.4958
Evaluate side-chains
  98 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain K residue   18 LEU
Chi-restraints excluded: chain K residue   22 CYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  191 HIS
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain R residue  147 HIS
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  284 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0570
   chunk 88 optimal weight:    8.9990
   chunk 59 optimal weight:    0.2980
   chunk 47 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 69 optimal weight:    0.0030
   overall best weight:    0.2046

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.139168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.095197 restraints weight = 12803.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 3.28
r_work: 0.3307 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7321  Z= 0.114
  Angle     :  0.668   9.800   9951  Z= 0.334
  Chirality :  0.044   0.208   1135
  Planarity :  0.004   0.059   1250
  Dihedral  :  4.979  39.766   1030
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 21.63 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.29), residues: 904
  helix:  0.31 (0.30), residues: 313
  sheet: -0.93 (0.33), residues: 241
  loop : -1.49 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP K 111 
 HIS   0.004   0.001   HIS R 281 
 PHE   0.010   0.001   PHE L 141 
 TYR   0.018   0.001   TYR R  69 
 ARG   0.011   0.001   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02969 (  344)
  hydrogen bonds       : angle       4.49858 ( 1008)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       0.82459 (   12)
  covalent geometry    : bond        0.00247 ( 7315)
  covalent geometry    : angle       0.66794 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLN cc_start: 0.8305 (tt0) cc_final: 0.7981 (pt0)
REVERT: H   46 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8102 (mppt)
REVERT: H   76 ASP cc_start: 0.7972 (t0) cc_final: 0.7268 (t0)
REVERT: H   79 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8627 (mtpt)
REVERT: H   92 GLU cc_start: 0.8848 (pm20) cc_final: 0.8525 (pm20)
REVERT: H  185 GLN cc_start: 0.8740 (tt0) cc_final: 0.8474 (mt0)
REVERT: H  209 ILE cc_start: 0.8868 (pt) cc_final: 0.8595 (pp)
REVERT: H  226 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8379 (mt-10)
REVERT: K   18 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7234 (mp)
REVERT: K   31 ARG cc_start: 0.8306 (ptm160) cc_final: 0.7891 (ttp-170)
REVERT: K   46 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7740 (mp0)
REVERT: K   87 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7393 (mmtm)
REVERT: K  101 ASP cc_start: 0.8599 (t0) cc_final: 0.8050 (t0)
REVERT: L  107 GLU cc_start: 0.8454 (pt0) cc_final: 0.7915 (pt0)
REVERT: L  192 LYS cc_start: 0.8346 (pttp) cc_final: 0.7869 (mmpt)
REVERT: R  144 ARG cc_start: 0.7602 (pmm-80) cc_final: 0.7339 (pmm-80)
REVERT: R  156 TRP cc_start: 0.8182 (t-100) cc_final: 0.7960 (m100)
REVERT: R  198 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6256 (mt)
REVERT: R  202 PHE cc_start: 0.8073 (t80) cc_final: 0.7498 (m-10)
REVERT: R 1091 GLU cc_start: 0.8310 (mp0) cc_final: 0.7762 (mp0)
REVERT: R  243 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.5770 (t80)
REVERT: R  284 VAL cc_start: 0.7617 (t) cc_final: 0.7262 (p)
REVERT: R  285 CYS cc_start: 0.8220 (m) cc_final: 0.7629 (m)
REVERT: R  288 ASN cc_start: 0.7974 (m-40) cc_final: 0.7025 (m110)
  outliers start: 22
  outliers final: 10
  residues processed: 120
  average time/residue: 1.0129
  time to fit residues: 129.4497
Evaluate side-chains
  107 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain H residue   53 TYR
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain K residue   18 LEU
Chi-restraints excluded: chain K residue   22 CYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain R residue  147 HIS
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue  240 ILE
Chi-restraints excluded: chain R residue  243 PHE
Chi-restraints excluded: chain R residue  281 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0870
   chunk 64 optimal weight:    0.7980
   chunk 58 optimal weight:   20.0000
   chunk 33 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.0960

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

Flipped N/Q/H residues before XYZ refinement:
H 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.135383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.089274 restraints weight = 12897.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.37
r_work: 0.3230 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7321  Z= 0.155
  Angle     :  0.689   9.765   9951  Z= 0.347
  Chirality :  0.044   0.175   1135
  Planarity :  0.004   0.056   1250
  Dihedral  :  5.150  40.034   1030
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 23.06 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.29), residues: 904
  helix:  0.28 (0.30), residues: 314
  sheet: -0.97 (0.33), residues: 248
  loop : -1.45 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP K 111 
 HIS   0.005   0.001   HIS R 147 
 PHE   0.010   0.001   PHE L 141 
 TYR   0.018   0.001   TYR L 142 
 ARG   0.010   0.001   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  344)
  hydrogen bonds       : angle       4.55231 ( 1008)
  SS BOND              : bond        0.00247 (    6)
  SS BOND              : angle       1.01096 (   12)
  covalent geometry    : bond        0.00362 ( 7315)
  covalent geometry    : angle       0.68832 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLN cc_start: 0.8371 (tt0) cc_final: 0.8049 (pt0)
REVERT: H   76 ASP cc_start: 0.7945 (t0) cc_final: 0.7195 (t0)
REVERT: H   79 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8503 (mtpt)
REVERT: H   92 GLU cc_start: 0.8859 (pm20) cc_final: 0.8494 (pm20)
REVERT: H  185 GLN cc_start: 0.8737 (tt0) cc_final: 0.8470 (mt0)
REVERT: H  209 ILE cc_start: 0.8848 (pt) cc_final: 0.8574 (pp)
REVERT: H  226 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8380 (mt-10)
REVERT: K   18 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7307 (mp)
REVERT: K   31 ARG cc_start: 0.8381 (ptm160) cc_final: 0.7843 (ttp-170)
REVERT: K   46 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7714 (mp0)
REVERT: K   87 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7472 (mmtm)
REVERT: K  101 ASP cc_start: 0.8707 (t0) cc_final: 0.8030 (t0)
REVERT: L  107 GLU cc_start: 0.8439 (pt0) cc_final: 0.8004 (pt0)
REVERT: R  156 TRP cc_start: 0.8195 (t-100) cc_final: 0.7964 (m100)
REVERT: R  198 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6131 (mt)
REVERT: R  202 PHE cc_start: 0.8081 (t80) cc_final: 0.7485 (m-10)
REVERT: R 1091 GLU cc_start: 0.8382 (mp0) cc_final: 0.7825 (mp0)
REVERT: R  243 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.5805 (t80)
REVERT: R  284 VAL cc_start: 0.7643 (t) cc_final: 0.7314 (p)
REVERT: R  285 CYS cc_start: 0.8228 (m) cc_final: 0.7660 (m)
REVERT: R  288 ASN cc_start: 0.8174 (m-40) cc_final: 0.7347 (m-40)
  outliers start: 22
  outliers final: 12
  residues processed: 111
  average time/residue: 0.9768
  time to fit residues: 115.9370
Evaluate side-chains
  106 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain K residue   18 LEU
Chi-restraints excluded: chain K residue   22 CYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain L residue  199 THR
Chi-restraints excluded: chain R residue  115 THR
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue  243 PHE
Chi-restraints excluded: chain R residue  281 HIS
Chi-restraints excluded: chain R residue  287 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 22 optimal weight:   20.0000
   chunk 65 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0980
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
** L 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 147 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.133000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.086502 restraints weight = 12986.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 3.38
r_work: 0.3186 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   7321  Z= 0.227
  Angle     :  0.742   9.726   9951  Z= 0.376
  Chirality :  0.046   0.198   1135
  Planarity :  0.004   0.055   1250
  Dihedral  :  5.487  39.838   1030
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.19 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.28), residues: 904
  helix:  0.09 (0.29), residues: 314
  sheet: -0.98 (0.33), residues: 239
  loop : -1.46 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP K 111 
 HIS   0.003   0.001   HIS R 147 
 PHE   0.010   0.001   PHE L 100 
 TYR   0.032   0.002   TYR R  69 
 ARG   0.009   0.001   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03629 (  344)
  hydrogen bonds       : angle       4.73202 ( 1008)
  SS BOND              : bond        0.00224 (    6)
  SS BOND              : angle       1.12147 (   12)
  covalent geometry    : bond        0.00537 ( 7315)
  covalent geometry    : angle       0.74147 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   76 ASP cc_start: 0.7971 (t0) cc_final: 0.7206 (t0)
REVERT: H   79 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8407 (mtpt)
REVERT: H   92 GLU cc_start: 0.8895 (pm20) cc_final: 0.8546 (pm20)
REVERT: H  185 GLN cc_start: 0.8729 (tt0) cc_final: 0.8466 (mt0)
REVERT: H  209 ILE cc_start: 0.8790 (pt) cc_final: 0.8522 (OUTLIER)
REVERT: H  226 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8364 (mt-10)
REVERT: K   18 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7394 (mp)
REVERT: K   46 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7801 (mm-30)
REVERT: K   87 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7506 (mmtm)
REVERT: K  101 ASP cc_start: 0.8691 (t0) cc_final: 0.7985 (t0)
REVERT: L  107 GLU cc_start: 0.8480 (pt0) cc_final: 0.8038 (pt0)
REVERT: R  146 GLU cc_start: 0.7222 (pp20) cc_final: 0.5643 (mm-30)
REVERT: R  156 TRP cc_start: 0.8246 (t-100) cc_final: 0.7992 (m100)
REVERT: R  202 PHE cc_start: 0.8179 (t80) cc_final: 0.7538 (m-10)
REVERT: R 1091 GLU cc_start: 0.8418 (mp0) cc_final: 0.7880 (mp0)
REVERT: R  243 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6014 (t80)
REVERT: R  288 ASN cc_start: 0.8401 (m-40) cc_final: 0.7568 (m-40)
  outliers start: 23
  outliers final: 14
  residues processed: 106
  average time/residue: 0.9979
  time to fit residues: 112.8944
Evaluate side-chains
  103 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain K residue   18 LEU
Chi-restraints excluded: chain K residue   22 CYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain K residue  109 ASP
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain L residue  199 THR
Chi-restraints excluded: chain R residue  115 THR
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue 1013 GLU
Chi-restraints excluded: chain R residue  243 PHE
Chi-restraints excluded: chain R residue  287 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0570
   chunk 41 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0020
   chunk 77 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.3706

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

Flipped N/Q/H residues before XYZ refinement:
R 147 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.137035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.091372 restraints weight = 13062.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.42
r_work: 0.3262 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7321  Z= 0.124
  Angle     :  0.701  10.054   9951  Z= 0.355
  Chirality :  0.044   0.185   1135
  Planarity :  0.004   0.057   1250
  Dihedral  :  5.120  37.416   1030
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 24.48 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.29), residues: 904
  helix:  0.27 (0.29), residues: 314
  sheet: -0.76 (0.34), residues: 225
  loop : -1.34 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP K 111 
 HIS   0.003   0.001   HIS R 147 
 PHE   0.009   0.001   PHE L 141 
 TYR   0.021   0.001   TYR R  69 
 ARG   0.015   0.001   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  344)
  hydrogen bonds       : angle       4.52408 ( 1008)
  SS BOND              : bond        0.00302 (    6)
  SS BOND              : angle       0.82310 (   12)
  covalent geometry    : bond        0.00274 ( 7315)
  covalent geometry    : angle       0.70117 ( 9939)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   76 ASP cc_start: 0.7949 (t0) cc_final: 0.7250 (t0)
REVERT: H   79 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8631 (mtpm)
REVERT: H   92 GLU cc_start: 0.8859 (pm20) cc_final: 0.8505 (pm20)
REVERT: H  185 GLN cc_start: 0.8729 (tt0) cc_final: 0.8449 (mt0)
REVERT: H  209 ILE cc_start: 0.8806 (pt) cc_final: 0.8520 (pp)
REVERT: H  226 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8367 (mt-10)
REVERT: K   18 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7259 (mp)
REVERT: K   31 ARG cc_start: 0.8381 (ptm160) cc_final: 0.8092 (ttp-110)
REVERT: K   46 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7718 (mp0)
REVERT: K   87 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7401 (mmtm)
REVERT: K  101 ASP cc_start: 0.8682 (t0) cc_final: 0.8045 (t0)
REVERT: L  107 GLU cc_start: 0.8477 (pt0) cc_final: 0.8049 (pt0)
REVERT: R  146 GLU cc_start: 0.7209 (pp20) cc_final: 0.5726 (mm-30)
REVERT: R  202 PHE cc_start: 0.8160 (t80) cc_final: 0.7531 (m-10)
REVERT: R 1091 GLU cc_start: 0.8349 (mp0) cc_final: 0.7800 (mp0)
REVERT: R  243 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.5843 (t80)
REVERT: R  284 VAL cc_start: 0.7652 (t) cc_final: 0.7309 (p)
REVERT: R  285 CYS cc_start: 0.8167 (m) cc_final: 0.7604 (m)
REVERT: R  288 ASN cc_start: 0.8178 (m-40) cc_final: 0.7293 (m-40)
  outliers start: 16
  outliers final: 8
  residues processed: 107
  average time/residue: 0.9545
  time to fit residues: 109.5070
Evaluate side-chains
  101 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain K residue   18 LEU
Chi-restraints excluded: chain K residue   22 CYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   78 THR
Chi-restraints excluded: chain K residue   91 THR
Chi-restraints excluded: chain K residue  115 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  193 VAL
Chi-restraints excluded: chain R residue 1005 LEU
Chi-restraints excluded: chain R residue  243 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 69 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
H  87 ASN
K   1 GLN
R 147 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.135790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.090072 restraints weight = 12904.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 3.40
r_work: 0.3245 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7321  Z= 0.138
  Angle     :  0.700  10.118   9951  Z= 0.352
  Chirality :  0.044   0.173   1135
  Planarity :  0.004   0.056   1250
  Dihedral  :  5.092  37.067   1030
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 24.87 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.29), residues: 904
  helix:  0.35 (0.29), residues: 314
  sheet: -0.72 (0.34), residues: 239
  loop : -1.32 (0.37), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP K 111 
 HIS   0.004   0.001   HIS R 147 
 PHE   0.010   0.001   PHE L 141 
 TYR   0.023   0.001   TYR R  69 
 ARG   0.014   0.001   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03290 (  344)
  hydrogen bonds       : angle       4.53032 ( 1008)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       0.93810 (   12)
  covalent geometry    : bond        0.00318 ( 7315)
  covalent geometry    : angle       0.69917 ( 9939)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5786.62 seconds
wall clock time: 102 minutes 1.48 seconds (6121.48 seconds total)