Starting phenix.real_space_refine
on Mon Jul 28 10:58:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y90_10731/07_2025/6y90_10731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y90_10731/07_2025/6y90_10731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6y90_10731/07_2025/6y90_10731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y90_10731/07_2025/6y90_10731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y90_10731/07_2025/6y90_10731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y90_10731/07_2025/6y90_10731.cif"
  }
  resolution = 3.69
  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=   0.004 sd=   0.057
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
     P       2      5.49       5
     S      56      5.16       5
     C    6368      2.51       5
     N    1520      2.21       5
     O    1832      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9778
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1341
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 7, 'TRANS': 164}
    Chain: "B"
      Number of atoms: 1341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1341
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 7, 'TRANS': 164}
    Chain: "C"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1669
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 210}
    Chain: "D"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1623
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199}
    Chain: "A"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 256
          Unusual residues: {'MYS': 5, 'PC1': 1, 'Y01': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 256
          Unusual residues: {'MYS': 5, 'PC1': 1, 'Y01': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    H, L
  Time building chain proxies: 6.95, per 1000 atoms: 0.71
  Number of scatterers: 9778
  At special positions: 0
  Unit cell: (103.378, 142.45, 134.31, 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)
     S      56     16.00
     P       2     15.00
     O    1832      8.00
     N    1520      7.00
     C    6368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 167 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 167 " - pdb=" SG  CYS B 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 148 " - pdb=" SG  CYS C 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 224 " - pdb=" SG  CYS D 213 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 148 " - pdb=" SG  CYS H 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 224 " - pdb=" SG  CYS L 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 133 " - pdb=" SG  CYS L 193 " 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2252

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 20 sheets defined
      24.7% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 4.004A  pdb=" N   VAL A  84 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 102
      removed outlier: 3.805A  pdb=" N   TRP A  89 " --> pdb=" O   TRP A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 143
      removed outlier: 4.010A  pdb=" N   MET A 117 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ILE A 118 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 177 through 215
      removed outlier: 3.859A  pdb=" N   CYS A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 71
      removed outlier: 3.567A  pdb=" N   LEU B  52 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   MET B  71 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.707A  pdb=" N   VAL B  84 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 102
      removed outlier: 3.889A  pdb=" N   TRP B  89 " --> pdb=" O   TRP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 143
      removed outlier: 4.054A  pdb=" N   MET B 117 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ILE B 118 " --> pdb=" O   LYS B 114 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 157
    Processing helix  chain 'B' and resid 171 through 175
    Processing helix  chain 'B' and resid 177 through 215
      removed outlier: 3.729A  pdb=" N   CYS B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 82
    Processing helix  chain 'D' and resid 120 through 127
      removed outlier: 3.540A  pdb=" N   LEU D 124 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY D 127 " --> pdb=" O   GLN D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 181 through 188
    Processing helix  chain 'L' and resid 78 through 82
    Processing helix  chain 'L' and resid 120 through 127
      removed outlier: 3.539A  pdb=" N   LEU L 124 " --> pdb=" O   SER L 120 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY L 127 " --> pdb=" O   GLN L 123 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 181 through 188
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5
      removed outlier: 3.752A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 59
      removed outlier: 3.620A  pdb=" N   ILE C  48 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102
      removed outlier: 3.817A  pdb=" N   ASP C 105 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 128 through 132
      removed outlier: 3.881A  pdb=" N   SER C 128 " --> pdb=" O   LYS C 151 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLY C 147 " --> pdb=" O   LEU C 132 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER C 188 " --> pdb=" O   CYS C 148 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   TYR C 184 " --> pdb=" O   ASP C 152 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   SER C 185 " --> pdb=" O   ALA C 176 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ALA C 176 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER C 187 " --> pdb=" O   PHE C 174 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 159 through 160
      removed outlier: 3.537A  pdb=" N   THR C 159 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.668A  pdb=" N   THR D  22 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D  74 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.558A  pdb=" N   LEU D  11 " --> pdb=" O   LYS D 102 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR D  84 " --> pdb=" O   GLN D  37 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   GLN D  36 " --> pdb=" O   PRO D  45 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TYR D  48 " --> pdb=" O   ASN D  52 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 113 through 117
      removed outlier: 3.516A  pdb=" N   SER D 113 " --> pdb=" O   ASN D 136 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASN D 136 " --> pdb=" O   SER D 113 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL D 132 " --> pdb=" O   PHE D 117 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA D 129 " --> pdb=" O   LEU D 180 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU D 180 " --> pdb=" O   ALA D 129 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER D 176 " --> pdb=" O   CYS D 133 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU D 135 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU D 174 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER D 161 " --> pdb=" O   SER D 175 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR D 177 " --> pdb=" O   GLN D 159 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLN D 159 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154
      removed outlier: 3.953A  pdb=" N   TRP D 147 " --> pdb=" O   GLN D 154 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS D 144 " --> pdb=" O   THR D 196 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLU D 194 " --> pdb=" O   GLN D 146 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TYR D 191 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE D 208 " --> pdb=" O   TYR D 191 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   CYS D 193 " --> pdb=" O   LYS D 206 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LYS D 206 " --> pdb=" O   CYS D 193 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.753A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59
      removed outlier: 3.620A  pdb=" N   ILE H  48 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 100 through 102
      removed outlier: 3.819A  pdb=" N   ASP H 105 " --> pdb=" O   TYR H 102 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 128 through 132
      removed outlier: 3.881A  pdb=" N   SER H 128 " --> pdb=" O   LYS H 151 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLY H 147 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   SER H 188 " --> pdb=" O   CYS H 148 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   TYR H 184 " --> pdb=" O   ASP H 152 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   SER H 185 " --> pdb=" O   ALA H 176 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   ALA H 176 " --> pdb=" O   SER H 185 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER H 187 " --> pdb=" O   PHE H 174 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 159 through 160
      removed outlier: 3.537A  pdb=" N   THR H 159 " --> pdb=" O   ASN H 207 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.668A  pdb=" N   THR L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  74 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.558A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 102 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR L  84 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   GLN L  36 " --> pdb=" O   PRO L  45 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   TYR L  48 " --> pdb=" O   ASN L  52 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 113 through 117
      removed outlier: 3.516A  pdb=" N   SER L 113 " --> pdb=" O   ASN L 136 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASN L 136 " --> pdb=" O   SER L 113 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL L 132 " --> pdb=" O   PHE L 117 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA L 129 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU L 180 " --> pdb=" O   ALA L 129 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER L 176 " --> pdb=" O   CYS L 133 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU L 135 " --> pdb=" O   LEU L 174 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU L 174 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER L 161 " --> pdb=" O   SER L 175 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   THR L 177 " --> pdb=" O   GLN L 159 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLN L 159 " --> pdb=" O   THR L 177 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 152 through 154
      removed outlier: 3.954A  pdb=" N   TRP L 147 " --> pdb=" O   GLN L 154 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS L 144 " --> pdb=" O   THR L 196 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLU L 194 " --> pdb=" O   GLN L 146 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TYR L 191 " --> pdb=" O   PHE L 208 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE L 208 " --> pdb=" O   TYR L 191 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   CYS L 193 " --> pdb=" O   LYS L 206 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LYS L 206 " --> pdb=" O   CYS L 193 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1077 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: 2.54

  Time building geometry restraints manager: 2.94 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1498
        1.31 -     1.44: 2686
        1.44 -     1.56: 5745
        1.56 -     1.69: 5
        1.69 -     1.81: 84
  Bond restraints: 10018
  Sorted by residual:
  bond pdb=" CAZ Y01 A 303 "
       pdb=" CBH Y01 A 303 "
    ideal  model  delta    sigma   weight residual
    1.519  1.405  0.114 2.00e-02 2.50e+03 3.26e+01
  bond pdb=" CAZ Y01 B 304 "
       pdb=" CBH Y01 B 304 "
    ideal  model  delta    sigma   weight residual
    1.519  1.405  0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" CAZ Y01 A 302 "
       pdb=" CBH Y01 A 302 "
    ideal  model  delta    sigma   weight residual
    1.519  1.406  0.113 2.00e-02 2.50e+03 3.18e+01
  bond pdb=" CAZ Y01 B 301 "
       pdb=" CBH Y01 B 301 "
    ideal  model  delta    sigma   weight residual
    1.519  1.406  0.113 2.00e-02 2.50e+03 3.17e+01
  bond pdb=" CAZ Y01 B 302 "
       pdb=" CBH Y01 B 302 "
    ideal  model  delta    sigma   weight residual
    1.519  1.406  0.113 2.00e-02 2.50e+03 3.17e+01
  ... (remaining 10013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 13126
        2.83 -     5.67: 438
        5.67 -     8.50: 18
        8.50 -    11.33: 6
       11.33 -    14.16: 2
  Bond angle restraints: 13590
  Sorted by residual:
  angle pdb=" O12 PC1 A 304 "
        pdb=" P   PC1 A 304 "
        pdb=" O14 PC1 A 304 "
      ideal   model   delta    sigma   weight residual
     123.67  109.51   14.16 3.00e+00 1.11e-01 2.23e+01
  angle pdb=" O12 PC1 B 305 "
        pdb=" P   PC1 B 305 "
        pdb=" O14 PC1 B 305 "
      ideal   model   delta    sigma   weight residual
     123.67  109.53   14.14 3.00e+00 1.11e-01 2.22e+01
  angle pdb=" CAY Y01 A 303 "
        pdb=" OAW Y01 A 303 "
        pdb=" CBC Y01 A 303 "
      ideal   model   delta    sigma   weight residual
     119.39  109.59    9.80 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" CAY Y01 B 304 "
        pdb=" OAW Y01 B 304 "
        pdb=" CBC Y01 B 304 "
      ideal   model   delta    sigma   weight residual
     119.39  109.65    9.74 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" C22 PC1 B 305 "
        pdb=" C21 PC1 B 305 "
        pdb=" O21 PC1 B 305 "
      ideal   model   delta    sigma   weight residual
     111.12  119.88   -8.76 3.00e+00 1.11e-01 8.52e+00
  ... (remaining 13585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.87: 5891
       20.87 -    41.75: 441
       41.75 -    62.62: 74
       62.62 -    83.49: 16
       83.49 -   104.36: 6
  Dihedral angle restraints: 6428
    sinusoidal: 2906
      harmonic: 3522
  Sorted by residual:
  dihedral pdb=" CA  PHE B 146 "
           pdb=" C   PHE B 146 "
           pdb=" N   LEU B 147 "
           pdb=" CA  LEU B 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.55   20.45     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CAR Y01 A 303 "
           pdb=" CAV Y01 A 303 "
           pdb=" CBC Y01 A 303 "
           pdb=" CAZ Y01 A 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.40  -48.96  104.36     1      3.00e+01 1.11e-03 1.33e+01
  dihedral pdb=" CAR Y01 B 304 "
           pdb=" CAV Y01 B 304 "
           pdb=" CBC Y01 B 304 "
           pdb=" CAZ Y01 B 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.40  -48.94  104.34     1      3.00e+01 1.11e-03 1.33e+01
  ... (remaining 6425 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1428
       0.096 -    0.192: 62
       0.192 -    0.288: 5
       0.288 -    0.384: 15
       0.384 -    0.480: 14
  Chirality restraints: 1524
  Sorted by residual:
  chirality pdb=" CBH Y01 B 301 "
            pdb=" CAT Y01 B 301 "
            pdb=" CAZ Y01 B 301 "
            pdb=" CBF Y01 B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.37   -0.48 2.00e-01 2.50e+01 5.76e+00
  chirality pdb=" CBH Y01 A 310 "
            pdb=" CAT Y01 A 310 "
            pdb=" CAZ Y01 A 310 "
            pdb=" CBF Y01 A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.38   -0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CBG Y01 B 301 "
            pdb=" CAQ Y01 B 301 "
            pdb=" CBD Y01 B 301 "
            pdb=" CBI Y01 B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.81    0.47 2.00e-01 2.50e+01 5.62e+00
  ... (remaining 1521 not shown)

  Planarity restraints: 1642
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  94 "   -0.007 2.00e-02 2.50e+03   1.03e-02 2.11e+00
        pdb=" CG  TYR A  94 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  94 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  94 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  94 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  57 "    0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO L  58 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO L  58 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO L  58 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D  57 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO D  58 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO D  58 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D  58 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1639 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2180
        2.79 -     3.32: 8677
        3.32 -     3.85: 15209
        3.85 -     4.37: 16780
        4.37 -     4.90: 29883
  Nonbonded interactions: 72729
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 163 "
            pdb=" OH  TYR B 182 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OD1 ASP C  90 "
            pdb=" OH  TYR C  94 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OD1 ASP H  90 "
            pdb=" OH  TYR H  94 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OD1 ASN L 136 "
            pdb=" OG  SER L 173 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OD1 ASN D 136 "
            pdb=" OG  SER D 173 "
     model   vdw
     2.287 3.040
  ... (remaining 72724 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 45 through 216 or resid 301 through 303 or resid 306 throu \ 
gh 309))
  selection = (chain 'B' and (resid 45 through 216 or resid 301 through 302 or (resid 303 and  \ 
(name CAA or name CAB or name CAD or name CAE or name CAI or name CAJ or name CA \ 
K or name CAL or name CAM or name CAN or name CAO or name CAP or name CAQ or nam \ 
e CAR or name CAS or name CAT or name CAU or name CAV or name CAX or name CAY or \ 
 name CAZ or name CBA or name CBB or name CBC or name CBD or name CBE or name CB \ 
F or name CBG or name CBH or name CBI or name OAF or name OAG or name OAH or nam \ 
e OAW)) or resid 306 through 309))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.670
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.770
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
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      :  0.007   0.114  10032  Z= 0.333
  Angle     :  0.902  14.163  13614  Z= 0.356
  Chirality :  0.068   0.480   1524
  Planarity :  0.003   0.032   1642
  Dihedral  : 14.795 104.364   4140
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.00 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.18 (0.25), residues: 1206
  helix:  2.02 (0.35), residues: 234
  sheet:  0.31 (0.28), residues: 352
  loop : -0.72 (0.26), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  89 
 HIS   0.002   0.000   HIS B 145 
 PHE   0.018   0.001   PHE A  62 
 TYR   0.024   0.001   TYR A  94 
 ARG   0.001   0.000   ARG B 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23071 (  385)
  hydrogen bonds       : angle       8.17755 ( 1077)
  SS BOND              : bond        0.00553 (   12)
  SS BOND              : angle       0.50249 (   24)
  covalent geometry    : bond        0.00671 (10018)
  covalent geometry    : angle       0.90266 (13590)
  Misc. bond           : bond        0.00363 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 191
  time to evaluate  : 0.975 
Fit side-chains
REVERT: B  106 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7933 (pttm)
REVERT: B  142 LYS cc_start: 0.8655 (tppt) cc_final: 0.8315 (tptt)
REVERT: D   89 GLN cc_start: 0.8320 (pp30) cc_final: 0.8114 (pp30)
REVERT: H   62 GLN cc_start: 0.7764 (mt0) cc_final: 0.7519 (mt0)
REVERT: L   89 GLN cc_start: 0.8291 (pp30) cc_final: 0.8079 (pp30)
  outliers start: 2
  outliers final: 2
  residues processed: 191
  average time/residue: 0.1988
  time to fit residues: 54.2118
Evaluate side-chains
  153 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain H residue   34 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 90 optimal weight:   40.0000
   chunk 50 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 48 optimal weight:   40.0000
   chunk 94 optimal weight:   20.0000
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 108 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 181 GLN
A 214 ASN
B  59 ASN
B 158 HIS
B 166 ASN
B 181 GLN
B 214 ASN
C  39 GLN
C 207 ASN
C 208 HIS
H  33 ASN
H  39 GLN
H 207 ASN
H 208 HIS
L   1 GLN
L 137 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.197786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.159003 restraints weight = 16869.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.158896 restraints weight = 10631.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.159699 restraints weight = 9524.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10032  Z= 0.124
  Angle     :  0.609   9.065  13614  Z= 0.289
  Chirality :  0.043   0.245   1524
  Planarity :  0.003   0.037   1642
  Dihedral  : 11.118  80.406   2056
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.34 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.13 (0.25), residues: 1206
  helix:  1.68 (0.34), residues: 248
  sheet:  0.44 (0.28), residues: 370
  loop : -0.84 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  89 
 HIS   0.003   0.001   HIS C 172 
 PHE   0.016   0.001   PHE B 146 
 TYR   0.020   0.001   TYR A  94 
 ARG   0.005   0.001   ARG L  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  385)
  hydrogen bonds       : angle       5.88200 ( 1077)
  SS BOND              : bond        0.00405 (   12)
  SS BOND              : angle       0.99385 (   24)
  covalent geometry    : bond        0.00281 (10018)
  covalent geometry    : angle       0.60793 (13590)
  Misc. bond           : bond        0.00325 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.7969 (ttmt) cc_final: 0.6970 (pttp)
REVERT: B  106 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8024 (pttp)
REVERT: C   48 ILE cc_start: 0.8511 (tp) cc_final: 0.8249 (tp)
REVERT: D   89 GLN cc_start: 0.8410 (pp30) cc_final: 0.8089 (pp30)
REVERT: D  168 LYS cc_start: 0.7761 (tttm) cc_final: 0.7140 (tppt)
REVERT: H   48 ILE cc_start: 0.8571 (tp) cc_final: 0.8279 (tp)
REVERT: H   62 GLN cc_start: 0.7952 (mt0) cc_final: 0.7717 (mt0)
REVERT: L   89 GLN cc_start: 0.8413 (pp30) cc_final: 0.8056 (pp30)
  outliers start: 11
  outliers final: 5
  residues processed: 177
  average time/residue: 0.2018
  time to fit residues: 51.6311
Evaluate side-chains
  153 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 148
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 81 optimal weight:    0.0070
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.7204

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 140 ASN
A 181 GLN
A 214 ASN
B 181 GLN
C  39 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.188978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.141637 restraints weight = 16768.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.143883 restraints weight = 9329.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.145304 restraints weight = 5706.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10032  Z= 0.165
  Angle     :  0.607   9.414  13614  Z= 0.293
  Chirality :  0.043   0.214   1524
  Planarity :  0.004   0.037   1642
  Dihedral  : 10.093  59.177   2050
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.26 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.14 (0.25), residues: 1206
  helix:  1.51 (0.33), residues: 254
  sheet:  0.30 (0.26), residues: 418
  loop : -0.72 (0.29), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  89 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.017   0.002   PHE B 146 
 TYR   0.017   0.001   TYR D  31 
 ARG   0.005   0.001   ARG D  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03836 (  385)
  hydrogen bonds       : angle       5.22234 ( 1077)
  SS BOND              : bond        0.00349 (   12)
  SS BOND              : angle       1.00846 (   24)
  covalent geometry    : bond        0.00382 (10018)
  covalent geometry    : angle       0.60634 (13590)
  Misc. bond           : bond        0.00183 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 1.033 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8306 (ttmt) cc_final: 0.6854 (pttp)
REVERT: B   50 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7202 (ttmm)
REVERT: B   93 MET cc_start: 0.8470 (tmm) cc_final: 0.8268 (tmm)
REVERT: B  106 LYS cc_start: 0.8526 (mmmt) cc_final: 0.7876 (pttp)
REVERT: B  118 ILE cc_start: 0.7264 (pt) cc_final: 0.7044 (pt)
REVERT: C   48 ILE cc_start: 0.8588 (tp) cc_final: 0.8308 (tp)
REVERT: H   48 ILE cc_start: 0.8638 (tp) cc_final: 0.8407 (tp)
REVERT: H   62 GLN cc_start: 0.8025 (mt0) cc_final: 0.7824 (mt0)
REVERT: H   64 PHE cc_start: 0.6679 (m-10) cc_final: 0.6250 (m-10)
REVERT: L   89 GLN cc_start: 0.8457 (pp30) cc_final: 0.8215 (pp30)
  outliers start: 18
  outliers final: 12
  residues processed: 172
  average time/residue: 0.1913
  time to fit residues: 48.0885
Evaluate side-chains
  163 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain B residue   59 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 110 optimal weight:   20.0000
   chunk 70 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 105 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 ASN
A 181 GLN
A 214 ASN
B 166 ASN
B 181 GLN
C  33 ASN
H  39 GLN
L  37 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.183502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.133443 restraints weight = 16641.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.136956 restraints weight = 8059.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.139002 restraints weight = 5303.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10032  Z= 0.206
  Angle     :  0.650   9.141  13614  Z= 0.314
  Chirality :  0.045   0.271   1524
  Planarity :  0.004   0.051   1642
  Dihedral  : 10.180  59.183   2050
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.86 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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: -0.08 (0.25), residues: 1206
  helix:  1.29 (0.33), residues: 254
  sheet:  0.21 (0.26), residues: 418
  loop : -0.87 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  89 
 HIS   0.004   0.001   HIS H 208 
 PHE   0.012   0.002   PHE B  45 
 TYR   0.023   0.002   TYR L  31 
 ARG   0.006   0.001   ARG L  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  385)
  hydrogen bonds       : angle       5.13400 ( 1077)
  SS BOND              : bond        0.00357 (   12)
  SS BOND              : angle       1.04149 (   24)
  covalent geometry    : bond        0.00475 (10018)
  covalent geometry    : angle       0.64871 (13590)
  Misc. bond           : bond        0.00263 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 168
  time to evaluate  : 1.153 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8337 (ttmt) cc_final: 0.6857 (pttp)
REVERT: A  119 MET cc_start: 0.7095 (mmt) cc_final: 0.6788 (mmt)
REVERT: B  106 LYS cc_start: 0.8522 (mmmt) cc_final: 0.7854 (pttp)
REVERT: B  109 ARG cc_start: 0.6589 (tmt-80) cc_final: 0.6167 (tpm170)
REVERT: D   89 GLN cc_start: 0.8413 (pp30) cc_final: 0.8196 (pp30)
REVERT: D  168 LYS cc_start: 0.7807 (tttm) cc_final: 0.7201 (tppt)
REVERT: H   64 PHE cc_start: 0.6909 (m-80) cc_final: 0.6703 (m-10)
REVERT: L   89 GLN cc_start: 0.8426 (pp30) cc_final: 0.8191 (pp30)
  outliers start: 25
  outliers final: 17
  residues processed: 186
  average time/residue: 0.1924
  time to fit residues: 52.0136
Evaluate side-chains
  169 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 98 optimal weight:   20.0000
   chunk 103 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 119 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 48 optimal weight:   20.0000
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 ASN
A 214 ASN
B 166 ASN
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.185570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.134627 restraints weight = 16959.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.138168 restraints weight = 8295.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.140362 restraints weight = 5516.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10032  Z= 0.151
  Angle     :  0.609  10.179  13614  Z= 0.290
  Chirality :  0.044   0.231   1524
  Planarity :  0.004   0.032   1642
  Dihedral  :  9.947  59.227   2050
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.79 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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: -0.05 (0.25), residues: 1206
  helix:  1.31 (0.32), residues: 252
  sheet:  0.23 (0.26), residues: 418
  loop : -0.86 (0.29), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  85 
 HIS   0.002   0.001   HIS H 172 
 PHE   0.017   0.001   PHE B 146 
 TYR   0.017   0.001   TYR C 107 
 ARG   0.006   0.000   ARG D  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 (  385)
  hydrogen bonds       : angle       5.02428 ( 1077)
  SS BOND              : bond        0.00328 (   12)
  SS BOND              : angle       0.89219 (   24)
  covalent geometry    : bond        0.00352 (10018)
  covalent geometry    : angle       0.60860 (13590)
  Misc. bond           : bond        0.00318 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 160
  time to evaluate  : 1.036 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8325 (ttmt) cc_final: 0.6834 (pttp)
REVERT: A   72 ILE cc_start: 0.9299 (mm) cc_final: 0.9025 (mm)
REVERT: B  106 LYS cc_start: 0.8524 (mmmt) cc_final: 0.7843 (pttp)
REVERT: B  109 ARG cc_start: 0.6641 (tmt-80) cc_final: 0.6011 (tpm170)
REVERT: C   64 PHE cc_start: 0.7191 (m-10) cc_final: 0.6950 (m-10)
REVERT: D   32 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8020 (tp)
  outliers start: 32
  outliers final: 18
  residues processed: 184
  average time/residue: 0.2182
  time to fit residues: 57.6467
Evaluate side-chains
  169 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 181 GLN
A 214 ASN
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.186674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.136821 restraints weight = 16658.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.140364 restraints weight = 8003.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.142482 restraints weight = 5262.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10032  Z= 0.120
  Angle     :  0.595   9.570  13614  Z= 0.285
  Chirality :  0.043   0.198   1524
  Planarity :  0.003   0.032   1642
  Dihedral  :  9.625  59.835   2050
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 21.10 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.02 (0.25), residues: 1206
  helix:  1.28 (0.32), residues: 252
  sheet:  0.41 (0.27), residues: 402
  loop : -0.85 (0.28), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  89 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.018   0.001   PHE H  64 
 TYR   0.014   0.001   TYR A  94 
 ARG   0.002   0.000   ARG D  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03317 (  385)
  hydrogen bonds       : angle       4.92498 ( 1077)
  SS BOND              : bond        0.00353 (   12)
  SS BOND              : angle       0.81329 (   24)
  covalent geometry    : bond        0.00279 (10018)
  covalent geometry    : angle       0.59468 (13590)
  Misc. bond           : bond        0.00246 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8281 (ttmt) cc_final: 0.6803 (pttp)
REVERT: A   72 ILE cc_start: 0.9297 (mm) cc_final: 0.9004 (mm)
REVERT: A   81 CYS cc_start: 0.8831 (m) cc_final: 0.8597 (t)
REVERT: B  106 LYS cc_start: 0.8500 (mmmt) cc_final: 0.7831 (pttp)
REVERT: B  109 ARG cc_start: 0.6547 (tmt-80) cc_final: 0.6205 (tpm170)
REVERT: B  193 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8542 (mt)
REVERT: L  171 THR cc_start: 0.6911 (OUTLIER) cc_final: 0.6670 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 169
  average time/residue: 0.1973
  time to fit residues: 48.1791
Evaluate side-chains
  165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue  171 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 21 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 116 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 120 ASN
A 214 ASN
D  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.185985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.141000 restraints weight = 17015.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.140653 restraints weight = 9647.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.141457 restraints weight = 6683.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10032  Z= 0.134
  Angle     :  0.586   8.694  13614  Z= 0.283
  Chirality :  0.043   0.197   1524
  Planarity :  0.003   0.032   1642
  Dihedral  :  9.460  59.374   2050
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.71 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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:  0.02 (0.25), residues: 1206
  helix:  1.28 (0.32), residues: 252
  sheet:  0.43 (0.27), residues: 402
  loop : -0.87 (0.28), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  89 
 HIS   0.002   0.001   HIS B 145 
 PHE   0.014   0.001   PHE C  64 
 TYR   0.015   0.001   TYR A  94 
 ARG   0.002   0.000   ARG D  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03271 (  385)
  hydrogen bonds       : angle       4.83118 ( 1077)
  SS BOND              : bond        0.00308 (   12)
  SS BOND              : angle       0.78927 (   24)
  covalent geometry    : bond        0.00318 (10018)
  covalent geometry    : angle       0.58572 (13590)
  Misc. bond           : bond        0.00237 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 1.083 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8329 (ttmt) cc_final: 0.6851 (pttp)
REVERT: A   72 ILE cc_start: 0.9302 (mm) cc_final: 0.9052 (mm)
REVERT: B  106 LYS cc_start: 0.8644 (mmmt) cc_final: 0.7834 (pttp)
REVERT: B  109 ARG cc_start: 0.6811 (tmt-80) cc_final: 0.6274 (tpm170)
REVERT: C   47 TRP cc_start: 0.8959 (OUTLIER) cc_final: 0.8705 (t60)
REVERT: L  171 THR cc_start: 0.6925 (OUTLIER) cc_final: 0.6686 (p)
  outliers start: 32
  outliers final: 23
  residues processed: 175
  average time/residue: 0.1913
  time to fit residues: 48.6908
Evaluate side-chains
  173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue  171 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 113 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 103 optimal weight:    0.0670
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.9722

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
D  37 GLN
D  52 ASN
H  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.187068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.141605 restraints weight = 16967.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.142264 restraints weight = 9364.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.143239 restraints weight = 6393.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10032  Z= 0.120
  Angle     :  0.580   9.489  13614  Z= 0.280
  Chirality :  0.043   0.193   1524
  Planarity :  0.003   0.030   1642
  Dihedral  :  9.128  58.655   2050
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.77 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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: -0.06 (0.25), residues: 1206
  helix:  0.98 (0.32), residues: 260
  sheet:  0.48 (0.27), residues: 402
  loop : -0.92 (0.29), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  89 
 HIS   0.002   0.001   HIS B 145 
 PHE   0.019   0.001   PHE H  64 
 TYR   0.026   0.001   TYR B  94 
 ARG   0.002   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03192 (  385)
  hydrogen bonds       : angle       4.75514 ( 1077)
  SS BOND              : bond        0.00302 (   12)
  SS BOND              : angle       0.69309 (   24)
  covalent geometry    : bond        0.00286 (10018)
  covalent geometry    : angle       0.57966 (13590)
  Misc. bond           : bond        0.00225 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 155
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8371 (ttmt) cc_final: 0.6791 (pttp)
REVERT: B   93 MET cc_start: 0.8721 (tmm) cc_final: 0.8434 (tmm)
REVERT: B  106 LYS cc_start: 0.8645 (mmmt) cc_final: 0.7799 (pttm)
REVERT: B  109 ARG cc_start: 0.6803 (tmt-80) cc_final: 0.6235 (tpm170)
REVERT: C   47 TRP cc_start: 0.8922 (OUTLIER) cc_final: 0.8609 (t60)
REVERT: L  171 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6706 (p)
  outliers start: 28
  outliers final: 21
  residues processed: 177
  average time/residue: 0.2121
  time to fit residues: 54.5800
Evaluate side-chains
  171 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue  171 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   chunk 59 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
D  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.184122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.138529 restraints weight = 16955.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.139199 restraints weight = 9402.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.139852 restraints weight = 6777.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10032  Z= 0.177
  Angle     :  0.621   8.904  13614  Z= 0.302
  Chirality :  0.044   0.205   1524
  Planarity :  0.004   0.031   1642
  Dihedral  :  9.189  58.833   2050
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 22.35 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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: -0.05 (0.25), residues: 1206
  helix:  1.10 (0.32), residues: 248
  sheet:  0.30 (0.26), residues: 424
  loop : -0.80 (0.29), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  89 
 HIS   0.003   0.001   HIS H 208 
 PHE   0.015   0.001   PHE H  64 
 TYR   0.027   0.002   TYR A  94 
 ARG   0.002   0.000   ARG D  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  385)
  hydrogen bonds       : angle       4.83815 ( 1077)
  SS BOND              : bond        0.00283 (   12)
  SS BOND              : angle       0.83803 (   24)
  covalent geometry    : bond        0.00422 (10018)
  covalent geometry    : angle       0.62007 (13590)
  Misc. bond           : bond        0.00244 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8359 (ttmt) cc_final: 0.6817 (pttp)
REVERT: B  106 LYS cc_start: 0.8639 (mmmt) cc_final: 0.7739 (pttm)
REVERT: B  109 ARG cc_start: 0.6782 (tmt-80) cc_final: 0.6276 (tpm170)
REVERT: L  171 THR cc_start: 0.6813 (OUTLIER) cc_final: 0.6556 (p)
  outliers start: 28
  outliers final: 24
  residues processed: 170
  average time/residue: 0.1903
  time to fit residues: 46.9567
Evaluate side-chains
  174 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue  171 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 28 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 117 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 166 ASN
A 214 ASN
D  37 GLN
D 137 ASN
H  39 GLN
L  37 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.185478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.140033 restraints weight = 16892.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.140949 restraints weight = 9163.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.141353 restraints weight = 6779.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10032  Z= 0.138
  Angle     :  0.602   8.460  13614  Z= 0.293
  Chirality :  0.044   0.198   1524
  Planarity :  0.003   0.029   1642
  Dihedral  :  9.024  59.123   2050
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.54 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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: -0.05 (0.25), residues: 1206
  helix:  1.11 (0.32), residues: 248
  sheet:  0.44 (0.27), residues: 404
  loop : -0.90 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  89 
 HIS   0.002   0.001   HIS B 145 
 PHE   0.017   0.001   PHE H  64 
 TYR   0.033   0.001   TYR B  94 
 ARG   0.002   0.000   ARG D  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  385)
  hydrogen bonds       : angle       4.79159 ( 1077)
  SS BOND              : bond        0.00275 (   12)
  SS BOND              : angle       0.75296 (   24)
  covalent geometry    : bond        0.00333 (10018)
  covalent geometry    : angle       0.60166 (13590)
  Misc. bond           : bond        0.00226 (    2)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8386 (ttmt) cc_final: 0.6805 (pttp)
REVERT: B   58 MET cc_start: 0.8593 (mmm) cc_final: 0.8320 (mmt)
REVERT: B   93 MET cc_start: 0.8818 (tmm) cc_final: 0.8529 (tmm)
REVERT: B  106 LYS cc_start: 0.8632 (mmmt) cc_final: 0.7732 (pttm)
REVERT: B  109 ARG cc_start: 0.6791 (tmt-80) cc_final: 0.6246 (tpm170)
REVERT: L  171 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.6619 (p)
  outliers start: 32
  outliers final: 26
  residues processed: 177
  average time/residue: 0.2027
  time to fit residues: 52.1604
Evaluate side-chains
  177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  166 ASN
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue  171 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 90 optimal weight:    0.0870
   chunk 68 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 119 optimal weight:   10.0000
   chunk 89 optimal weight:    7.9990
   chunk 115 optimal weight:    4.9990
   chunk 100 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.4764

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.185056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.139434 restraints weight = 16742.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.140573 restraints weight = 9170.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.141308 restraints weight = 6150.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10032  Z= 0.152
  Angle     :  0.618  10.140  13614  Z= 0.301
  Chirality :  0.044   0.206   1524
  Planarity :  0.003   0.030   1642
  Dihedral  :  8.959  59.541   2050
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.45 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    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: -0.10 (0.25), residues: 1206
  helix:  1.03 (0.32), residues: 248
  sheet:  0.43 (0.27), residues: 404
  loop : -0.92 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  89 
 HIS   0.002   0.001   HIS H 208 
 PHE   0.013   0.001   PHE H  64 
 TYR   0.031   0.001   TYR A  94 
 ARG   0.002   0.000   ARG D  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03352 (  385)
  hydrogen bonds       : angle       4.80223 ( 1077)
  SS BOND              : bond        0.00237 (   12)
  SS BOND              : angle       0.76378 (   24)
  covalent geometry    : bond        0.00362 (10018)
  covalent geometry    : angle       0.61741 (13590)
  Misc. bond           : bond        0.00261 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3578.50 seconds
wall clock time: 64 minutes 1.54 seconds (3841.54 seconds total)