Starting phenix.real_space_refine
on Tue Jul 29 22:22:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8go9_34174/07_2025/8go9_34174.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8go9_34174/07_2025/8go9_34174.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8go9_34174/07_2025/8go9_34174.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8go9_34174/07_2025/8go9_34174.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8go9_34174/07_2025/8go9_34174.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8go9_34174/07_2025/8go9_34174.cif"
  }
  resolution = 3.35
  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=   0.000 sd=   0.039
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      12      5.49       5
     S      26      5.16       5
     C    7376      2.51       5
     N    1988      2.21       5
     O    2260      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11662
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2888
          Classifications: {'peptide': 363}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 335}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1479
          Classifications: {'peptide': 202}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1359
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 26
    Chain: "D"
      Number of atoms: 1479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1479
          Classifications: {'peptide': 202}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "E"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1359
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 26
    Chain: "F"
      Number of atoms: 2888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2888
          Classifications: {'peptide': 363}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 335}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 105
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 105
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 6.91, per 1000 atoms: 0.59
  Number of scatterers: 11662
  At special positions: 0
  Unit cell: (186.038, 87.6375, 121.463, 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      26     16.00
     P      12     15.00
     O    2260      8.00
     N    1988      7.00
     C    7376      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 150 " - pdb=" SG  CYS B 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 150 " - pdb=" SG  CYS D 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.57
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2868

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 30 sheets defined
      7.0% alpha, 42.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.920A  pdb=" N   LEU A  49 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 110
    Processing helix  chain 'A' and resid 393 through 408
    Processing helix  chain 'B' and resid 90 through 94
      removed outlier: 4.022A  pdb=" N   THR B  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 128
    Processing helix  chain 'C' and resid 184 through 190
      removed outlier: 4.003A  pdb=" N   HIS C 190 " --> pdb=" O   ASP C 186 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 94
      removed outlier: 4.022A  pdb=" N   THR D  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 128
    Processing helix  chain 'E' and resid 184 through 190
      removed outlier: 4.002A  pdb=" N   HIS E 190 " --> pdb=" O   ASP E 186 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 50
      removed outlier: 3.920A  pdb=" N   LEU F  49 " --> pdb=" O   ASP F  45 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 99 through 110
    Processing helix  chain 'F' and resid 393 through 408
    Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118
    Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30
      removed outlier: 3.605A  pdb=" N   ILE A 169 " --> pdb=" O   PHE A 145 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   LYS A 171 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 10.267A  pdb=" N   VAL A 143 " --> pdb=" O   LYS A 171 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG A  63 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   VAL A  54 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   GLN A  86 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL A  56 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ASN A  84 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   LEU A  58 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE A  82 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL A  60 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS A  78 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189
      removed outlier: 3.530A  pdb=" N   THR A 187 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS A 271 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209
      removed outlier: 3.845A  pdb=" N   VAL A 336 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TYR A 322 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   LEU A 344 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
      removed outlier: 9.520A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LYS A 231 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 232 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA A 255 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   GLN A 238 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ALA A 240 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   LYS A 251 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ILE A 242 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   GLN A 249 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 10
      removed outlier: 3.668A  pdb=" N   VAL B   8 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER B  24 " --> pdb=" O   SER B  10 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 15
      removed outlier: 3.729A  pdb=" N   ALA B  52 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARG B  41 " --> pdb=" O   TRP B  50 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   TRP B  50 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 13 through 15
    Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 134
      removed outlier: 3.735A  pdb=" N   GLY B 149 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   TYR B 186 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 134
      removed outlier: 3.735A  pdb=" N   GLY B 149 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   TYR B 186 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 163
    Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 8
    Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 14
      removed outlier: 3.581A  pdb=" N   GLU C 106 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55
      removed outlier: 6.485A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   TYR C  50 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 117 through 119
      removed outlier: 6.331A  pdb=" N   TYR C 174 " --> pdb=" O   ASN C 139 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 6 through 10
      removed outlier: 3.668A  pdb=" N   VAL D   8 " --> pdb=" O   ALA D  26 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER D  24 " --> pdb=" O   SER D  10 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 13 through 15
      removed outlier: 3.730A  pdb=" N   ALA D  52 " --> pdb=" O   TRP D  39 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARG D  41 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   TRP D  50 " --> pdb=" O   ARG D  41 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15
    Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 134
      removed outlier: 3.735A  pdb=" N   GLY D 149 " --> pdb=" O   LEU D 134 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   TYR D 186 " --> pdb=" O   ASP D 154 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 130 through 134
      removed outlier: 3.735A  pdb=" N   GLY D 149 " --> pdb=" O   LEU D 134 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   TYR D 186 " --> pdb=" O   ASP D 154 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 161 through 163
    Processing sheet with id=AC4, first strand: chain 'E' and resid 5 through 8
    Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 14
      removed outlier: 3.581A  pdb=" N   GLU E 106 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 54 through 55
      removed outlier: 6.484A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   TYR E  50 " --> pdb=" O   VAL E  34 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 117 through 119
      removed outlier: 6.331A  pdb=" N   TYR E 174 " --> pdb=" O   ASN E 139 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 113 through 118
    Processing sheet with id=AC9, first strand: chain 'F' and resid 27 through 30
      removed outlier: 3.605A  pdb=" N   ILE F 169 " --> pdb=" O   PHE F 145 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE F 145 " --> pdb=" O   ILE F 169 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   LYS F 171 " --> pdb=" O   VAL F 143 " (cutoff:3.500A)
      removed outlier: 10.268A  pdb=" N   VAL F 143 " --> pdb=" O   LYS F 171 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG F  63 " --> pdb=" O   GLY F 142 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   VAL F  54 " --> pdb=" O   GLN F  86 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   GLN F  86 " --> pdb=" O   VAL F  54 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL F  56 " --> pdb=" O   ASN F  84 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ASN F  84 " --> pdb=" O   VAL F  56 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   LEU F  58 " --> pdb=" O   ILE F  82 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ILE F  82 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL F  60 " --> pdb=" O   LEU F  80 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS F  78 " --> pdb=" O   PHE F  62 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'F' and resid 128 through 130
    Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 189
      removed outlier: 3.529A  pdb=" N   THR F 187 " --> pdb=" O   LEU F 200 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS F 271 " --> pdb=" O   VAL F 219 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 208 through 209
      removed outlier: 3.844A  pdb=" N   VAL F 336 " --> pdb=" O   LEU F 328 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TYR F 322 " --> pdb=" O   PHE F 342 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   LEU F 344 " --> pdb=" O   VAL F 320 " (cutoff:3.500A)
      removed outlier: 9.521A  pdb=" N   VAL F 320 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LYS F 231 " --> pdb=" O   VAL F 329 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE F 232 " --> pdb=" O   GLN F 259 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA F 255 " --> pdb=" O   VAL F 236 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   GLN F 238 " --> pdb=" O   PRO F 253 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ALA F 240 " --> pdb=" O   LYS F 251 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   LYS F 251 " --> pdb=" O   ALA F 240 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   ILE F 242 " --> pdb=" O   GLN F 249 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   GLN F 249 " --> pdb=" O   ILE F 242 " (cutoff:3.500A)

    480 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.88

  Time building geometry restraints manager: 3.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3752
        1.34 -     1.46: 2723
        1.46 -     1.58: 5375
        1.58 -     1.69: 46
        1.69 -     1.81: 34
  Bond restraints: 11930
  Sorted by residual:
  bond pdb=" OG1 TPO G 354 "
       pdb=" P   TPO G 354 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" OG1 TPO H 354 "
       pdb=" P   TPO H 354 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" O3P TPO G 354 "
       pdb=" P   TPO G 354 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" O2P TPO G 354 "
       pdb=" P   TPO G 354 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" O2P TPO H 354 "
       pdb=" P   TPO H 354 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.66e+01
  ... (remaining 11925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 16096
        2.42 -     4.84: 134
        4.84 -     7.25: 14
        7.25 -     9.67: 4
        9.67 -    12.09: 2
  Bond angle restraints: 16250
  Sorted by residual:
  angle pdb=" CB  TPO H 354 "
        pdb=" OG1 TPO H 354 "
        pdb=" P   TPO H 354 "
      ideal   model   delta    sigma   weight residual
     119.31  107.22   12.09 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" CB  TPO G 354 "
        pdb=" OG1 TPO G 354 "
        pdb=" P   TPO G 354 "
      ideal   model   delta    sigma   weight residual
     119.31  107.27   12.04 3.00e+00 1.11e-01 1.61e+01
  angle pdb=" OG1 TPO G 354 "
        pdb=" P   TPO G 354 "
        pdb=" O1P TPO G 354 "
      ideal   model   delta    sigma   weight residual
     100.43  109.46   -9.03 3.00e+00 1.11e-01 9.06e+00
  angle pdb=" OG1 TPO H 354 "
        pdb=" P   TPO H 354 "
        pdb=" O1P TPO H 354 "
      ideal   model   delta    sigma   weight residual
     100.43  109.43   -9.00 3.00e+00 1.11e-01 8.99e+00
  angle pdb=" C   LEU F  49 "
        pdb=" N   LYS F  50 "
        pdb=" CA  LYS F  50 "
      ideal   model   delta    sigma   weight residual
     121.54  127.26   -5.72 1.91e+00 2.74e-01 8.97e+00
  ... (remaining 16245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6599
       17.99 -    35.99: 463
       35.99 -    53.98: 86
       53.98 -    71.97: 16
       71.97 -    89.96: 8
  Dihedral angle restraints: 7172
    sinusoidal: 2730
      harmonic: 4442
  Sorted by residual:
  dihedral pdb=" CA  ARG A  96 "
           pdb=" C   ARG A  96 "
           pdb=" N   PRO A  97 "
           pdb=" CA  PRO A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.99   32.01     0      5.00e+00 4.00e-02 4.10e+01
  dihedral pdb=" CA  ARG F  96 "
           pdb=" C   ARG F  96 "
           pdb=" N   PRO F  97 "
           pdb=" CA  PRO F  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.06   31.94     0      5.00e+00 4.00e-02 4.08e+01
  dihedral pdb=" CA  PRO F  95 "
           pdb=" C   PRO F  95 "
           pdb=" N   ARG F  96 "
           pdb=" CA  ARG F  96 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -30.10   30.10     0      5.00e+00 4.00e-02 3.62e+01
  ... (remaining 7169 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1290
       0.035 -    0.071: 337
       0.071 -    0.106: 157
       0.106 -    0.141: 56
       0.141 -    0.177: 4
  Chirality restraints: 1844
  Sorted by residual:
  chirality pdb=" CA  LYS A 295 "
            pdb=" N   LYS A 295 "
            pdb=" C   LYS A 295 "
            pdb=" CB  LYS A 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CA  LYS A 108 "
            pdb=" N   LYS A 108 "
            pdb=" C   LYS A 108 "
            pdb=" CB  LYS A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.15 2.00e-01 2.50e+01 5.98e-01
  chirality pdb=" CA  LYS F 108 "
            pdb=" N   LYS F 108 "
            pdb=" C   LYS F 108 "
            pdb=" CB  LYS F 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 1841 not shown)

  Planarity restraints: 2078
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  96 "    0.075 5.00e-02 4.00e+02   1.14e-01 2.10e+01
        pdb=" N   PRO A  97 "   -0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO A  97 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A  97 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F  96 "   -0.075 5.00e-02 4.00e+02   1.14e-01 2.09e+01
        pdb=" N   PRO F  97 "    0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO F  97 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO F  97 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  91 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO A  92 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A  92 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  92 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 2075 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2837
        2.80 -     3.33: 9646
        3.33 -     3.85: 17971
        3.85 -     4.38: 20008
        4.38 -     4.90: 36855
  Nonbonded interactions: 87317
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C   7 "
            pdb=" OG1 THR C 103 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OE1 GLN E   7 "
            pdb=" OG1 THR E 103 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" NZ  LYS F  11 "
            pdb=" OE2 GLU H 349 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" O   PHE E 140 "
            pdb=" OG1 THR E 173 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   PHE C 140 "
            pdb=" OG1 THR C 173 "
     model   vdw
     2.282 3.040
  ... (remaining 87312 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

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=0.65 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.080
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.080
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
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      :  0.003   0.108  11936  Z= 0.152
  Angle     :  0.554  12.092  16262  Z= 0.275
  Chirality :  0.042   0.177   1844
  Planarity :  0.006   0.114   2078
  Dihedral  : 13.071  89.963   4286
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  0.24 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 2.13 %
    Twisted General : 0.14 %

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:  0.51 (0.23), residues: 1472
  helix:  2.08 (0.60), residues: 80
  sheet:  1.27 (0.22), residues: 656
  loop : -0.77 (0.23), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  50 
 HIS   0.002   0.000   HIS F 346 
 PHE   0.008   0.001   PHE F 278 
 TYR   0.006   0.001   TYR A 250 
 ARG   0.007   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22647 (  434)
  hydrogen bonds       : angle       9.36260 ( 1242)
  SS BOND              : bond        0.00197 (    6)
  SS BOND              : angle       0.23271 (   12)
  covalent geometry    : bond        0.00307 (11930)
  covalent geometry    : angle       0.55415 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 1.236 
Fit side-chains
REVERT: A  108 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7923 (tttm)
REVERT: B   77 THR cc_start: 0.8264 (p) cc_final: 0.8018 (p)
REVERT: B  185 LEU cc_start: 0.7506 (mm) cc_final: 0.7219 (mm)
REVERT: D   22 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.7120 (tpt-90)
REVERT: D  132 PHE cc_start: 0.6250 (m-10) cc_final: 0.5801 (m-80)
REVERT: D  151 LEU cc_start: 0.7352 (tt) cc_final: 0.7145 (tt)
REVERT: F  108 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7960 (ttpt)
  outliers start: 4
  outliers final: 1
  residues processed: 128
  average time/residue: 0.2625
  time to fit residues: 47.0676
Evaluate side-chains
  107 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LYS
Chi-restraints excluded: chain F residue  108 LYS
Chi-restraints excluded: chain F residue  295 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0570
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    0.1980
   chunk 87 optimal weight:    4.9990
   chunk 136 optimal weight:    0.8980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
B  85 GLN
B  87 ASN
C   7 GLN
D  87 ASN
E   7 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.179372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.123871 restraints weight = 13935.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.60
r_work: 0.3198 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11936  Z= 0.126
  Angle     :  0.531   7.596  16262  Z= 0.272
  Chirality :  0.044   0.148   1844
  Planarity :  0.005   0.091   2078
  Dihedral  :  5.799  62.750   1688
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  5.50 %
    Favored  : 93.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.28 %
    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:  0.45 (0.23), residues: 1472
  helix:  2.06 (0.59), residues: 84
  sheet:  1.11 (0.21), residues: 672
  loop : -0.73 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  50 
 HIS   0.002   0.001   HIS F 199 
 PHE   0.022   0.001   PHE F  81 
 TYR   0.013   0.001   TYR E  92 
 ARG   0.006   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 (  434)
  hydrogen bonds       : angle       6.00916 ( 1242)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       0.36726 (   12)
  covalent geometry    : bond        0.00295 (11930)
  covalent geometry    : angle       0.53139 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.211 
Fit side-chains
REVERT: A  308 LYS cc_start: 0.7423 (ptpp) cc_final: 0.7076 (mtpp)
REVERT: C   25 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7432 (mmm160)
REVERT: C   28 GLN cc_start: 0.8110 (mp10) cc_final: 0.7853 (mm-40)
REVERT: D  185 LEU cc_start: 0.7158 (mm) cc_final: 0.6310 (mm)
REVERT: E  106 GLU cc_start: 0.8304 (pm20) cc_final: 0.8093 (pm20)
REVERT: F  153 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8281 (mttp)
REVERT: F  230 LYS cc_start: 0.7119 (mtmm) cc_final: 0.6740 (mtpp)
REVERT: F  308 LYS cc_start: 0.7427 (ptpp) cc_final: 0.7058 (mtpp)
  outliers start: 15
  outliers final: 13
  residues processed: 124
  average time/residue: 0.2870
  time to fit residues: 48.8378
Evaluate side-chains
  111 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  296 HIS
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain F residue  295 LYS
Chi-restraints excluded: chain F residue  296 HIS
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0670
   chunk 2 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 125 optimal weight:    0.3980
   chunk 8 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9990
   chunk 128 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.5920

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.178129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.120881 restraints weight = 14183.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.69
r_work: 0.3112 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11936  Z= 0.122
  Angle     :  0.513   6.904  16262  Z= 0.260
  Chirality :  0.044   0.148   1844
  Planarity :  0.005   0.064   2078
  Dihedral  :  5.696  62.779   1680
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.53 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.46 (0.23), residues: 1472
  helix:  2.24 (0.59), residues: 82
  sheet:  1.03 (0.20), residues: 690
  loop : -0.69 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  50 
 HIS   0.002   0.001   HIS F 199 
 PHE   0.023   0.001   PHE F 269 
 TYR   0.014   0.001   TYR F 250 
 ARG   0.004   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02961 (  434)
  hydrogen bonds       : angle       5.39047 ( 1242)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       0.21143 (   12)
  covalent geometry    : bond        0.00289 (11930)
  covalent geometry    : angle       0.51329 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 1.361 
Fit side-chains
REVERT: A  308 LYS cc_start: 0.7285 (ptpp) cc_final: 0.7068 (mtpp)
REVERT: C   25 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7255 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8126 (mp10) cc_final: 0.7848 (mm-40)
REVERT: D   22 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7665 (tpt-90)
REVERT: D  185 LEU cc_start: 0.7048 (mm) cc_final: 0.6207 (mm)
REVERT: E  106 GLU cc_start: 0.8298 (pm20) cc_final: 0.7684 (pm20)
REVERT: F  230 LYS cc_start: 0.7081 (mtmm) cc_final: 0.6679 (mtpp)
REVERT: F  308 LYS cc_start: 0.7330 (ptpp) cc_final: 0.7086 (mtpp)
  outliers start: 15
  outliers final: 13
  residues processed: 118
  average time/residue: 0.2894
  time to fit residues: 47.3067
Evaluate side-chains
  111 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 1.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  231 LYS
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 139 optimal weight:    0.0870
   chunk 138 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 133 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.178753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.122871 restraints weight = 14044.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.73
r_work: 0.3090 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11936  Z= 0.130
  Angle     :  0.514   6.872  16262  Z= 0.262
  Chirality :  0.044   0.151   1844
  Planarity :  0.005   0.088   2078
  Dihedral  :  5.627  64.175   1676
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  9.81 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.42 (0.23), residues: 1472
  helix:  2.28 (0.60), residues: 84
  sheet:  0.97 (0.20), residues: 692
  loop : -0.68 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  50 
 HIS   0.002   0.001   HIS F 199 
 PHE   0.013   0.001   PHE A  81 
 TYR   0.015   0.001   TYR E  92 
 ARG   0.003   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02764 (  434)
  hydrogen bonds       : angle       5.08009 ( 1242)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       0.20545 (   12)
  covalent geometry    : bond        0.00312 (11930)
  covalent geometry    : angle       0.51449 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 1.673 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.6915 (t80) cc_final: 0.6703 (t80)
REVERT: A  308 LYS cc_start: 0.7330 (ptpp) cc_final: 0.7111 (mtpp)
REVERT: C   25 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7271 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8188 (mp10) cc_final: 0.7885 (mm-40)
REVERT: C  106 GLU cc_start: 0.8264 (pm20) cc_final: 0.7774 (pm20)
REVERT: D   22 ARG cc_start: 0.7930 (tpt-90) cc_final: 0.7619 (tpt-90)
REVERT: E   43 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8248 (mmtt)
REVERT: E  106 GLU cc_start: 0.8433 (pm20) cc_final: 0.8109 (pm20)
REVERT: F  230 LYS cc_start: 0.7040 (mtmm) cc_final: 0.6660 (mtpp)
REVERT: F  308 LYS cc_start: 0.7451 (ptpp) cc_final: 0.6988 (mtpp)
  outliers start: 24
  outliers final: 19
  residues processed: 115
  average time/residue: 0.3737
  time to fit residues: 60.2972
Evaluate side-chains
  112 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 2.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 26 optimal weight:    0.0670
   chunk 1 optimal weight:    1.9990
   chunk 125 optimal weight:    2.9990
   chunk 143 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0670
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.178658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.121052 restraints weight = 14035.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.69
r_work: 0.3095 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11936  Z= 0.131
  Angle     :  0.518   6.438  16262  Z= 0.265
  Chirality :  0.044   0.152   1844
  Planarity :  0.005   0.074   2078
  Dihedral  :  5.628  65.242   1676
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.13 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.39 (0.23), residues: 1472
  helix:  2.36 (0.60), residues: 84
  sheet:  0.90 (0.20), residues: 692
  loop : -0.67 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  50 
 HIS   0.002   0.001   HIS F 346 
 PHE   0.012   0.001   PHE A  81 
 TYR   0.013   0.001   TYR F 250 
 ARG   0.002   0.000   ARG F 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02687 (  434)
  hydrogen bonds       : angle       4.87508 ( 1242)
  SS BOND              : bond        0.00386 (    6)
  SS BOND              : angle       0.22226 (   12)
  covalent geometry    : bond        0.00314 (11930)
  covalent geometry    : angle       0.51806 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 1.398 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.6729 (mtmm) cc_final: 0.6437 (mtpp)
REVERT: A  308 LYS cc_start: 0.7503 (ptpp) cc_final: 0.6878 (mtpp)
REVERT: B   85 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8086 (tp40)
REVERT: B  185 LEU cc_start: 0.6601 (mm) cc_final: 0.6328 (mm)
REVERT: C   25 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7267 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8218 (mp10) cc_final: 0.7867 (mm-40)
REVERT: C  106 GLU cc_start: 0.8228 (pm20) cc_final: 0.7623 (pm20)
REVERT: D   22 ARG cc_start: 0.7864 (tpt-90) cc_final: 0.7558 (tpt-90)
REVERT: F  230 LYS cc_start: 0.6973 (mtmm) cc_final: 0.6612 (mtpp)
REVERT: F  308 LYS cc_start: 0.7475 (ptpp) cc_final: 0.6926 (mtpp)
  outliers start: 28
  outliers final: 24
  residues processed: 122
  average time/residue: 0.2834
  time to fit residues: 48.2675
Evaluate side-chains
  118 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 7 optimal weight:    0.1980
   chunk 72 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 117 optimal weight:    0.5980
   chunk 134 optimal weight:    3.9990
   chunk 130 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 146 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
B  87 ASN
D  87 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.176328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.120580 restraints weight = 14239.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.80
r_work: 0.3230 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11936  Z= 0.138
  Angle     :  0.529   6.359  16262  Z= 0.268
  Chirality :  0.044   0.153   1844
  Planarity :  0.005   0.095   2078
  Dihedral  :  5.654  66.341   1676
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.45 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.36 (0.23), residues: 1472
  helix:  2.51 (0.60), residues: 82
  sheet:  0.86 (0.20), residues: 692
  loop : -0.67 (0.24), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  50 
 HIS   0.002   0.001   HIS A 346 
 PHE   0.011   0.001   PHE A  81 
 TYR   0.015   0.001   TYR C  92 
 ARG   0.007   0.000   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02645 (  434)
  hydrogen bonds       : angle       4.85532 ( 1242)
  SS BOND              : bond        0.00393 (    6)
  SS BOND              : angle       0.25063 (   12)
  covalent geometry    : bond        0.00332 (11930)
  covalent geometry    : angle       0.52922 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 1.351 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.6820 (mtmm) cc_final: 0.6519 (mtpp)
REVERT: A  308 LYS cc_start: 0.7513 (ptpp) cc_final: 0.6976 (mtpp)
REVERT: B   85 GLN cc_start: 0.8369 (tp-100) cc_final: 0.7970 (tp40)
REVERT: B  185 LEU cc_start: 0.6749 (mm) cc_final: 0.6522 (mm)
REVERT: C   25 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7572 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8359 (mp10) cc_final: 0.8028 (mm-40)
REVERT: C  106 GLU cc_start: 0.8601 (pm20) cc_final: 0.8401 (pm20)
REVERT: D   22 ARG cc_start: 0.7773 (tpt-90) cc_final: 0.7510 (tpt-90)
REVERT: E  106 GLU cc_start: 0.8356 (pm20) cc_final: 0.7962 (pm20)
REVERT: F  230 LYS cc_start: 0.7083 (mtmm) cc_final: 0.6727 (mtpp)
REVERT: F  308 LYS cc_start: 0.7520 (ptpp) cc_final: 0.6884 (mtpp)
  outliers start: 30
  outliers final: 26
  residues processed: 115
  average time/residue: 0.2890
  time to fit residues: 45.9186
Evaluate side-chains
  119 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 2.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0980
   chunk 107 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
B  87 ASN
D  87 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.176673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.122659 restraints weight = 14326.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.68
r_work: 0.3085 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11936  Z= 0.130
  Angle     :  0.521   6.092  16262  Z= 0.265
  Chirality :  0.044   0.151   1844
  Planarity :  0.005   0.098   2078
  Dihedral  :  5.658  66.980   1676
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.56 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.37 (0.23), residues: 1472
  helix:  2.59 (0.61), residues: 82
  sheet:  0.86 (0.20), residues: 692
  loop : -0.67 (0.24), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  50 
 HIS   0.002   0.000   HIS F 346 
 PHE   0.011   0.001   PHE F  81 
 TYR   0.014   0.001   TYR A 250 
 ARG   0.006   0.000   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02547 (  434)
  hydrogen bonds       : angle       4.75516 ( 1242)
  SS BOND              : bond        0.00376 (    6)
  SS BOND              : angle       0.23906 (   12)
  covalent geometry    : bond        0.00313 (11930)
  covalent geometry    : angle       0.52090 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 1.370 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.6720 (mtmm) cc_final: 0.6440 (mtpp)
REVERT: A  308 LYS cc_start: 0.7530 (ptpp) cc_final: 0.6980 (mtpp)
REVERT: B   85 GLN cc_start: 0.8452 (tp-100) cc_final: 0.7956 (tp40)
REVERT: C   25 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7265 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8326 (mp10) cc_final: 0.7964 (mm-40)
REVERT: C  106 GLU cc_start: 0.8591 (pm20) cc_final: 0.8354 (pm20)
REVERT: D   22 ARG cc_start: 0.7856 (tpt-90) cc_final: 0.7503 (tpt-90)
REVERT: E   25 ARG cc_start: 0.7813 (ttm110) cc_final: 0.7564 (ttm110)
REVERT: E  106 GLU cc_start: 0.8224 (pm20) cc_final: 0.7950 (pm20)
REVERT: E  109 ARG cc_start: 0.7388 (ptm160) cc_final: 0.7160 (ptm160)
REVERT: F  230 LYS cc_start: 0.6997 (mtmm) cc_final: 0.6646 (mtpp)
REVERT: F  308 LYS cc_start: 0.7536 (ptpp) cc_final: 0.6942 (mtpp)
  outliers start: 26
  outliers final: 25
  residues processed: 113
  average time/residue: 0.3549
  time to fit residues: 55.9459
Evaluate side-chains
  111 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 131 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9980
   chunk 126 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 82 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN
E  28 GLN
F 190 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.176151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.142377 restraints weight = 14285.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.65
r_work: 0.3339 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11936  Z= 0.140
  Angle     :  0.526   6.078  16262  Z= 0.268
  Chirality :  0.044   0.155   1844
  Planarity :  0.005   0.095   2078
  Dihedral  :  5.686  67.663   1676
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.80 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.34 (0.23), residues: 1472
  helix:  2.44 (0.61), residues: 84
  sheet:  0.82 (0.20), residues: 696
  loop : -0.67 (0.25), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  50 
 HIS   0.002   0.001   HIS F 346 
 PHE   0.011   0.001   PHE B 105 
 TYR   0.016   0.001   TYR E  92 
 ARG   0.005   0.000   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02591 (  434)
  hydrogen bonds       : angle       4.79235 ( 1242)
  SS BOND              : bond        0.00393 (    6)
  SS BOND              : angle       0.26371 (   12)
  covalent geometry    : bond        0.00337 (11930)
  covalent geometry    : angle       0.52642 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 86
  time to evaluate  : 1.510 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.6883 (mtmm) cc_final: 0.6590 (mtpp)
REVERT: A  308 LYS cc_start: 0.7552 (ptpp) cc_final: 0.7078 (mtpp)
REVERT: B   85 GLN cc_start: 0.8273 (tp-100) cc_final: 0.8042 (tp40)
REVERT: C   25 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7614 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8388 (mp10) cc_final: 0.8099 (mm-40)
REVERT: D   22 ARG cc_start: 0.7558 (tpt-90) cc_final: 0.7349 (tpt-90)
REVERT: E  106 GLU cc_start: 0.8226 (pm20) cc_final: 0.8001 (pm20)
REVERT: F  230 LYS cc_start: 0.7095 (mtmm) cc_final: 0.6751 (mtpp)
REVERT: F  308 LYS cc_start: 0.7566 (ptpp) cc_final: 0.7048 (mtpp)
  outliers start: 30
  outliers final: 30
  residues processed: 107
  average time/residue: 0.3096
  time to fit residues: 45.3059
Evaluate side-chains
  113 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   28 GLN
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0030
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 134 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    1.1996

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN
E  28 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.174684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140022 restraints weight = 14316.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.68
r_work: 0.3298 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11936  Z= 0.199
  Angle     :  0.570   6.123  16262  Z= 0.293
  Chirality :  0.045   0.167   1844
  Planarity :  0.005   0.083   2078
  Dihedral  :  5.872  68.858   1676
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.20 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.26 (0.23), residues: 1472
  helix:  2.40 (0.60), residues: 84
  sheet:  0.90 (0.20), residues: 676
  loop : -0.84 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  50 
 HIS   0.004   0.001   HIS A 211 
 PHE   0.013   0.002   PHE B 105 
 TYR   0.021   0.002   TYR E  92 
 ARG   0.005   0.000   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02915 (  434)
  hydrogen bonds       : angle       5.00983 ( 1242)
  SS BOND              : bond        0.00468 (    6)
  SS BOND              : angle       0.41317 (   12)
  covalent geometry    : bond        0.00482 (11930)
  covalent geometry    : angle       0.57041 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 1.268 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.6926 (mtmm) cc_final: 0.6595 (mtpp)
REVERT: A  308 LYS cc_start: 0.7705 (ptpp) cc_final: 0.7134 (mtpp)
REVERT: B   68 LYS cc_start: 0.8145 (tptt) cc_final: 0.7933 (tptp)
REVERT: C   28 GLN cc_start: 0.8391 (mp10) cc_final: 0.8094 (mm-40)
REVERT: D   22 ARG cc_start: 0.7523 (tpt-90) cc_final: 0.7297 (tpt-90)
REVERT: D   68 LYS cc_start: 0.8131 (tptt) cc_final: 0.7915 (tptp)
REVERT: E   25 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7503 (ttm110)
REVERT: F  230 LYS cc_start: 0.7112 (mtmm) cc_final: 0.6475 (mtpp)
REVERT: F  308 LYS cc_start: 0.7663 (ptpp) cc_final: 0.7082 (mtpp)
  outliers start: 30
  outliers final: 28
  residues processed: 112
  average time/residue: 0.3958
  time to fit residues: 61.8445
Evaluate side-chains
  117 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   28 GLN
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 145 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9990
   chunk 126 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 140 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN
E  28 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.177594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.145162 restraints weight = 14148.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 1.57
r_work: 0.3348 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11936  Z= 0.152
  Angle     :  0.542   6.857  16262  Z= 0.278
  Chirality :  0.044   0.154   1844
  Planarity :  0.005   0.084   2078
  Dihedral  :  5.832  68.146   1676
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.60 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.26 (0.23), residues: 1472
  helix:  2.43 (0.60), residues: 84
  sheet:  0.90 (0.20), residues: 676
  loop : -0.84 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  50 
 HIS   0.002   0.001   HIS A 346 
 PHE   0.010   0.001   PHE F  81 
 TYR   0.016   0.001   TYR C  92 
 ARG   0.014   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02679 (  434)
  hydrogen bonds       : angle       4.89914 ( 1242)
  SS BOND              : bond        0.00369 (    6)
  SS BOND              : angle       0.26295 (   12)
  covalent geometry    : bond        0.00369 (11930)
  covalent geometry    : angle       0.54225 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 2.550 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7659 (mtp85)
REVERT: A  230 LYS cc_start: 0.6936 (mtmm) cc_final: 0.6610 (mtpp)
REVERT: A  308 LYS cc_start: 0.7694 (ptpp) cc_final: 0.7152 (mtpp)
REVERT: B   68 LYS cc_start: 0.8072 (tptt) cc_final: 0.7857 (tptp)
REVERT: C   25 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7796 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8404 (mp10) cc_final: 0.8129 (mm-40)
REVERT: D   22 ARG cc_start: 0.7465 (tpt-90) cc_final: 0.7264 (tpt-90)
REVERT: D   68 LYS cc_start: 0.8067 (tptt) cc_final: 0.7850 (tptp)
REVERT: E   25 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7442 (ttm110)
REVERT: F  308 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7116 (mtpp)
  outliers start: 29
  outliers final: 29
  residues processed: 106
  average time/residue: 0.3960
  time to fit residues: 56.5846
Evaluate side-chains
  114 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 2.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   28 GLN
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 81 optimal weight:    0.0970
   chunk 137 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0020
   chunk 124 optimal weight:    0.5980
   chunk 99 optimal weight:    0.6980
   chunk 122 optimal weight:    0.0870
   chunk 15 optimal weight:    0.4980
   chunk 65 optimal weight:    0.0670
   overall best weight:    0.1502

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN
E  28 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.178721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.122361 restraints weight = 14112.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.61
r_work: 0.3288 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11936  Z= 0.086
  Angle     :  0.498   6.670  16262  Z= 0.251
  Chirality :  0.043   0.150   1844
  Planarity :  0.005   0.081   2078
  Dihedral  :  5.617  66.327   1676
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.64 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.48 (0.23), residues: 1472
  helix:  2.47 (0.60), residues: 84
  sheet:  1.07 (0.20), residues: 676
  loop : -0.71 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  36 
 HIS   0.002   0.000   HIS F 211 
 PHE   0.011   0.001   PHE A  81 
 TYR   0.008   0.001   TYR E  50 
 ARG   0.013   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02183 (  434)
  hydrogen bonds       : angle       4.51644 ( 1242)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       0.17822 (   12)
  covalent geometry    : bond        0.00205 (11930)
  covalent geometry    : angle       0.49806 (16250)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7940.73 seconds
wall clock time: 146 minutes 32.09 seconds (8792.09 seconds total)