Starting phenix.real_space_refine
on Sat Aug 23 11:26:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8go9_34174/08_2025/8go9_34174.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8go9_34174/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8go9_34174/08_2025/8go9_34174.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8go9_34174/08_2025/8go9_34174.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8go9_34174/08_2025/8go9_34174.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8go9_34174/08_2025/8go9_34174.map"
  }
  resolution = 3.35
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'GLU:plan': 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, 'ASP:plan': 3, 'HIS:plan': 1}
          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: {'ASN:plan1': 1, 'GLU:plan': 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, 'ASP:plan': 3, 'HIS:plan': 1}
          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: 2.47, per 1000 atoms: 0.21
  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: 0.89
  Conformation dependent library (CDL) restraints added in 516.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.45
  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: 1.91

  Time building geometry restraints manager: 1.17 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}

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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.790
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.450
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.000   ARG E  25 
 TYR   0.006   0.001   TYR A 250 
 PHE   0.008   0.001   PHE F 278 
 TRP   0.003   0.001   TRP B  50 
 HIS   0.002   0.000   HIS F 346 

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

*********************** 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  : 0.430 
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: 0.1178
  time to fit residues: 21.2263
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  : 0.349 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.3980
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    0.6980
   overall best weight:    0.7982

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.177648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.141676 restraints weight = 13985.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 1.73
r_work: 0.3335 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11936  Z= 0.151
  Angle     :  0.548   7.467  16262  Z= 0.281
  Chirality :  0.044   0.153   1844
  Planarity :  0.005   0.091   2078
  Dihedral  :  5.864  63.558   1688
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  5.66 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.23), residues: 1472
  helix:  2.06 (0.59), residues: 84
  sheet:  1.04 (0.21), residues: 672
  loop : -0.76 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  25 
 TYR   0.017   0.002   TYR E  92 
 PHE   0.021   0.002   PHE A  81 
 TRP   0.012   0.001   TRP D  50 
 HIS   0.003   0.001   HIS F 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11930)
  covalent geometry    : angle       0.54765 (16250)
  SS BOND              : bond        0.00433 (    6)
  SS BOND              : angle       0.32491 (   12)
  hydrogen bonds       : bond        0.03705 (  434)
  hydrogen bonds       : angle       6.07081 ( 1242)

*********************** 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
  128 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.531 
Fit side-chains
REVERT: A  308 LYS cc_start: 0.7437 (ptpp) cc_final: 0.7155 (mtpp)
REVERT: D  185 LEU cc_start: 0.7490 (mm) cc_final: 0.6573 (mm)
REVERT: E  106 GLU cc_start: 0.8267 (pm20) cc_final: 0.7899 (pm20)
REVERT: F  153 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8394 (mttp)
REVERT: F  230 LYS cc_start: 0.7174 (mtmm) cc_final: 0.6621 (ttpp)
REVERT: F  308 LYS cc_start: 0.7430 (ptpp) cc_final: 0.7126 (mtpp)
  outliers start: 14
  outliers final: 14
  residues processed: 121
  average time/residue: 0.1252
  time to fit residues: 20.8009
Evaluate side-chains
  112 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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 C residue   77 SER
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  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 135 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0010
   chunk 34 optimal weight:    0.0270
   chunk 70 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0870
   chunk 104 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.3422

-------------------------------------------------------------------------------
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 = 0.4090 r_free = 0.4090 target = 0.178717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.125985 restraints weight = 14190.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.71
r_work: 0.3173 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11936  Z= 0.097
  Angle     :  0.502   7.108  16262  Z= 0.253
  Chirality :  0.043   0.140   1844
  Planarity :  0.005   0.067   2078
  Dihedral  :  5.564  62.405   1676
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  8.61 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.23), residues: 1472
  helix:  2.27 (0.59), residues: 82
  sheet:  1.04 (0.20), residues: 690
  loop : -0.69 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  22 
 TYR   0.014   0.001   TYR F  48 
 PHE   0.022   0.001   PHE F 269 
 TRP   0.006   0.001   TRP B  50 
 HIS   0.002   0.000   HIS F 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (11930)
  covalent geometry    : angle       0.50182 (16250)
  SS BOND              : bond        0.00361 (    6)
  SS BOND              : angle       0.18095 (   12)
  hydrogen bonds       : bond        0.02817 (  434)
  hydrogen bonds       : angle       5.38450 ( 1242)

*********************** 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
  118 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.309 
Fit side-chains
REVERT: C  119 PHE cc_start: 0.4223 (m-80) cc_final: 0.3973 (m-80)
REVERT: D   22 ARG cc_start: 0.8075 (tpt-90) cc_final: 0.7860 (tpt-90)
REVERT: D  185 LEU cc_start: 0.7093 (mm) cc_final: 0.6214 (mm)
REVERT: E  106 GLU cc_start: 0.8360 (pm20) cc_final: 0.8020 (pm20)
REVERT: F  230 LYS cc_start: 0.7167 (mtmm) cc_final: 0.6760 (mtpp)
REVERT: F  308 LYS cc_start: 0.7307 (ptpp) cc_final: 0.6954 (mtpp)
  outliers start: 13
  outliers final: 9
  residues processed: 113
  average time/residue: 0.1294
  time to fit residues: 20.0444
Evaluate side-chains
  104 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain F residue  147 ILE
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 114 optimal weight:    0.3980
   chunk 6 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 83 optimal weight:    0.3980
   chunk 21 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 120 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.174249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 103)---------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.124208 restraints weight = 14251.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.32
r_work: 0.3092 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3023
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  11936  Z= 0.222
  Angle     :  0.594   8.186  16262  Z= 0.304
  Chirality :  0.046   0.173   1844
  Planarity :  0.005   0.088   2078
  Dihedral  :  5.943  66.935   1676
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.23), residues: 1472
  helix:  2.16 (0.60), residues: 84
  sheet:  0.83 (0.20), residues: 692
  loop : -0.84 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 101 
 TYR   0.024   0.002   TYR E  92 
 PHE   0.014   0.002   PHE B 105 
 TRP   0.015   0.002   TRP D  50 
 HIS   0.005   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 (11930)
  covalent geometry    : angle       0.59422 (16250)
  SS BOND              : bond        0.00496 (    6)
  SS BOND              : angle       0.33469 (   12)
  hydrogen bonds       : bond        0.03327 (  434)
  hydrogen bonds       : angle       5.51537 ( 1242)

*********************** 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
  122 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.6776 (mtmm) cc_final: 0.6441 (mtpp)
REVERT: C  106 GLU cc_start: 0.7916 (pm20) cc_final: 0.7676 (pm20)
REVERT: C  119 PHE cc_start: 0.4834 (m-80) cc_final: 0.4619 (m-80)
REVERT: D   22 ARG cc_start: 0.7909 (tpt-90) cc_final: 0.7587 (tpt-90)
REVERT: E  106 GLU cc_start: 0.7939 (pm20) cc_final: 0.7670 (pm20)
REVERT: F  230 LYS cc_start: 0.7087 (mtmm) cc_final: 0.6708 (mtpp)
REVERT: F  308 LYS cc_start: 0.7488 (ptpp) cc_final: 0.7115 (mtpp)
  outliers start: 22
  outliers final: 17
  residues processed: 115
  average time/residue: 0.1531
  time to fit residues: 23.5327
Evaluate side-chains
  111 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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 C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
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  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 63 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 123 optimal weight:    0.3980
   chunk 111 optimal weight:    9.9990
   chunk 83 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.176485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.119645 restraints weight = 14155.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.65
r_work: 0.3082 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2088

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= 0.123
  Angle     :  0.516   6.724  16262  Z= 0.262
  Chirality :  0.044   0.147   1844
  Planarity :  0.005   0.075   2078
  Dihedral  :  5.767  66.312   1676
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.85 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.23), residues: 1472
  helix:  2.28 (0.60), residues: 84
  sheet:  0.83 (0.20), residues: 690
  loop : -0.81 (0.24), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 406 
 TYR   0.013   0.001   TYR F 250 
 PHE   0.013   0.001   PHE A  81 
 TRP   0.009   0.001   TRP B  50 
 HIS   0.002   0.000   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (11930)
  covalent geometry    : angle       0.51587 (16250)
  SS BOND              : bond        0.00366 (    6)
  SS BOND              : angle       0.20993 (   12)
  hydrogen bonds       : bond        0.02684 (  434)
  hydrogen bonds       : angle       5.02511 ( 1242)

*********************** 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
  124 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  230 LYS cc_start: 0.6758 (mtmm) cc_final: 0.6449 (mtpp)
REVERT: D   22 ARG cc_start: 0.7904 (tpt-90) cc_final: 0.7546 (tpt-90)
REVERT: E  106 GLU cc_start: 0.8388 (pm20) cc_final: 0.8147 (pm20)
REVERT: F   63 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7737 (mtp85)
REVERT: F  106 LEU cc_start: 0.7838 (mm) cc_final: 0.7507 (mp)
REVERT: F  230 LYS cc_start: 0.7062 (mtmm) cc_final: 0.6702 (mtpp)
REVERT: F  308 LYS cc_start: 0.7494 (ptpp) cc_final: 0.6963 (mtpp)
  outliers start: 25
  outliers final: 20
  residues processed: 117
  average time/residue: 0.1511
  time to fit residues: 23.6986
Evaluate side-chains
  113 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
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  151 LEU
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain E residue    5 MET
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  295 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    0.0470
   chunk 146 optimal weight:    0.8980
   chunk 142 optimal weight:    0.0370
   chunk 58 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 83 optimal weight:    0.0970
   chunk 122 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.3354

-------------------------------------------------------------------------------
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 = 0.4087 r_free = 0.4087 target = 0.178362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.122070 restraints weight = 14176.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.57
r_work: 0.3155 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2993
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2137

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= 0.095
  Angle     :  0.505   6.484  16262  Z= 0.254
  Chirality :  0.043   0.136   1844
  Planarity :  0.005   0.063   2078
  Dihedral  :  5.589  65.769   1676
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.24 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.23), residues: 1472
  helix:  2.41 (0.60), residues: 84
  sheet:  0.88 (0.20), residues: 692
  loop : -0.69 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  22 
 TYR   0.009   0.001   TYR A 250 
 PHE   0.012   0.001   PHE F  81 
 TRP   0.006   0.001   TRP C  36 
 HIS   0.001   0.000   HIS F 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (11930)
  covalent geometry    : angle       0.50474 (16250)
  SS BOND              : bond        0.00336 (    6)
  SS BOND              : angle       0.21156 (   12)
  hydrogen bonds       : bond        0.02385 (  434)
  hydrogen bonds       : angle       4.72157 ( 1242)

*********************** 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
  119 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7572 (mtp85)
REVERT: A  230 LYS cc_start: 0.6702 (mtmm) cc_final: 0.6409 (mtpp)
REVERT: B  185 LEU cc_start: 0.6649 (mm) cc_final: 0.6419 (mm)
REVERT: D   22 ARG cc_start: 0.7982 (tpt-90) cc_final: 0.7675 (tpt-90)
REVERT: E  106 GLU cc_start: 0.8627 (pm20) cc_final: 0.8181 (pm20)
REVERT: E  109 ARG cc_start: 0.7364 (ptm160) cc_final: 0.7155 (ptm160)
REVERT: F  230 LYS cc_start: 0.7014 (mtmm) cc_final: 0.6655 (mtpp)
REVERT: F  308 LYS cc_start: 0.7530 (ptpp) cc_final: 0.6883 (mtpp)
  outliers start: 21
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1466
  time to fit residues: 21.9949
Evaluate side-chains
  106 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain E residue    5 MET
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  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 131 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0980
   chunk 4 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 146 optimal weight:    0.6980
   chunk 125 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4091 r_free = 0.4091 target = 0.178428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.142955 restraints weight = 14188.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.69
r_work: 0.3325 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11936  Z= 0.157
  Angle     :  0.554   7.886  16262  Z= 0.280
  Chirality :  0.045   0.162   1844
  Planarity :  0.005   0.099   2078
  Dihedral  :  5.759  67.703   1676
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.88 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.23), residues: 1472
  helix:  2.55 (0.61), residues: 82
  sheet:  0.81 (0.20), residues: 692
  loop : -0.77 (0.24), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  22 
 TYR   0.016   0.001   TYR C  92 
 PHE   0.011   0.001   PHE A  62 
 TRP   0.011   0.001   TRP B  50 
 HIS   0.004   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (11930)
  covalent geometry    : angle       0.55365 (16250)
  SS BOND              : bond        0.00414 (    6)
  SS BOND              : angle       0.28457 (   12)
  hydrogen bonds       : bond        0.02701 (  434)
  hydrogen bonds       : angle       4.90035 ( 1242)

*********************** 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
  114 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7635 (mtp85)
REVERT: A  230 LYS cc_start: 0.6857 (mtmm) cc_final: 0.6556 (mtpp)
REVERT: F  230 LYS cc_start: 0.7036 (mtmm) cc_final: 0.6703 (mtpp)
REVERT: F  308 LYS cc_start: 0.7570 (ptpp) cc_final: 0.7007 (mtpp)
  outliers start: 23
  outliers final: 22
  residues processed: 106
  average time/residue: 0.1684
  time to fit residues: 23.6989
Evaluate side-chains
  105 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
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  296 HIS
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  107 ILE
Chi-restraints excluded: chain D residue   77 THR
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  200 LEU
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 143 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9990
   chunk 130 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 129 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.0584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.176901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.144368 restraints weight = 14131.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 1.56
r_work: 0.3337 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  11936  Z= 0.181
  Angle     :  0.572   7.568  16262  Z= 0.291
  Chirality :  0.045   0.164   1844
  Planarity :  0.005   0.093   2078
  Dihedral  :  5.890  68.902   1676
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.80 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.23), residues: 1472
  helix:  2.49 (0.61), residues: 82
  sheet:  0.87 (0.20), residues: 676
  loop : -0.94 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  22 
 TYR   0.019   0.002   TYR C  92 
 PHE   0.012   0.002   PHE F  62 
 TRP   0.013   0.002   TRP B  50 
 HIS   0.004   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (11930)
  covalent geometry    : angle       0.57219 (16250)
  SS BOND              : bond        0.00444 (    6)
  SS BOND              : angle       0.32545 (   12)
  hydrogen bonds       : bond        0.02837 (  434)
  hydrogen bonds       : angle       5.05348 ( 1242)

*********************** 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
  123 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7638 (mtp85)
REVERT: A  230 LYS cc_start: 0.6925 (mtmm) cc_final: 0.6592 (mtpp)
REVERT: B   68 LYS cc_start: 0.8075 (tptt) cc_final: 0.7859 (tptp)
REVERT: C   25 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7690 (ttm110)
REVERT: D   68 LYS cc_start: 0.8080 (tptt) cc_final: 0.7857 (tptp)
REVERT: E   25 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7515 (ttm110)
REVERT: F  230 LYS cc_start: 0.7102 (mtmm) cc_final: 0.6786 (mtpp)
REVERT: F  308 LYS cc_start: 0.7603 (ptpp) cc_final: 0.7051 (mtpp)
  outliers start: 27
  outliers final: 26
  residues processed: 115
  average time/residue: 0.1473
  time to fit residues: 22.9723
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  : 0.453 
-------------------------------------------------------------------------------
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  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   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   60 VAL
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  200 LEU
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 71 optimal weight:    2.9990
   chunk 145 optimal weight:    0.9990
   chunk 143 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 125 optimal weight:    0.0980
   chunk 91 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 88 optimal weight:    0.2980
   chunk 136 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.178811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.146726 restraints weight = 14055.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.56
r_work: 0.3366 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2451

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= 0.117
  Angle     :  0.526   6.764  16262  Z= 0.265
  Chirality :  0.044   0.144   1844
  Planarity :  0.005   0.084   2078
  Dihedral  :  5.751  67.610   1676
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.23), residues: 1472
  helix:  2.51 (0.61), residues: 82
  sheet:  0.94 (0.20), residues: 676
  loop : -0.89 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  22 
 TYR   0.012   0.001   TYR C  92 
 PHE   0.011   0.001   PHE F  81 
 TRP   0.008   0.001   TRP D  50 
 HIS   0.002   0.000   HIS F 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (11930)
  covalent geometry    : angle       0.52580 (16250)
  SS BOND              : bond        0.00350 (    6)
  SS BOND              : angle       0.22722 (   12)
  hydrogen bonds       : bond        0.02481 (  434)
  hydrogen bonds       : angle       4.79620 ( 1242)

*********************** 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
  117 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7612 (mtp85)
REVERT: A  230 LYS cc_start: 0.6926 (mtmm) cc_final: 0.6411 (ttpp)
REVERT: B   68 LYS cc_start: 0.8031 (tptt) cc_final: 0.7806 (tptp)
REVERT: E   25 ARG cc_start: 0.7640 (ttm110) cc_final: 0.7409 (ttm110)
REVERT: F   63 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7597 (mtp85)
REVERT: F  230 LYS cc_start: 0.7103 (mtmm) cc_final: 0.6785 (mtpp)
REVERT: F  308 LYS cc_start: 0.7588 (ptpp) cc_final: 0.7066 (mtpp)
  outliers start: 25
  outliers final: 23
  residues processed: 111
  average time/residue: 0.1556
  time to fit residues: 23.2069
Evaluate side-chains
  111 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
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  336 VAL
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   28 GLN
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 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  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  200 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 132 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 118 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 122 optimal weight:    0.4980
   chunk 15 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 0 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.177341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.143845 restraints weight = 14168.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.64
r_work: 0.3343 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2480

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= 0.126
  Angle     :  0.529   6.027  16262  Z= 0.268
  Chirality :  0.044   0.151   1844
  Planarity :  0.005   0.085   2078
  Dihedral  :  5.729  67.746   1676
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.23), residues: 1472
  helix:  2.52 (0.60), residues: 82
  sheet:  0.95 (0.20), residues: 676
  loop : -0.87 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  22 
 TYR   0.013   0.001   TYR E  92 
 PHE   0.011   0.001   PHE F  81 
 TRP   0.009   0.001   TRP D  50 
 HIS   0.002   0.001   HIS F 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (11930)
  covalent geometry    : angle       0.52868 (16250)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       0.23178 (   12)
  hydrogen bonds       : bond        0.02532 (  434)
  hydrogen bonds       : angle       4.76249 ( 1242)

********************** 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
  113 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7654 (mtp85)
REVERT: A  230 LYS cc_start: 0.6928 (mtmm) cc_final: 0.6631 (mtpp)
REVERT: B   68 LYS cc_start: 0.8078 (tptt) cc_final: 0.7848 (tptp)
REVERT: C   25 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7723 (ttm110)
REVERT: E   25 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7505 (ttm110)
REVERT: F   63 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7654 (mtp85)
REVERT: F  230 LYS cc_start: 0.7127 (mtmm) cc_final: 0.6803 (mtpp)
REVERT: F  308 LYS cc_start: 0.7587 (ptpp) cc_final: 0.7068 (mtpp)
  outliers start: 25
  outliers final: 25
  residues processed: 107
  average time/residue: 0.1549
  time to fit residues: 22.1709
Evaluate side-chains
  112 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
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  205 ASP
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
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   28 GLN
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 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  200 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 124 optimal weight:    0.5980
   chunk 132 optimal weight:    1.9990
   chunk 116 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0770
   chunk 99 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 144 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 133 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.5738

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.178547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.145501 restraints weight = 14137.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.61
r_work: 0.3356 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2500

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= 0.119
  Angle     :  0.522   6.023  16262  Z= 0.264
  Chirality :  0.044   0.148   1844
  Planarity :  0.005   0.081   2078
  Dihedral  :  5.704  67.654   1676
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.23), residues: 1472
  helix:  2.52 (0.60), residues: 82
  sheet:  0.96 (0.20), residues: 676
  loop : -0.85 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  22 
 TYR   0.012   0.001   TYR C  92 
 PHE   0.011   0.001   PHE F  81 
 TRP   0.008   0.001   TRP D  50 
 HIS   0.002   0.000   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (11930)
  covalent geometry    : angle       0.52223 (16250)
  SS BOND              : bond        0.00356 (    6)
  SS BOND              : angle       0.22275 (   12)
  hydrogen bonds       : bond        0.02476 (  434)
  hydrogen bonds       : angle       4.71630 ( 1242)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3483.73 seconds
wall clock time: 60 minutes 25.37 seconds (3625.37 seconds total)