Starting phenix.real_space_refine
on Tue Dec 31 20:30:04 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c21_45135/12_2024/9c21_45135_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c21_45135/12_2024/9c21_45135.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c21_45135/12_2024/9c21_45135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c21_45135/12_2024/9c21_45135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c21_45135/12_2024/9c21_45135_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c21_45135/12_2024/9c21_45135_neut.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     126      5.16       5
     C   10656      2.51       5
     N    2886      2.21       5
     O    3036      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 16704
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2784
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 370, 2774
          Classifications: {'peptide': 370}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 19, 'TRANS': 350}
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'HIC:plan-2': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 82
      Conformer: "B"
        Number of residues, atoms: 371, 2774
          Classifications: {'peptide': 371}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved chain links: 2
          Unresolved chain link angles: 6
          Unresolved chain link dihedrals: 6
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 148
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIC:plan-2': 1, 'HIC:plan-1': 1, 'ASP:plan': 8, 'GLU:plan': 12, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 91
          bond proxies already assigned to first conformer: 2823
  Restraints were copied for chains:
    C, B, E, D, F
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  BHIS A  73 " occ=0.50
      ... (8 atoms not shown)
      pdb=" NE2BHIS A  73 " occ=0.50
    residue:
      pdb=" N  BHIS B  73 " occ=0.50
      ... (8 atoms not shown)
      pdb=" NE2BHIS B  73 " occ=0.50
    residue:
      pdb=" N  BHIS C  73 " occ=0.50
      ... (8 atoms not shown)
      pdb=" NE2BHIS C  73 " occ=0.50
    residue:
      pdb=" N  BHIS D  73 " occ=0.50
      ... (8 atoms not shown)
      pdb=" NE2BHIS D  73 " occ=0.50
    residue:
      pdb=" N  BHIS E  73 " occ=0.50
      ... (8 atoms not shown)
      pdb=" NE2BHIS E  73 " occ=0.50
    residue:
      pdb=" N  BHIS F  73 " occ=0.50
      ... (8 atoms not shown)
      pdb=" NE2BHIS F  73 " occ=0.50
  Time building chain proxies: 7.67, per 1000 atoms: 0.46
  Number of scatterers: 16704
  At special positions: 0
  Unit cell: (91.67, 95.79, 218.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     126     16.00
     O    3036      8.00
     N    2886      7.00
     C   10656      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Links applied
    TRANS
      "BHIS A  73 " - " GLU A  72 " : altloc "B" - ""
      "BHIS B  73 " - " GLU B  72 " : altloc "B" - ""
      "BHIS C  73 " - " GLU C  72 " : altloc "B" - ""
      "BHIS D  73 " - " GLU D  72 " : altloc "B" - ""
      "BHIS E  73 " - " GLU E  72 " : altloc "B" - ""
      "BHIS F  73 " - " GLU F  72 " : altloc "B" - ""
  Time building additional restraints: 4.52
  Conformation dependent library (CDL) restraints added in 3.8 seconds
  

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4116

  Finding SS restraints...
    Secondary structure from input PDB file:
      108 helices and 36 sheets defined
      48.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 78 through 93
      removed outlier: 3.682A  pdb=" N   GLU A  93 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
      removed outlier: 3.531A  pdb=" N   GLU A 100 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS A 101 " --> pdb=" O   PRO A  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 97 through 101'
    Processing helix  chain 'A' and resid 112 through 126
    Processing helix  chain 'A' and resid 137 through 146
    Processing helix  chain 'A' and resid 172 through 175
      removed outlier: 3.800A  pdb=" N   ILE A 175 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 172 through 175'
    Processing helix  chain 'A' and resid 181 through 197
    Processing helix  chain 'A' and resid 202 through 217
    Processing helix  chain 'A' and resid 222 through 233
    Processing helix  chain 'A' and resid 252 through 257
    Processing helix  chain 'A' and resid 258 through 262
      removed outlier: 3.512A  pdb=" N   LEU A 261 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.653A  pdb=" N   CYS A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 296
    Processing helix  chain 'A' and resid 308 through 321
    Processing helix  chain 'A' and resid 337 through 349
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 3.556A  pdb=" N   GLN A 354 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 365
    Processing helix  chain 'A' and resid 366 through 372
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 78 through 93
      removed outlier: 3.682A  pdb=" N   GLU B  93 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.531A  pdb=" N   GLU B 100 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS B 101 " --> pdb=" O   PRO B  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 97 through 101'
    Processing helix  chain 'B' and resid 112 through 126
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 172 through 175
      removed outlier: 3.801A  pdb=" N   ILE B 175 " --> pdb=" O   PRO B 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 172 through 175'
    Processing helix  chain 'B' and resid 181 through 197
    Processing helix  chain 'B' and resid 202 through 217
    Processing helix  chain 'B' and resid 222 through 233
    Processing helix  chain 'B' and resid 252 through 257
    Processing helix  chain 'B' and resid 258 through 262
      removed outlier: 3.513A  pdb=" N   LEU B 261 " --> pdb=" O   PRO B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 285
      removed outlier: 3.653A  pdb=" N   CYS B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 296
    Processing helix  chain 'B' and resid 308 through 321
    Processing helix  chain 'B' and resid 337 through 349
    Processing helix  chain 'B' and resid 350 through 355
      removed outlier: 3.556A  pdb=" N   GLN B 354 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 365
    Processing helix  chain 'B' and resid 366 through 372
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 93
      removed outlier: 3.683A  pdb=" N   GLU C  93 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
      removed outlier: 3.530A  pdb=" N   GLU C 100 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   HIS C 101 " --> pdb=" O   PRO C  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 97 through 101'
    Processing helix  chain 'C' and resid 112 through 126
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 172 through 175
      removed outlier: 3.800A  pdb=" N   ILE C 175 " --> pdb=" O   PRO C 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 172 through 175'
    Processing helix  chain 'C' and resid 181 through 197
    Processing helix  chain 'C' and resid 202 through 217
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 252 through 257
    Processing helix  chain 'C' and resid 258 through 262
      removed outlier: 3.512A  pdb=" N   LEU C 261 " --> pdb=" O   PRO C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 285
      removed outlier: 3.653A  pdb=" N   CYS C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 296
    Processing helix  chain 'C' and resid 308 through 321
    Processing helix  chain 'C' and resid 337 through 349
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 3.557A  pdb=" N   GLN C 354 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 365
    Processing helix  chain 'C' and resid 366 through 372
    Processing helix  chain 'D' and resid 55 through 61
    Processing helix  chain 'D' and resid 78 through 93
      removed outlier: 3.682A  pdb=" N   GLU D  93 " --> pdb=" O   THR D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 101
      removed outlier: 3.531A  pdb=" N   GLU D 100 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS D 101 " --> pdb=" O   PRO D  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 97 through 101'
    Processing helix  chain 'D' and resid 112 through 126
    Processing helix  chain 'D' and resid 137 through 146
    Processing helix  chain 'D' and resid 172 through 175
      removed outlier: 3.800A  pdb=" N   ILE D 175 " --> pdb=" O   PRO D 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 172 through 175'
    Processing helix  chain 'D' and resid 181 through 197
    Processing helix  chain 'D' and resid 202 through 217
    Processing helix  chain 'D' and resid 222 through 233
    Processing helix  chain 'D' and resid 252 through 257
    Processing helix  chain 'D' and resid 258 through 262
      removed outlier: 3.513A  pdb=" N   LEU D 261 " --> pdb=" O   PRO D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 285
      removed outlier: 3.653A  pdb=" N   CYS D 285 " --> pdb=" O   SER D 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 289 through 296
    Processing helix  chain 'D' and resid 308 through 321
    Processing helix  chain 'D' and resid 337 through 349
    Processing helix  chain 'D' and resid 350 through 355
      removed outlier: 3.556A  pdb=" N   GLN D 354 " --> pdb=" O   THR D 351 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 359 through 365
    Processing helix  chain 'D' and resid 366 through 372
    Processing helix  chain 'E' and resid 55 through 61
    Processing helix  chain 'E' and resid 78 through 93
      removed outlier: 3.682A  pdb=" N   GLU E  93 " --> pdb=" O   THR E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 101
      removed outlier: 3.531A  pdb=" N   GLU E 100 " --> pdb=" O   ALA E  97 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS E 101 " --> pdb=" O   PRO E  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 97 through 101'
    Processing helix  chain 'E' and resid 112 through 126
    Processing helix  chain 'E' and resid 137 through 146
    Processing helix  chain 'E' and resid 172 through 175
      removed outlier: 3.801A  pdb=" N   ILE E 175 " --> pdb=" O   PRO E 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 172 through 175'
    Processing helix  chain 'E' and resid 181 through 197
    Processing helix  chain 'E' and resid 202 through 217
    Processing helix  chain 'E' and resid 222 through 233
    Processing helix  chain 'E' and resid 252 through 257
    Processing helix  chain 'E' and resid 258 through 262
      removed outlier: 3.513A  pdb=" N   LEU E 261 " --> pdb=" O   PRO E 258 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 273 through 285
      removed outlier: 3.652A  pdb=" N   CYS E 285 " --> pdb=" O   SER E 281 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 289 through 296
    Processing helix  chain 'E' and resid 308 through 321
    Processing helix  chain 'E' and resid 337 through 349
    Processing helix  chain 'E' and resid 350 through 355
      removed outlier: 3.557A  pdb=" N   GLN E 354 " --> pdb=" O   THR E 351 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 359 through 365
    Processing helix  chain 'E' and resid 366 through 372
    Processing helix  chain 'F' and resid 55 through 61
    Processing helix  chain 'F' and resid 78 through 93
      removed outlier: 3.681A  pdb=" N   GLU F  93 " --> pdb=" O   THR F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 101
      removed outlier: 3.531A  pdb=" N   GLU F 100 " --> pdb=" O   ALA F  97 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   HIS F 101 " --> pdb=" O   PRO F  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 97 through 101'
    Processing helix  chain 'F' and resid 112 through 126
    Processing helix  chain 'F' and resid 137 through 146
    Processing helix  chain 'F' and resid 172 through 175
      removed outlier: 3.800A  pdb=" N   ILE F 175 " --> pdb=" O   PRO F 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 172 through 175'
    Processing helix  chain 'F' and resid 181 through 197
    Processing helix  chain 'F' and resid 202 through 217
    Processing helix  chain 'F' and resid 222 through 233
    Processing helix  chain 'F' and resid 252 through 257
    Processing helix  chain 'F' and resid 258 through 262
      removed outlier: 3.512A  pdb=" N   LEU F 261 " --> pdb=" O   PRO F 258 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 273 through 285
      removed outlier: 3.652A  pdb=" N   CYS F 285 " --> pdb=" O   SER F 281 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 289 through 296
    Processing helix  chain 'F' and resid 308 through 321
    Processing helix  chain 'F' and resid 337 through 349
    Processing helix  chain 'F' and resid 350 through 355
      removed outlier: 3.557A  pdb=" N   GLN F 354 " --> pdb=" O   THR F 351 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 359 through 365
    Processing helix  chain 'F' and resid 366 through 372
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 6.273A  pdb=" N   LEU A   8 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   THR A 106 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   VAL A  10 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.581A  pdb=" N   VAL A  35 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178
      removed outlier: 6.221A  pdb=" N   THR A 297 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 166
    Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32
      removed outlier: 6.273A  pdb=" N   LEU B   8 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   THR B 106 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   VAL B  10 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.581A  pdb=" N   VAL B  35 " --> pdb=" O   LYS B  68 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178
      removed outlier: 6.222A  pdb=" N   THR B 297 " --> pdb=" O   ILE B 330 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166
    Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32
      removed outlier: 6.273A  pdb=" N   LEU C   8 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   THR C 106 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 8.045A  pdb=" N   VAL C  10 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54
      removed outlier: 3.581A  pdb=" N   VAL C  35 " --> pdb=" O   LYS C  68 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178
      removed outlier: 6.221A  pdb=" N   THR C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 165 through 166
    Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32
      removed outlier: 6.274A  pdb=" N   LEU D   8 " --> pdb=" O   LEU D 104 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   THR D 106 " --> pdb=" O   LEU D   8 " (cutoff:3.500A)
      removed outlier: 8.045A  pdb=" N   VAL D  10 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54
      removed outlier: 3.581A  pdb=" N   VAL D  35 " --> pdb=" O   LYS D  68 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72
    Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178
      removed outlier: 6.222A  pdb=" N   THR D 297 " --> pdb=" O   ILE D 330 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 165 through 166
    Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241
    Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32
      removed outlier: 6.273A  pdb=" N   LEU E   8 " --> pdb=" O   LEU E 104 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   THR E 106 " --> pdb=" O   LEU E   8 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   VAL E  10 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54
      removed outlier: 3.580A  pdb=" N   VAL E  35 " --> pdb=" O   LYS E  68 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72
    Processing sheet with id=AD1, first strand: chain 'E' and resid 176 through 178
      removed outlier: 6.221A  pdb=" N   THR E 297 " --> pdb=" O   ILE E 330 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 165 through 166
    Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241
    Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32
      removed outlier: 6.274A  pdb=" N   LEU F   8 " --> pdb=" O   LEU F 104 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   THR F 106 " --> pdb=" O   LEU F   8 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   VAL F  10 " --> pdb=" O   THR F 106 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54
      removed outlier: 3.582A  pdb=" N   VAL F  35 " --> pdb=" O   LYS F  68 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72
    Processing sheet with id=AD7, first strand: chain 'F' and resid 176 through 178
      removed outlier: 6.222A  pdb=" N   THR F 297 " --> pdb=" O   ILE F 330 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'F' and resid 165 through 166
    Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241

    846 hydrogen bonds defined for protein.
    2322 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: 6.31

  Time building geometry restraints manager: 5.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3391
        1.33 -     1.45: 3890
        1.45 -     1.57: 9585
        1.57 -     1.69: 0
        1.69 -     1.81: 216
  Bond restraints: 17082
  Sorted by residual:
  bond pdb=" CG BHIS E  73 "
       pdb=" ND1BHIS E  73 "
    ideal  model  delta    sigma   weight residual
    1.378  1.312  0.066 1.10e-02 8.26e+03 3.59e+01
  bond pdb=" CG BHIS D  73 "
       pdb=" ND1BHIS D  73 "
    ideal  model  delta    sigma   weight residual
    1.378  1.312  0.066 1.10e-02 8.26e+03 3.55e+01
  bond pdb=" CG BHIS F  73 "
       pdb=" ND1BHIS F  73 "
    ideal  model  delta    sigma   weight residual
    1.378  1.312  0.066 1.10e-02 8.26e+03 3.55e+01
  bond pdb=" CG BHIS C  73 "
       pdb=" ND1BHIS C  73 "
    ideal  model  delta    sigma   weight residual
    1.378  1.313  0.065 1.10e-02 8.26e+03 3.50e+01
  bond pdb=" CG BHIS A  73 "
       pdb=" ND1BHIS A  73 "
    ideal  model  delta    sigma   weight residual
    1.378  1.313  0.065 1.10e-02 8.26e+03 3.47e+01
  ... (remaining 17077 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 22707
        2.12 -     4.24: 460
        4.24 -     6.36: 29
        6.36 -     8.48: 12
        8.48 -    10.60: 18
  Bond angle restraints: 23226
  Sorted by residual:
  angle pdb=" CA BHIS E  73 "
        pdb=" CB BHIS E  73 "
        pdb=" CG BHIS E  73 "
      ideal   model   delta    sigma   weight residual
     113.80  108.89    4.91 1.00e+00 1.00e+00 2.41e+01
  angle pdb=" CA BHIS C  73 "
        pdb=" CB BHIS C  73 "
        pdb=" CG BHIS C  73 "
      ideal   model   delta    sigma   weight residual
     113.80  108.93    4.87 1.00e+00 1.00e+00 2.37e+01
  angle pdb=" CA BHIS A  73 "
        pdb=" CB BHIS A  73 "
        pdb=" CG BHIS A  73 "
      ideal   model   delta    sigma   weight residual
     113.80  108.95    4.85 1.00e+00 1.00e+00 2.36e+01
  angle pdb=" CA BHIS D  73 "
        pdb=" CB BHIS D  73 "
        pdb=" CG BHIS D  73 "
      ideal   model   delta    sigma   weight residual
     113.80  108.95    4.85 1.00e+00 1.00e+00 2.35e+01
  angle pdb=" CA BHIS F  73 "
        pdb=" CB BHIS F  73 "
        pdb=" CG BHIS F  73 "
      ideal   model   delta    sigma   weight residual
     113.80  108.95    4.85 1.00e+00 1.00e+00 2.35e+01
  ... (remaining 23221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 9120
       17.97 -    35.94: 831
       35.94 -    53.91: 231
       53.91 -    71.88: 18
       71.88 -    89.85: 18
  Dihedral angle restraints: 10218
    sinusoidal: 3786
      harmonic: 6432
  Sorted by residual:
  dihedral pdb=" C   MET D 305 "
           pdb=" N   MET D 305 "
           pdb=" CA  MET D 305 "
           pdb=" CB  MET D 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.34   13.74     0      2.50e+00 1.60e-01 3.02e+01
  dihedral pdb=" C   MET B 305 "
           pdb=" N   MET B 305 "
           pdb=" CA  MET B 305 "
           pdb=" CB  MET B 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.32   13.72     0      2.50e+00 1.60e-01 3.01e+01
  dihedral pdb=" C   MET C 305 "
           pdb=" N   MET C 305 "
           pdb=" CA  MET C 305 "
           pdb=" CB  MET C 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.31   13.71     0      2.50e+00 1.60e-01 3.01e+01
  ... (remaining 10215 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 2505
       0.091 -    0.182: 147
       0.182 -    0.272: 6
       0.272 -    0.363: 0
       0.363 -    0.454: 6
  Chirality restraints: 2664
  Sorted by residual:
  chirality pdb=" CA  MET D 305 "
            pdb=" N   MET D 305 "
            pdb=" C   MET D 305 "
            pdb=" CB  MET D 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.16e+00
  chirality pdb=" CA  MET B 305 "
            pdb=" N   MET B 305 "
            pdb=" C   MET B 305 "
            pdb=" CB  MET B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.09e+00
  chirality pdb=" CA  MET A 305 "
            pdb=" N   MET A 305 "
            pdb=" C   MET A 305 "
            pdb=" CB  MET A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.08e+00
  ... (remaining 2661 not shown)

  Planarity restraints: 2964
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 368 "    0.025 2.00e-02 2.50e+03   4.92e-02 2.42e+01
        pdb=" C   SER C 368 "   -0.085 2.00e-02 2.50e+03
        pdb=" O   SER C 368 "    0.032 2.00e-02 2.50e+03
        pdb=" N   ILE C 369 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 368 "    0.025 2.00e-02 2.50e+03   4.91e-02 2.42e+01
        pdb=" C   SER D 368 "   -0.085 2.00e-02 2.50e+03
        pdb=" O   SER D 368 "    0.032 2.00e-02 2.50e+03
        pdb=" N   ILE D 369 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER F 368 "    0.025 2.00e-02 2.50e+03   4.91e-02 2.41e+01
        pdb=" C   SER F 368 "   -0.085 2.00e-02 2.50e+03
        pdb=" O   SER F 368 "    0.032 2.00e-02 2.50e+03
        pdb=" N   ILE F 369 "    0.028 2.00e-02 2.50e+03
  ... (remaining 2961 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 1020
        2.73 -     3.27: 16970
        3.27 -     3.81: 28761
        3.81 -     4.36: 32259
        4.36 -     4.90: 57017
  Nonbonded interactions: 136027
  Sorted by model distance:
  nonbonded pdb=" O   GLY D 168 "
            pdb=" NE2 GLN E  49 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" OD2 ASP D 288 "
            pdb=" NE  ARG E  62 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" OD2 ASP B 288 "
            pdb=" NE  ARG C  62 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OD2 ASP E 288 "
            pdb=" NE  ARG F  62 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" O   GLY B 168 "
            pdb=" NE2 GLN C  49 "
     model   vdw
     2.205 3.120
  ... (remaining 136022 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 72 or resid 74 through 373))
  selection = (chain 'B' and (resid 5 through 72 or resid 74 through 373))
  selection = (chain 'C' and (resid 5 through 72 or resid 74 through 373))
  selection = (chain 'D' and (resid 5 through 72 or resid 74 through 373))
  selection = (chain 'E' and (resid 5 through 72 or resid 74 through 373))
  selection = (chain 'F' and (resid 5 through 72 or resid 74 through 373))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     39.670
  Find NCS groups from input model:        0.710
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  17082  Z= 0.304
  Angle     :  0.714  10.600  23226  Z= 0.398
  Chirality :  0.049   0.454   2664
  Planarity :  0.006   0.099   2958
  Dihedral  : 15.188  89.853   6084
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 18.74 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.19), residues: 2208
  helix:  1.27 (0.18), residues: 948
  sheet:  0.92 (0.26), residues: 366
  loop : -0.37 (0.22), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 356 
 HIS   0.002   0.000  BHIS B  73 
 PHE   0.009   0.001   PHE B 279 
 TYR   0.009   0.001   TYR D 362 
 ARG   0.003   0.000   ARG C 177 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 280
  time to evaluate  : 1.989 
Fit side-chains
REVERT: A  370 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7215 (p)
REVERT: B   59 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8202 (mm-40)
REVERT: B  119 MET cc_start: 0.8356 (ttm) cc_final: 0.8123 (ttm)
REVERT: C   16 MET cc_start: 0.7897 (mtp) cc_final: 0.7612 (mtp)
REVERT: C   94 LEU cc_start: 0.9133 (mp) cc_final: 0.8832 (mt)
REVERT: C  153 MET cc_start: 0.8590 (tmm) cc_final: 0.8309 (tmm)
REVERT: D  227 MET cc_start: 0.8788 (mmm) cc_final: 0.8212 (tpp)
REVERT: D  313 MET cc_start: 0.8697 (ttm) cc_final: 0.8115 (ttt)
REVERT: E   81 ASP cc_start: 0.8043 (m-30) cc_final: 0.7805 (m-30)
REVERT: F   44 MET cc_start: 0.8370 (mmm) cc_final: 0.7934 (mmp)
REVERT: F  159 VAL cc_start: 0.8841 (t) cc_final: 0.8572 (m)
  outliers start: 24
  outliers final: 14
  residues processed: 298
  average time/residue: 0.2298
  time to fit residues: 112.5207
Evaluate side-chains
  236 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 221
  time to evaluate  : 2.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  368 SER
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 187 optimal weight:    4.9990
   chunk 168 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 174 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 129 optimal weight:    2.9990
   chunk 201 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 371 HIS
D 225 GLN
E  49 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  17082  Z= 0.303
  Angle     :  0.594   7.884  23226  Z= 0.314
  Chirality :  0.046   0.156   2664
  Planarity :  0.006   0.087   2958
  Dihedral  :  5.134  46.356   2445
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.61 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.18), residues: 2208
  helix:  1.33 (0.18), residues: 966
  sheet:  0.85 (0.27), residues: 366
  loop : -0.34 (0.20), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 356 
 HIS   0.008   0.001   HIS E 371 
 PHE   0.035   0.001   PHE F 279 
 TYR   0.017   0.001   TYR C 306 
 ARG   0.004   0.000   ARG E 116 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 217
  time to evaluate  : 1.948 
Fit side-chains
REVERT: B  119 MET cc_start: 0.8429 (ttm) cc_final: 0.8209 (ttm)
REVERT: B  190 MET cc_start: 0.8104 (mmm) cc_final: 0.7902 (mtt)
REVERT: C   94 LEU cc_start: 0.9152 (mp) cc_final: 0.8834 (mt)
REVERT: D   82 MET cc_start: 0.8547 (tpp) cc_final: 0.8252 (ttp)
REVERT: D  222 ASP cc_start: 0.7417 (p0) cc_final: 0.6852 (p0)
REVERT: D  227 MET cc_start: 0.8817 (mmm) cc_final: 0.8144 (tpt)
REVERT: D  313 MET cc_start: 0.8755 (ttm) cc_final: 0.8188 (ttt)
REVERT: E   78 ASN cc_start: 0.7830 (t0) cc_final: 0.7473 (t0)
REVERT: F  279 PHE cc_start: 0.8117 (t80) cc_final: 0.7752 (t80)
  outliers start: 51
  outliers final: 37
  residues processed: 256
  average time/residue: 0.2273
  time to fit residues: 96.6920
Evaluate side-chains
  233 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 196
  time to evaluate  : 2.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   17 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   17 CYS
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   71 ILE
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  123 MET
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  313 MET
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 167 optimal weight:    8.9990
   chunk 137 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 201 optimal weight:    0.8980
   chunk 218 optimal weight:   10.0000
   chunk 179 optimal weight:    3.9990
   chunk 200 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 162 optimal weight:    0.9980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
F  92 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  17082  Z= 0.238
  Angle     :  0.551  10.491  23226  Z= 0.288
  Chirality :  0.045   0.136   2664
  Planarity :  0.005   0.075   2958
  Dihedral  :  4.618  44.588   2438
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.85 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.18), residues: 2208
  helix:  1.41 (0.18), residues: 966
  sheet:  1.03 (0.27), residues: 366
  loop : -0.25 (0.20), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 356 
 HIS   0.004   0.000   HIS E 371 
 PHE   0.018   0.001   PHE F 279 
 TYR   0.018   0.001   TYR A 143 
 ARG   0.003   0.000   ARG F 147 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 211
  time to evaluate  : 2.370 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.6862 (tp30) cc_final: 0.6509 (tp30)
REVERT: A  222 ASP cc_start: 0.7395 (p0) cc_final: 0.6916 (p0)
REVERT: B  159 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8454 (p)
REVERT: C   94 LEU cc_start: 0.9120 (mp) cc_final: 0.8795 (mt)
REVERT: D   82 MET cc_start: 0.8628 (tpp) cc_final: 0.8155 (tpp)
REVERT: D  227 MET cc_start: 0.8816 (mmm) cc_final: 0.8104 (tpp)
REVERT: D  241 GLU cc_start: 0.7494 (tp30) cc_final: 0.6974 (tt0)
REVERT: E  159 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8573 (m)
REVERT: F  279 PHE cc_start: 0.8106 (t80) cc_final: 0.7703 (t80)
  outliers start: 60
  outliers final: 46
  residues processed: 257
  average time/residue: 0.2249
  time to fit residues: 97.3739
Evaluate side-chains
  246 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 198
  time to evaluate  : 2.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   17 CYS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  272 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  159 VAL
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   12 ASN
Chi-restraints excluded: chain F residue   17 CYS
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   96 VAL
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  272 CYS
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 199 optimal weight:    6.9990
   chunk 151 optimal weight:    8.9990
   chunk 104 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   chunk 135 optimal weight:    0.0470
   chunk 202 optimal weight:    9.9990
   chunk 214 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   chunk 192 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    2.0084

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  17082  Z= 0.260
  Angle     :  0.559  11.928  23226  Z= 0.292
  Chirality :  0.045   0.137   2664
  Planarity :  0.005   0.071   2958
  Dihedral  :  4.624  46.635   2436
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 17.85 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.18), residues: 2208
  helix:  1.42 (0.17), residues: 966
  sheet:  1.02 (0.27), residues: 372
  loop : -0.19 (0.20), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 356 
 HIS   0.003   0.001   HIS E 371 
 PHE   0.013   0.001   PHE F 279 
 TYR   0.018   0.001   TYR E 143 
 ARG   0.003   0.000   ARG D 116 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 209
  time to evaluate  : 1.902 
Fit side-chains
REVERT: A  222 ASP cc_start: 0.7440 (p0) cc_final: 0.6989 (p0)
REVERT: B  159 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8464 (p)
REVERT: C   94 LEU cc_start: 0.9176 (mp) cc_final: 0.8879 (mt)
REVERT: D  227 MET cc_start: 0.8842 (mmm) cc_final: 0.8117 (tpt)
REVERT: E  159 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8572 (m)
REVERT: F  279 PHE cc_start: 0.8151 (t80) cc_final: 0.7663 (t80)
  outliers start: 66
  outliers final: 59
  residues processed: 262
  average time/residue: 0.2185
  time to fit residues: 96.6682
Evaluate side-chains
  256 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 195
  time to evaluate  : 1.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   17 CYS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue   17 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   17 CYS
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  159 VAL
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   12 ASN
Chi-restraints excluded: chain F residue   17 CYS
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  123 MET
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  272 CYS
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 178 optimal weight:    3.9990
   chunk 121 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 159 optimal weight:    0.9980
   chunk 88 optimal weight:    8.9990
   chunk 183 optimal weight:    7.9990
   chunk 148 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 109 optimal weight:    7.9990
   chunk 192 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
C  59 GLN
C 225 GLN
D 225 GLN
F 173 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  17082  Z= 0.439
  Angle     :  0.650  11.844  23226  Z= 0.345
  Chirality :  0.049   0.152   2664
  Planarity :  0.005   0.073   2958
  Dihedral  :  5.374  48.644   2436
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 17.49 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.18), residues: 2208
  helix:  1.14 (0.17), residues: 966
  sheet:  0.88 (0.28), residues: 372
  loop : -0.43 (0.20), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B 356 
 HIS   0.004   0.001   HIS A 101 
 PHE   0.017   0.002   PHE C 200 
 TYR   0.022   0.002   TYR A 143 
 ARG   0.004   0.000   ARG F 116 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 198
  time to evaluate  : 1.704 
Fit side-chains
REVERT: B   78 ASN cc_start: 0.8158 (t0) cc_final: 0.7757 (t0)
REVERT: D  227 MET cc_start: 0.8836 (mmm) cc_final: 0.8102 (tpt)
REVERT: D  241 GLU cc_start: 0.7600 (tp30) cc_final: 0.6997 (tt0)
REVERT: D  313 MET cc_start: 0.8770 (ttm) cc_final: 0.8247 (ttt)
REVERT: E   78 ASN cc_start: 0.8080 (t0) cc_final: 0.7627 (t0)
REVERT: E  159 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8582 (m)
  outliers start: 76
  outliers final: 68
  residues processed: 261
  average time/residue: 0.2159
  time to fit residues: 95.1917
Evaluate side-chains
  255 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 186
  time to evaluate  : 1.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   17 CYS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue   17 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  327 ILE
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   12 ASN
Chi-restraints excluded: chain E residue   17 CYS
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  159 VAL
Chi-restraints excluded: chain E residue  327 ILE
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   12 ASN
Chi-restraints excluded: chain F residue   17 CYS
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   96 VAL
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  123 MET
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  272 CYS
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 193 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 125 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 214 optimal weight:    3.9990
   chunk 178 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 173 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  17082  Z= 0.174
  Angle     :  0.537  13.439  23226  Z= 0.279
  Chirality :  0.043   0.135   2664
  Planarity :  0.005   0.065   2958
  Dihedral  :  4.630  49.152   2436
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.97 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.18), residues: 2208
  helix:  1.38 (0.17), residues: 966
  sheet:  1.45 (0.29), residues: 318
  loop : -0.20 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 356 
 HIS   0.004   0.000   HIS F 101 
 PHE   0.010   0.001   PHE F 279 
 TYR   0.017   0.001   TYR D 143 
 ARG   0.003   0.000   ARG F 147 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 209
  time to evaluate  : 1.997 
Fit side-chains
REVERT: B  159 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8547 (p)
REVERT: D  227 MET cc_start: 0.8813 (mmm) cc_final: 0.8064 (tpt)
REVERT: D  241 GLU cc_start: 0.7537 (tp30) cc_final: 0.7269 (tp30)
REVERT: E  159 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8569 (m)
REVERT: F  279 PHE cc_start: 0.8147 (t80) cc_final: 0.7780 (t80)
  outliers start: 63
  outliers final: 59
  residues processed: 261
  average time/residue: 0.2219
  time to fit residues: 97.7877
Evaluate side-chains
  256 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 195
  time to evaluate  : 1.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   17 CYS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue   17 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   12 ASN
Chi-restraints excluded: chain E residue   17 CYS
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  159 VAL
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   12 ASN
Chi-restraints excluded: chain F residue   17 CYS
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   96 VAL
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  123 MET
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  272 CYS
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  355 MET
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 207 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 156 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0040
   chunk 180 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 213 optimal weight:    0.1980
   chunk 133 optimal weight:   10.0000
   chunk 130 optimal weight:   10.0000
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.6398

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

Flipped N/Q/H residues before XYZ refinement:
C  92 ASN
** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  17082  Z= 0.229
  Angle     :  0.547  13.819  23226  Z= 0.286
  Chirality :  0.044   0.154   2664
  Planarity :  0.005   0.063   2958
  Dihedral  :  4.573  49.026   2434
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 19.27 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.18), residues: 2208
  helix:  1.44 (0.17), residues: 966
  sheet:  1.02 (0.28), residues: 372
  loop : -0.18 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP D 356 
 HIS   0.005   0.001   HIS F 101 
 PHE   0.022   0.001   PHE D 352 
 TYR   0.025   0.001   TYR E 143 
 ARG   0.002   0.000   ARG F 116 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 199
  time to evaluate  : 2.035 
Fit side-chains
REVERT: A   76 VAL cc_start: 0.8704 (t) cc_final: 0.8480 (t)
REVERT: B  159 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8519 (p)
REVERT: D  117 GLU cc_start: 0.7018 (tp30) cc_final: 0.6815 (tp30)
REVERT: D  227 MET cc_start: 0.8860 (mmm) cc_final: 0.8128 (tpt)
REVERT: D  241 GLU cc_start: 0.7552 (tp30) cc_final: 0.7312 (tp30)
REVERT: E  159 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8565 (m)
REVERT: F  241 GLU cc_start: 0.7897 (tp30) cc_final: 0.7673 (tp30)
REVERT: F  279 PHE cc_start: 0.8135 (t80) cc_final: 0.7727 (t80)
  outliers start: 70
  outliers final: 64
  residues processed: 257
  average time/residue: 0.2224
  time to fit residues: 96.4692
Evaluate side-chains
  264 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 198
  time to evaluate  : 2.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   17 CYS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue   17 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   12 ASN
Chi-restraints excluded: chain E residue   17 CYS
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  159 VAL
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   12 ASN
Chi-restraints excluded: chain F residue   17 CYS
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   96 VAL
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  123 MET
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  272 CYS
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  355 MET
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 132 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 127 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 136 optimal weight:    0.5980
   chunk 145 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 168 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
F 101 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  17082  Z= 0.195
  Angle     :  0.536  14.404  23226  Z= 0.278
  Chirality :  0.044   0.146   2664
  Planarity :  0.005   0.061   2958
  Dihedral  :  4.342  49.212   2432
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.50 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.18), residues: 2208
  helix:  1.49 (0.17), residues: 966
  sheet:  1.05 (0.28), residues: 372
  loop : -0.14 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D 356 
 HIS   0.005   0.001   HIS F 101 
 PHE   0.015   0.001   PHE D 352 
 TYR   0.025   0.001   TYR D 143 
 ARG   0.002   0.000   ARG F 147 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 209
  time to evaluate  : 2.004 
Fit side-chains
REVERT: B  159 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8581 (p)
REVERT: C  143 TYR cc_start: 0.7462 (m-80) cc_final: 0.7061 (m-10)
REVERT: D  227 MET cc_start: 0.8859 (mmm) cc_final: 0.8137 (tpt)
REVERT: E  159 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8575 (m)
REVERT: F  241 GLU cc_start: 0.7862 (tp30) cc_final: 0.7650 (tp30)
REVERT: F  279 PHE cc_start: 0.8052 (t80) cc_final: 0.7693 (t80)
  outliers start: 68
  outliers final: 59
  residues processed: 262
  average time/residue: 0.2188
  time to fit residues: 97.0188
Evaluate side-chains
  261 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 200
  time to evaluate  : 1.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   17 CYS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue   17 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   17 CYS
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  159 VAL
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   12 ASN
Chi-restraints excluded: chain F residue   17 CYS
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   96 VAL
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  123 MET
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  272 CYS
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  355 MET
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 194 optimal weight:    0.0980
   chunk 204 optimal weight:    1.9990
   chunk 187 optimal weight:    1.9990
   chunk 199 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0060
   chunk 86 optimal weight:    2.9990
   chunk 156 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 180 optimal weight:    5.9990
   chunk 188 optimal weight:    4.9990
   chunk 198 optimal weight:    4.9990
   overall best weight:    0.9800

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

Flipped N/Q/H residues before XYZ refinement:
F 101 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  17082  Z= 0.172
  Angle     :  0.532  14.645  23226  Z= 0.274
  Chirality :  0.043   0.143   2664
  Planarity :  0.005   0.058   2958
  Dihedral  :  4.245  49.414   2432
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.80 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.18), residues: 2208
  helix:  1.56 (0.17), residues: 966
  sheet:  1.11 (0.28), residues: 372
  loop : -0.11 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 356 
 HIS   0.008   0.001   HIS F 101 
 PHE   0.013   0.001   PHE D 352 
 TYR   0.015   0.001   TYR B 143 
 ARG   0.002   0.000   ARG F 147 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 216
  time to evaluate  : 2.003 
Fit side-chains
REVERT: C  143 TYR cc_start: 0.7292 (m-80) cc_final: 0.6894 (m-10)
REVERT: E  159 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8555 (m)
REVERT: F  279 PHE cc_start: 0.8031 (t80) cc_final: 0.7709 (t80)
  outliers start: 65
  outliers final: 59
  residues processed: 268
  average time/residue: 0.2317
  time to fit residues: 103.5263
Evaluate side-chains
  267 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 207
  time to evaluate  : 2.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   17 CYS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue   17 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   12 ASN
Chi-restraints excluded: chain E residue   17 CYS
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  159 VAL
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   12 ASN
Chi-restraints excluded: chain F residue   17 CYS
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   96 VAL
Chi-restraints excluded: chain F residue  101 HIS
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  272 CYS
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 130 optimal weight:    9.9990
   chunk 210 optimal weight:    8.9990
   chunk 128 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 146 optimal weight:    4.9990
   chunk 221 optimal weight:    1.9990
   chunk 203 optimal weight:    0.9980
   chunk 176 optimal weight:    0.0980
   chunk 18 optimal weight:    1.9990
   chunk 136 optimal weight:    0.8980
   chunk 107 optimal weight:   10.0000
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
F 101 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  17082  Z= 0.171
  Angle     :  0.535  15.140  23226  Z= 0.276
  Chirality :  0.043   0.158   2664
  Planarity :  0.005   0.065   2958
  Dihedral  :  4.221  49.742   2432
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 20.09 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.18), residues: 2208
  helix:  1.58 (0.17), residues: 966
  sheet:  1.17 (0.28), residues: 372
  loop : -0.12 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 356 
 HIS   0.013   0.001   HIS F 101 
 PHE   0.009   0.001   PHE F 279 
 TYR   0.027   0.001   TYR D 143 
 ARG   0.002   0.000   ARG F 147 

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 212
  time to evaluate  : 1.937 
Fit side-chains
REVERT: B  119 MET cc_start: 0.8510 (ttm) cc_final: 0.8272 (ttm)
REVERT: C  143 TYR cc_start: 0.7293 (m-80) cc_final: 0.6896 (m-10)
REVERT: D  241 GLU cc_start: 0.7639 (tp30) cc_final: 0.7085 (tt0)
REVERT: E  159 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8560 (m)
REVERT: F  279 PHE cc_start: 0.8015 (t80) cc_final: 0.7725 (t80)
  outliers start: 60
  outliers final: 59
  residues processed: 262
  average time/residue: 0.2220
  time to fit residues: 99.1140
Evaluate side-chains
  269 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 209
  time to evaluate  : 2.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   17 CYS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain C residue   12 ASN
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain D residue   12 ASN
Chi-restraints excluded: chain D residue   17 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain E residue   12 ASN
Chi-restraints excluded: chain E residue   17 CYS
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  159 VAL
Chi-restraints excluded: chain E residue  369 ILE
Chi-restraints excluded: chain F residue   12 ASN
Chi-restraints excluded: chain F residue   17 CYS
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   96 VAL
Chi-restraints excluded: chain F residue  101 HIS
Chi-restraints excluded: chain F residue  122 ILE
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  178 LEU
Chi-restraints excluded: chain F residue  272 CYS
Chi-restraints excluded: chain F residue  327 ILE
Chi-restraints excluded: chain F residue  369 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 139 optimal weight:    1.9990
   chunk 187 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0870
   chunk 162 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 176 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0030
   chunk 181 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.4768

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

Flipped N/Q/H residues before XYZ refinement:
F 101 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.102979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.085407 restraints weight = 115097.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 6.20
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  17082  Z= 0.145
  Angle     :  0.526  14.574  23226  Z= 0.272
  Chirality :  0.043   0.146   2664
  Planarity :  0.005   0.074   2958
  Dihedral  :  4.152  49.807   2432
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.27 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.18), residues: 2208
  helix:  1.63 (0.17), residues: 966
  sheet:  1.22 (0.28), residues: 372
  loop : -0.06 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 356 
 HIS   0.015   0.001   HIS F 101 
 PHE   0.010   0.001   PHE F 279 
 TYR   0.014   0.001   TYR F 198 
 ARG   0.003   0.000   ARG F 147 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3169.16 seconds
wall clock time: 60 minutes 29.83 seconds (3629.83 seconds total)