Starting phenix.real_space_refine
on Tue Jul 29 04:05:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pch_13320/07_2025/7pch_13320.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pch_13320/07_2025/7pch_13320.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pch_13320/07_2025/7pch_13320.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pch_13320/07_2025/7pch_13320.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pch_13320/07_2025/7pch_13320.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pch_13320/07_2025/7pch_13320.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      32      5.16       5
     C    6608      2.51       5
     N    1734      2.21       5
     O    2420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10798
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 1069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
    Chain: "B"
      Number of atoms: 1159
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
      Conformer: "B"
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
          bond proxies already assigned to first conformer: 1113
    Chain: "E"
      Number of atoms: 2830
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 340, 2800
          Classifications: {'peptide': 340}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 327}
      Conformer: "B"
        Number of residues, atoms: 340, 2800
          Classifications: {'peptide': 340}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 327}
          bond proxies already assigned to first conformer: 2822
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 82
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 82
          Classifications: {'water': 82}
          Link IDs: {None: 81}
    Chain: "B"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 103
          Classifications: {'water': 103}
          Link IDs: {None: 102}
    Chain: "E"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
    Chain: "C"
      Number of atoms: 82
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 82
          Classifications: {'water': 82}
          Link IDs: {None: 81}
    Chain: "D"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 103
          Classifications: {'water': 103}
          Link IDs: {None: 102}
    Chain: "F"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
  Restraints were copied for chains:
    C, D, F
  Residues with excluded nonbonded symmetry interactions: 14
    residue:
      pdb=" N  ALYS B  61 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  61 " occ=0.50
    residue:
      pdb=" N  ALYS B  65 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  65 " occ=0.50
    residue:
      pdb=" N  ALYS B  82 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  82 " occ=0.50
    residue:
      pdb=" N  AGLU B 101 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU B 101 " occ=0.50
    residue:
      pdb=" N  ALYS E 141 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS E 141 " occ=0.50
    residue:
      pdb=" N  ALYS E 210 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS E 210 " occ=0.50
    residue:
      pdb=" N  ATYR E 214 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR E 214 " occ=0.50
    residue:
      pdb=" N  ALYS D  61 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS D  61 " occ=0.50
    residue:
      pdb=" N  ALYS D  65 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS D  65 " occ=0.50
    residue:
      pdb=" N  ALYS D  82 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS D  82 " occ=0.50
    residue:
      pdb=" N  AGLU D 101 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU D 101 " occ=0.50
    residue:
      pdb=" N  ALYS F 141 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS F 141 " occ=0.50
    ... (remaining 2 not shown)
  Time building chain proxies: 9.74, per 1000 atoms: 0.90
  Number of scatterers: 10798
  At special positions: 0
  Unit cell: (101.06, 132.356, 93.236, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      32     16.00
     O    2420      8.00
     N    1734      7.00
     C    6608      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.50
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2416

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 10 sheets defined
      53.9% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.655A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 139
      removed outlier: 4.219A  pdb=" N   LYS A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 4.197A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 42
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 57 through 77
      removed outlier: 3.571A  pdb=" N  ALYS B  61 " --> pdb=" O   ASN B  57 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS B  66 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 95
      removed outlier: 5.334A  pdb=" N   THR B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   LEU B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 3.636A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'E' and resid 128 through 134
      removed outlier: 4.187A  pdb=" N   LYS E 134 " --> pdb=" O   ARG E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 163 through 169
    Processing helix  chain 'E' and resid 269 through 285
      Proline residue:  E 281  - end of helix
    Processing helix  chain 'E' and resid 287 through 300
      removed outlier: 4.572A  pdb=" N   ASP E 300 " --> pdb=" O   ASN E 296 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 303 through 332
      removed outlier: 4.183A  pdb=" N   ALA E 308 " --> pdb=" O   GLU E 304 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   GLU E 309 " --> pdb=" O   LYS E 305 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 361 through 365
    Processing helix  chain 'E' and resid 451 through 463
      removed outlier: 3.673A  pdb=" N   LYS E 456 " --> pdb=" O   GLU E 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.655A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS C  99 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 139
      removed outlier: 4.219A  pdb=" N   LYS C 139 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 16
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 4.197A  pdb=" N   GLY D  24 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   GLY D  25 " --> pdb=" O   ASP D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 42
    Processing helix  chain 'D' and resid 50 through 57
    Processing helix  chain 'D' and resid 57 through 77
      removed outlier: 3.571A  pdb=" N  ALYS D  61 " --> pdb=" O   ASN D  57 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS D  66 " --> pdb=" O   ALA D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 95
      removed outlier: 5.334A  pdb=" N   THR D  87 " --> pdb=" O   GLY D  83 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   LEU D  88 " --> pdb=" O   THR D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 3.636A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 142
    Processing helix  chain 'F' and resid 128 through 134
      removed outlier: 4.187A  pdb=" N   LYS F 134 " --> pdb=" O   ARG F 130 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 163 through 169
    Processing helix  chain 'F' and resid 269 through 285
      Proline residue:  F 281  - end of helix
    Processing helix  chain 'F' and resid 287 through 300
      removed outlier: 4.572A  pdb=" N   ASP F 300 " --> pdb=" O   ASN F 296 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 303 through 332
      removed outlier: 4.183A  pdb=" N   ALA F 308 " --> pdb=" O   GLU F 304 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   GLU F 309 " --> pdb=" O   LYS F 305 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 361 through 365
    Processing helix  chain 'F' and resid 451 through 463
      removed outlier: 3.673A  pdb=" N   LYS F 456 " --> pdb=" O   GLU F 452 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 148 through 151
      removed outlier: 3.610A  pdb=" N   ALA E 174 " --> pdb=" O   ILE E 151 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL E 171 " --> pdb=" O   GLN E 190 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   GLN E 190 " --> pdb=" O   VAL E 171 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   GLY E 188 " --> pdb=" O   PRO E 173 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ARG E 224 " --> pdb=" O   LEU E 211 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   LEU E 211 " --> pdb=" O   ARG E 224 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   SER E 226 " --> pdb=" O   ILE E 209 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ILE E 209 " --> pdb=" O   SER E 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 153 through 156
      removed outlier: 11.269A  pdb=" N   MET E 254 " --> pdb=" O   VAL E 237 " (cutoff:3.500A)
      removed outlier: 10.530A  pdb=" N   VAL E 237 " --> pdb=" O   MET E 254 " (cutoff:3.500A)
      removed outlier: 11.244A  pdb=" N   PHE E 256 " --> pdb=" O   LYS E 235 " (cutoff:3.500A)
      removed outlier: 11.512A  pdb=" N   LYS E 235 " --> pdb=" O   PHE E 256 " (cutoff:3.500A)
      removed outlier: 10.517A  pdb=" N   GLN E 258 " --> pdb=" O   ALA E 233 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ALA E 233 " --> pdb=" O   GLN E 258 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   THR E 231 " --> pdb=" O   ILE E 260 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   HIS E 241 " --> pdb=" O   TRP E 195 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   TRP E 195 " --> pdb=" O   HIS E 241 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   VAL E 200 " --> pdb=" O   LEU E 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 153 through 156
      removed outlier: 11.269A  pdb=" N   MET E 254 " --> pdb=" O   VAL E 237 " (cutoff:3.500A)
      removed outlier: 10.530A  pdb=" N   VAL E 237 " --> pdb=" O   MET E 254 " (cutoff:3.500A)
      removed outlier: 11.244A  pdb=" N   PHE E 256 " --> pdb=" O   LYS E 235 " (cutoff:3.500A)
      removed outlier: 11.512A  pdb=" N   LYS E 235 " --> pdb=" O   PHE E 256 " (cutoff:3.500A)
      removed outlier: 10.517A  pdb=" N   GLN E 258 " --> pdb=" O   ALA E 233 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ALA E 233 " --> pdb=" O   GLN E 258 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   THR E 231 " --> pdb=" O   ILE E 260 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER E 238 " --> pdb=" O   TYR E 249 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 344 through 348
      removed outlier: 3.854A  pdb=" N   ASP E 344 " --> pdb=" O   MET E 375 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   MET E 375 " --> pdb=" O   ASP E 344 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ILE E 371 " --> pdb=" O   THR E 348 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   GLU E 385 " --> pdb=" O   PRO E 370 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   SER E 406 " --> pdb=" O   THR E 415 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ILE E 417 " --> pdb=" O   THR E 404 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   THR E 404 " --> pdb=" O   ILE E 417 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 350 through 353
      removed outlier: 7.274A  pdb=" N   ASP E 428 " --> pdb=" O   VAL E 397 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   VAL E 397 " --> pdb=" O   ASP E 428 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ILE E 430 " --> pdb=" O   PHE E 395 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   PHE E 395 " --> pdb=" O   ILE E 430 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LYS E 432 " --> pdb=" O   LYS E 393 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 148 through 151
      removed outlier: 3.610A  pdb=" N   ALA F 174 " --> pdb=" O   ILE F 151 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL F 171 " --> pdb=" O   GLN F 190 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   GLN F 190 " --> pdb=" O   VAL F 171 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   GLY F 188 " --> pdb=" O   PRO F 173 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ARG F 224 " --> pdb=" O   LEU F 211 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   LEU F 211 " --> pdb=" O   ARG F 224 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   SER F 226 " --> pdb=" O   ILE F 209 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ILE F 209 " --> pdb=" O   SER F 226 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 153 through 156
      removed outlier: 11.269A  pdb=" N   MET F 254 " --> pdb=" O   VAL F 237 " (cutoff:3.500A)
      removed outlier: 10.530A  pdb=" N   VAL F 237 " --> pdb=" O   MET F 254 " (cutoff:3.500A)
      removed outlier: 11.244A  pdb=" N   PHE F 256 " --> pdb=" O   LYS F 235 " (cutoff:3.500A)
      removed outlier: 11.512A  pdb=" N   LYS F 235 " --> pdb=" O   PHE F 256 " (cutoff:3.500A)
      removed outlier: 10.517A  pdb=" N   GLN F 258 " --> pdb=" O   ALA F 233 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ALA F 233 " --> pdb=" O   GLN F 258 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   THR F 231 " --> pdb=" O   ILE F 260 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   HIS F 241 " --> pdb=" O   TRP F 195 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   TRP F 195 " --> pdb=" O   HIS F 241 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   VAL F 200 " --> pdb=" O   LEU F 207 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 153 through 156
      removed outlier: 11.269A  pdb=" N   MET F 254 " --> pdb=" O   VAL F 237 " (cutoff:3.500A)
      removed outlier: 10.530A  pdb=" N   VAL F 237 " --> pdb=" O   MET F 254 " (cutoff:3.500A)
      removed outlier: 11.244A  pdb=" N   PHE F 256 " --> pdb=" O   LYS F 235 " (cutoff:3.500A)
      removed outlier: 11.512A  pdb=" N   LYS F 235 " --> pdb=" O   PHE F 256 " (cutoff:3.500A)
      removed outlier: 10.517A  pdb=" N   GLN F 258 " --> pdb=" O   ALA F 233 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   ALA F 233 " --> pdb=" O   GLN F 258 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   THR F 231 " --> pdb=" O   ILE F 260 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER F 238 " --> pdb=" O   TYR F 249 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 344 through 348
      removed outlier: 3.854A  pdb=" N   ASP F 344 " --> pdb=" O   MET F 375 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   MET F 375 " --> pdb=" O   ASP F 344 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ILE F 371 " --> pdb=" O   THR F 348 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   GLU F 385 " --> pdb=" O   PRO F 370 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   SER F 406 " --> pdb=" O   THR F 415 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ILE F 417 " --> pdb=" O   THR F 404 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   THR F 404 " --> pdb=" O   ILE F 417 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 350 through 353
      removed outlier: 7.274A  pdb=" N   ASP F 428 " --> pdb=" O   VAL F 397 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   VAL F 397 " --> pdb=" O   ASP F 428 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ILE F 430 " --> pdb=" O   PHE F 395 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   PHE F 395 " --> pdb=" O   ILE F 430 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LYS F 432 " --> pdb=" O   LYS F 393 " (cutoff:3.500A)

    610 hydrogen bonds defined for protein.
    1714 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.73

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.18 -     1.36: 3334
        1.36 -     1.54: 6968
        1.54 -     1.72: 184
        1.72 -     1.90: 58
        1.90 -     2.08: 16
  Bond restraints: 10560
  Sorted by residual:
  bond pdb=" C   LEU B  88 "
       pdb=" O   LEU B  88 "
    ideal  model  delta    sigma   weight residual
    1.237  1.176  0.061 1.19e-02 7.06e+03 2.61e+01
  bond pdb=" C   LEU D  88 "
       pdb=" O   LEU D  88 "
    ideal  model  delta    sigma   weight residual
    1.237  1.176  0.061 1.19e-02 7.06e+03 2.61e+01
  bond pdb=" CA  SER D  89 "
       pdb=" CB  SER D  89 "
    ideal  model  delta    sigma   weight residual
    1.529  1.457  0.072 1.55e-02 4.16e+03 2.13e+01
  bond pdb=" CA  SER B  89 "
       pdb=" CB  SER B  89 "
    ideal  model  delta    sigma   weight residual
    1.529  1.457  0.072 1.55e-02 4.16e+03 2.13e+01
  bond pdb=" C   ARG F 447 "
       pdb=" O   ARG F 447 "
    ideal  model  delta    sigma   weight residual
    1.236  1.183  0.052 1.22e-02 6.72e+03 1.84e+01
  ... (remaining 10555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 12108
        2.23 -     4.47: 2110
        4.47 -     6.70: 106
        6.70 -     8.93: 8
        8.93 -    11.16: 12
  Bond angle restraints: 14344
  Sorted by residual:
  angle pdb=" N   HIS E 143 "
        pdb=" CA  HIS E 143 "
        pdb=" C   HIS E 143 "
      ideal   model   delta    sigma   weight residual
     113.15  105.67    7.48 1.19e+00 7.06e-01 3.95e+01
  angle pdb=" N   HIS F 143 "
        pdb=" CA  HIS F 143 "
        pdb=" C   HIS F 143 "
      ideal   model   delta    sigma   weight residual
     113.15  105.67    7.48 1.19e+00 7.06e-01 3.95e+01
  angle pdb=" N   SER E 213 "
        pdb=" CA  SER E 213 "
        pdb=" C   SER E 213 "
      ideal   model   delta    sigma   weight residual
     108.99  117.44   -8.45 1.57e+00 4.06e-01 2.90e+01
  angle pdb=" N   SER F 213 "
        pdb=" CA  SER F 213 "
        pdb=" C   SER F 213 "
      ideal   model   delta    sigma   weight residual
     108.99  117.44   -8.45 1.57e+00 4.06e-01 2.90e+01
  angle pdb=" CA  GLN D 127 "
        pdb=" C   GLN D 127 "
        pdb=" O   GLN D 127 "
      ideal   model   delta    sigma   weight residual
     120.55  115.29    5.26 1.06e+00 8.90e-01 2.46e+01
  ... (remaining 14339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 5784
       17.57 -    35.14: 398
       35.14 -    52.70: 94
       52.70 -    70.27: 26
       70.27 -    87.84: 12
  Dihedral angle restraints: 6314
    sinusoidal: 2566
      harmonic: 3748
  Sorted by residual:
  dihedral pdb=" C2C HEM C 201 "
           pdb=" C3C HEM C 201 "
           pdb=" CAC HEM C 201 "
           pdb=" CBC HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.51   87.51     2      1.00e+01 1.00e-02 4.79e+01
  dihedral pdb=" C2C HEM A 201 "
           pdb=" C3C HEM A 201 "
           pdb=" CAC HEM A 201 "
           pdb=" CBC HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -87.51   87.51     2      1.00e+01 1.00e-02 4.79e+01
  dihedral pdb=" C2B HEM B 201 "
           pdb=" C3B HEM B 201 "
           pdb=" CAB HEM B 201 "
           pdb=" CBB HEM B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  114.03   65.97     2      1.00e+01 1.00e-02 4.00e+01
  ... (remaining 6311 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 616
       0.053 -    0.106: 396
       0.106 -    0.159: 336
       0.159 -    0.212: 156
       0.212 -    0.265: 38
  Chirality restraints: 1542
  Sorted by residual:
  chirality pdb=" CA  VAL D  54 "
            pdb=" N   VAL D  54 "
            pdb=" C   VAL D  54 "
            pdb=" CB  VAL D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  VAL B  54 "
            pdb=" N   VAL B  54 "
            pdb=" C   VAL B  54 "
            pdb=" CB  VAL B  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  VAL F 237 "
            pdb=" N   VAL F 237 "
            pdb=" C   VAL F 237 "
            pdb=" CB  VAL F 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 1539 not shown)

  Planarity restraints: 1818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  60 "   -0.027 2.00e-02 2.50e+03   5.50e-02 3.02e+01
        pdb=" C   VAL B  60 "    0.095 2.00e-02 2.50e+03
        pdb=" O   VAL B  60 "   -0.035 2.00e-02 2.50e+03
        pdb=" N  BLYS B  61 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  60 "    0.027 2.00e-02 2.50e+03   5.50e-02 3.02e+01
        pdb=" C   VAL D  60 "   -0.095 2.00e-02 2.50e+03
        pdb=" O   VAL D  60 "    0.035 2.00e-02 2.50e+03
        pdb=" N  BLYS D  61 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA BLYS B  61 "   -0.026 2.00e-02 2.50e+03   5.45e-02 2.97e+01
        pdb=" C  BLYS B  61 "    0.094 2.00e-02 2.50e+03
        pdb=" O  BLYS B  61 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   ALA B  62 "   -0.033 2.00e-02 2.50e+03
  ... (remaining 1815 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 3426
        2.85 -     3.37: 10214
        3.37 -     3.88: 19380
        3.88 -     4.39: 23989
        4.39 -     4.90: 37494
  Nonbonded interactions: 94503
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D  43 "
            pdb=" O   HOH D 301 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OE2 GLU B  43 "
            pdb=" O   HOH B 301 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" O   THR B  84 "
            pdb=" O   HOH B 302 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" O   THR D  84 "
            pdb=" O   HOH D 302 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" O   VAL E 367 "
            pdb=" O   HOH E 501 "
     model   vdw
     2.486 3.040
  ... (remaining 94498 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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=0.00 max=1.00 mean=0.99
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:             7.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.340
  Set scattering table:                    0.090
  Process input model:                     31.330
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
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      :  0.013   0.250  10564  Z= 0.914
  Angle     :  1.542  11.164  14344  Z= 1.142
  Chirality :  0.101   0.265   1542
  Planarity :  0.008   0.055   1818
  Dihedral  : 13.622  87.838   3898
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.92 %
    Favored  : 92.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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 (0.23), residues: 1284
  helix:  2.20 (0.21), residues: 614
  sheet:  0.41 (0.43), residues: 154
  loop : -0.80 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP F 392 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.013   0.002   PHE F 454 
 TYR   0.017   0.002   TYR F 444 
 ARG   0.007   0.001   ARG F 414 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17366 (  600)
  hydrogen bonds       : angle       8.11861 ( 1714)
  covalent geometry    : bond        0.01242 (10560)
  covalent geometry    : angle       1.54155 (14344)
  Misc. bond           : bond        0.21502 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 1.253 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8732 (tt0) cc_final: 0.8409 (tt0)
REVERT: B   21 ASP cc_start: 0.8833 (m-30) cc_final: 0.8175 (m-30)
REVERT: B   90 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7972 (mt-10)
REVERT: E  382 MET cc_start: 0.8760 (ttm) cc_final: 0.8466 (ttm)
REVERT: E  396 MET cc_start: 0.8244 (mtm) cc_final: 0.7958 (mtm)
REVERT: C   27 GLU cc_start: 0.8727 (tt0) cc_final: 0.8402 (tt0)
REVERT: D   21 ASP cc_start: 0.8835 (m-30) cc_final: 0.8187 (m-30)
REVERT: D   90 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7972 (mt-10)
REVERT: F  382 MET cc_start: 0.8763 (ttm) cc_final: 0.8467 (ttm)
REVERT: F  396 MET cc_start: 0.8244 (mtm) cc_final: 0.7961 (mtm)
  outliers start: 4
  outliers final: 0
  residues processed: 127
  average time/residue: 1.5090
  time to fit residues: 205.1259
Evaluate side-chains
  83 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 112 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  77 HIS
B 102 ASN
D  77 HIS
D 102 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.063275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.041608 restraints weight = 221165.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2675 rms_B_bonded: 7.60
r_work: 0.2389 rms_B_bonded: 7.21 restraints_weight: 2.0000
r_work (final): 0.2389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2443 r_free = 0.2443    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2439 r_free = 0.2439    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10564  Z= 0.128
  Angle     :  0.586   9.739  14344  Z= 0.301
  Chirality :  0.041   0.150   1542
  Planarity :  0.004   0.035   1818
  Dihedral  :  7.930  81.795   1400
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.84 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.23), residues: 1284
  helix:  2.84 (0.20), residues: 628
  sheet:  0.64 (0.42), residues: 158
  loop : -0.34 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  14 
 HIS   0.007   0.001   HIS E 369 
 PHE   0.008   0.001   PHE F 178 
 TYR   0.015   0.001   TYR F 310 
 ARG   0.006   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  600)
  hydrogen bonds       : angle       5.28787 ( 1714)
  covalent geometry    : bond        0.00319 (10560)
  covalent geometry    : angle       0.58627 (14344)
  Misc. bond           : bond        0.02462 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 1.328 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.9473 (tt0) cc_final: 0.9173 (tt0)
REVERT: B    7 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8694 (mt-10)
REVERT: B   90 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8797 (tt0)
REVERT: B  104 ARG cc_start: 0.9158 (ttm-80) cc_final: 0.8505 (ttp-110)
REVERT: E  396 MET cc_start: 0.8628 (mtm) cc_final: 0.8265 (mtt)
REVERT: C   27 GLU cc_start: 0.9469 (tt0) cc_final: 0.9169 (tt0)
REVERT: D    7 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8702 (mt-10)
REVERT: D   22 GLU cc_start: 0.8737 (mp0) cc_final: 0.8528 (mp0)
REVERT: D   90 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8798 (tt0)
REVERT: D  104 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8541 (ttp-110)
REVERT: F  276 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8974 (tm-30)
REVERT: F  396 MET cc_start: 0.8628 (mtm) cc_final: 0.8262 (mtt)
  outliers start: 12
  outliers final: 2
  residues processed: 100
  average time/residue: 1.4059
  time to fit residues: 151.5473
Evaluate side-chains
  90 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain C residue   74 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 123 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0270
   chunk 79 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 122 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0870
   chunk 51 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    0.5616

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

Flipped N/Q/H residues before XYZ refinement:
E 333 GLN
F 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.061863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.040777 restraints weight = 217385.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.2674 rms_B_bonded: 7.24
r_work: 0.2397 rms_B_bonded: 6.95 restraints_weight: 2.0000
r_work (final): 0.2397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2443 r_free = 0.2443    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2443 r_free = 0.2443    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10564  Z= 0.105
  Angle     :  0.535   9.389  14344  Z= 0.271
  Chirality :  0.040   0.155   1542
  Planarity :  0.004   0.035   1818
  Dihedral  :  6.846  85.832   1400
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.20 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.23), residues: 1284
  helix:  2.91 (0.20), residues: 628
  sheet:  0.62 (0.39), residues: 166
  loop : -0.09 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.005   0.000   HIS E 369 
 PHE   0.008   0.001   PHE E 225 
 TYR   0.012   0.001   TYR F 310 
 ARG   0.004   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03302 (  600)
  hydrogen bonds       : angle       4.79095 ( 1714)
  covalent geometry    : bond        0.00262 (10560)
  covalent geometry    : angle       0.53489 (14344)
  Misc. bond           : bond        0.05673 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 1.232 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.9498 (tt0) cc_final: 0.9296 (tt0)
REVERT: B    7 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8678 (mt-10)
REVERT: B  104 ARG cc_start: 0.9132 (ttm-80) cc_final: 0.8499 (ttp-110)
REVERT: E  152 ASP cc_start: 0.9419 (OUTLIER) cc_final: 0.9191 (m-30)
REVERT: E  180 ASP cc_start: 0.9270 (m-30) cc_final: 0.8872 (p0)
REVERT: E  276 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8929 (tm-30)
REVERT: E  375 MET cc_start: 0.9244 (tpp) cc_final: 0.8921 (tpp)
REVERT: E  382 MET cc_start: 0.9155 (ttm) cc_final: 0.8910 (ttm)
REVERT: E  396 MET cc_start: 0.8714 (mtm) cc_final: 0.8351 (mtt)
REVERT: E  403 ARG cc_start: 0.9495 (mtp180) cc_final: 0.9068 (mtp-110)
REVERT: C   27 GLU cc_start: 0.9495 (tt0) cc_final: 0.9292 (tt0)
REVERT: D    7 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8682 (mt-10)
REVERT: D   26 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.9038 (mm-30)
REVERT: D  104 ARG cc_start: 0.9140 (ttm-80) cc_final: 0.8528 (ttp-110)
REVERT: F  180 ASP cc_start: 0.9269 (m-30) cc_final: 0.8872 (p0)
REVERT: F  276 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8812 (tm-30)
REVERT: F  375 MET cc_start: 0.9244 (tpp) cc_final: 0.8918 (tpp)
REVERT: F  382 MET cc_start: 0.9161 (ttm) cc_final: 0.8915 (ttm)
REVERT: F  396 MET cc_start: 0.8701 (mtm) cc_final: 0.8314 (mtt)
REVERT: F  403 ARG cc_start: 0.9494 (mtp180) cc_final: 0.9065 (mtp-110)
  outliers start: 16
  outliers final: 4
  residues processed: 103
  average time/residue: 1.6150
  time to fit residues: 177.6554
Evaluate side-chains
  96 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain E residue  152 ASP
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   50 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 15 optimal weight:    0.3980
   chunk 114 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0970
   chunk 121 optimal weight:    0.0010
   chunk 93 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0000
   overall best weight:    0.4990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.061973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.041206 restraints weight = 207638.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 7.12
r_work: 0.2393 rms_B_bonded: 6.89 restraints_weight: 2.0000
r_work (final): 0.2393
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2438
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2438 r_free = 0.2438    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2438 r_free = 0.2438    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2438
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10564  Z= 0.102
  Angle     :  0.536   8.618  14344  Z= 0.268
  Chirality :  0.039   0.143   1542
  Planarity :  0.004   0.039   1818
  Dihedral  :  6.930  86.707   1400
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.39 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.24), residues: 1284
  helix:  2.86 (0.21), residues: 630
  sheet:  0.73 (0.40), residues: 166
  loop :  0.09 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS F 369 
 PHE   0.008   0.001   PHE E 418 
 TYR   0.011   0.001   TYR F 310 
 ARG   0.003   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03016 (  600)
  hydrogen bonds       : angle       4.58760 ( 1714)
  covalent geometry    : bond        0.00264 (10560)
  covalent geometry    : angle       0.53625 (14344)
  Misc. bond           : bond        0.03791 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.308 
Fit side-chains
REVERT: B  104 ARG cc_start: 0.9131 (ttm-80) cc_final: 0.8471 (ttp-110)
REVERT: E  124 MET cc_start: 0.7857 (pp-130) cc_final: 0.7606 (ppp)
REVERT: E  180 ASP cc_start: 0.9282 (m-30) cc_final: 0.8872 (p0)
REVERT: E  276 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8874 (tm-30)
REVERT: E  375 MET cc_start: 0.9257 (tpp) cc_final: 0.8946 (tpp)
REVERT: E  396 MET cc_start: 0.8770 (mtm) cc_final: 0.8407 (mtt)
REVERT: E  403 ARG cc_start: 0.9511 (mtp180) cc_final: 0.9146 (mtp-110)
REVERT: D  104 ARG cc_start: 0.9136 (ttm-80) cc_final: 0.8499 (ttp-110)
REVERT: F  124 MET cc_start: 0.7868 (pp-130) cc_final: 0.7613 (ppp)
REVERT: F  180 ASP cc_start: 0.9275 (m-30) cc_final: 0.8866 (p0)
REVERT: F  276 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8949 (tm-30)
REVERT: F  375 MET cc_start: 0.9274 (tpp) cc_final: 0.8960 (tpp)
REVERT: F  396 MET cc_start: 0.8751 (mtm) cc_final: 0.8376 (mtt)
REVERT: F  403 ARG cc_start: 0.9511 (mtp180) cc_final: 0.9148 (mtp-110)
  outliers start: 12
  outliers final: 2
  residues processed: 98
  average time/residue: 1.7443
  time to fit residues: 182.3769
Evaluate side-chains
  90 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain C residue   74 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 95 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 120 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
B 146 HIS
C  97 ASN
D 146 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.057935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.035878 restraints weight = 236519.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.2585 rms_B_bonded: 7.34
r_work: 0.2305 rms_B_bonded: 6.92 restraints_weight: 2.0000
r_work (final): 0.2305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2321 r_free = 0.2321    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2320 r_free = 0.2320    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8995
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  10564  Z= 0.172
  Angle     :  0.586   9.318  14344  Z= 0.295
  Chirality :  0.041   0.147   1542
  Planarity :  0.004   0.037   1818
  Dihedral  :  7.062  85.568   1400
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.48 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.24), residues: 1284
  helix:  2.94 (0.21), residues: 622
  sheet:  0.52 (0.40), residues: 162
  loop :  0.23 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  14 
 HIS   0.004   0.001   HIS F 369 
 PHE   0.010   0.001   PHE F 164 
 TYR   0.014   0.001   TYR F 310 
 ARG   0.004   0.000   ARG F 401 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03559 (  600)
  hydrogen bonds       : angle       4.55058 ( 1714)
  covalent geometry    : bond        0.00450 (10560)
  covalent geometry    : angle       0.58628 (14344)
  Misc. bond           : bond        0.05655 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 ASP cc_start: 0.9432 (m-30) cc_final: 0.8887 (p0)
REVERT: B   22 GLU cc_start: 0.9183 (pm20) cc_final: 0.8912 (pm20)
REVERT: B  104 ARG cc_start: 0.9249 (ttm-80) cc_final: 0.8587 (ttp-110)
REVERT: E  124 MET cc_start: 0.7867 (pp-130) cc_final: 0.7568 (ppp)
REVERT: E  180 ASP cc_start: 0.9264 (m-30) cc_final: 0.8882 (p0)
REVERT: E  276 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8960 (tm-30)
REVERT: E  396 MET cc_start: 0.8992 (mtm) cc_final: 0.8606 (mtt)
REVERT: E  403 ARG cc_start: 0.9564 (mtp180) cc_final: 0.9116 (mtp-110)
REVERT: D  104 ARG cc_start: 0.9252 (ttm-80) cc_final: 0.8602 (ttp-110)
REVERT: F  124 MET cc_start: 0.7871 (pp-130) cc_final: 0.7572 (ppp)
REVERT: F  180 ASP cc_start: 0.9262 (m-30) cc_final: 0.8878 (p0)
REVERT: F  276 GLU cc_start: 0.9304 (tm-30) cc_final: 0.8867 (tm-30)
REVERT: F  396 MET cc_start: 0.8983 (mtm) cc_final: 0.8597 (mtt)
REVERT: F  403 ARG cc_start: 0.9563 (mtp180) cc_final: 0.9114 (mtp-110)
  outliers start: 8
  outliers final: 2
  residues processed: 96
  average time/residue: 1.5984
  time to fit residues: 164.0098
Evaluate side-chains
  90 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain C residue   74 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 104 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 27 optimal weight:    0.4980
   chunk 119 optimal weight:   10.0000
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.059645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.037596 restraints weight = 238409.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.2641 rms_B_bonded: 7.44
r_work: 0.2365 rms_B_bonded: 7.02 restraints_weight: 2.0000
r_work (final): 0.2365
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2381 r_free = 0.2381    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2381 r_free = 0.2381    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  10564  Z= 0.104
  Angle     :  0.548   9.931  14344  Z= 0.273
  Chirality :  0.040   0.142   1542
  Planarity :  0.004   0.038   1818
  Dihedral  :  7.038  89.177   1400
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 13.11 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.24), residues: 1284
  helix:  3.02 (0.21), residues: 616
  sheet:  0.57 (0.40), residues: 166
  loop :  0.12 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.003   0.001   HIS F 369 
 PHE   0.008   0.001   PHE E 418 
 TYR   0.010   0.001   TYR F 310 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02899 (  600)
  hydrogen bonds       : angle       4.39244 ( 1714)
  covalent geometry    : bond        0.00273 (10560)
  covalent geometry    : angle       0.54795 (14344)
  Misc. bond           : bond        0.05589 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9141 (m-30) cc_final: 0.8735 (p0)
REVERT: A   78 ASN cc_start: 0.9533 (t0) cc_final: 0.9226 (t0)
REVERT: B   21 ASP cc_start: 0.9379 (m-30) cc_final: 0.8792 (p0)
REVERT: B   22 GLU cc_start: 0.9137 (pm20) cc_final: 0.8836 (pm20)
REVERT: E  180 ASP cc_start: 0.9279 (m-30) cc_final: 0.8900 (p0)
REVERT: E  276 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8926 (tm-30)
REVERT: E  375 MET cc_start: 0.9084 (tpp) cc_final: 0.8647 (tpp)
REVERT: E  396 MET cc_start: 0.8950 (mtm) cc_final: 0.8574 (mtt)
REVERT: E  403 ARG cc_start: 0.9568 (mtp180) cc_final: 0.9213 (mtp-110)
REVERT: C    6 ASP cc_start: 0.9149 (m-30) cc_final: 0.8745 (p0)
REVERT: C   78 ASN cc_start: 0.9537 (t0) cc_final: 0.9282 (t0)
REVERT: D   21 ASP cc_start: 0.9351 (m-30) cc_final: 0.8738 (p0)
REVERT: D   22 GLU cc_start: 0.9191 (pm20) cc_final: 0.8944 (pm20)
REVERT: F  180 ASP cc_start: 0.9283 (m-30) cc_final: 0.8898 (p0)
REVERT: F  276 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8849 (tm-30)
REVERT: F  375 MET cc_start: 0.9085 (tpp) cc_final: 0.8648 (tpp)
REVERT: F  396 MET cc_start: 0.8947 (mtm) cc_final: 0.8572 (mtt)
REVERT: F  403 ARG cc_start: 0.9566 (mtp180) cc_final: 0.9212 (mtp-110)
  outliers start: 2
  outliers final: 4
  residues processed: 92
  average time/residue: 1.7235
  time to fit residues: 169.4975
Evaluate side-chains
  94 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain D residue   52 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0670
   chunk 107 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 114 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.7124

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.059728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.037717 restraints weight = 228285.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.2656 rms_B_bonded: 7.29
r_work: 0.2377 rms_B_bonded: 6.95 restraints_weight: 2.0000
r_work (final): 0.2377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2407
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2407 r_free = 0.2407    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2406 r_free = 0.2406    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8990
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10564  Z= 0.108
  Angle     :  0.574  12.116  14344  Z= 0.282
  Chirality :  0.039   0.139   1542
  Planarity :  0.004   0.049   1818
  Dihedral  :  7.048  89.228   1400
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 13.11 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.24), residues: 1284
  helix:  3.08 (0.21), residues: 616
  sheet:  0.33 (0.37), residues: 196
  loop :  0.26 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  14 
 HIS   0.003   0.000   HIS D 146 
 PHE   0.009   0.001   PHE E 418 
 TYR   0.010   0.001   TYR F 310 
 ARG   0.013   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02873 (  600)
  hydrogen bonds       : angle       4.35522 ( 1714)
  covalent geometry    : bond        0.00287 (10560)
  covalent geometry    : angle       0.57406 (14344)
  Misc. bond           : bond        0.04791 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9152 (m-30) cc_final: 0.8753 (p0)
REVERT: A   78 ASN cc_start: 0.9540 (t0) cc_final: 0.9239 (t0)
REVERT: B   21 ASP cc_start: 0.9368 (m-30) cc_final: 0.8796 (OUTLIER)
REVERT: B   22 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8877 (pm20)
REVERT: B   90 GLU cc_start: 0.9259 (tt0) cc_final: 0.8949 (tm-30)
REVERT: E  124 MET cc_start: 0.7992 (ppp) cc_final: 0.7748 (ppp)
REVERT: E  180 ASP cc_start: 0.9281 (m-30) cc_final: 0.8905 (p0)
REVERT: E  276 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8941 (tm-30)
REVERT: E  375 MET cc_start: 0.9086 (tpp) cc_final: 0.8679 (tpp)
REVERT: E  396 MET cc_start: 0.8997 (mtm) cc_final: 0.8626 (mtt)
REVERT: E  403 ARG cc_start: 0.9548 (mtp180) cc_final: 0.9140 (mtp-110)
REVERT: C    6 ASP cc_start: 0.9151 (m-30) cc_final: 0.8750 (p0)
REVERT: C   78 ASN cc_start: 0.9539 (t0) cc_final: 0.9236 (t0)
REVERT: D   21 ASP cc_start: 0.9322 (m-30) cc_final: 0.8721 (p0)
REVERT: D   22 GLU cc_start: 0.9179 (pm20) cc_final: 0.8965 (pm20)
REVERT: D   90 GLU cc_start: 0.9255 (tt0) cc_final: 0.8946 (tm-30)
REVERT: F  124 MET cc_start: 0.8005 (ppp) cc_final: 0.7763 (ppp)
REVERT: F  180 ASP cc_start: 0.9280 (m-30) cc_final: 0.8904 (p0)
REVERT: F  276 GLU cc_start: 0.9292 (tm-30) cc_final: 0.8871 (tm-30)
REVERT: F  375 MET cc_start: 0.9091 (tpp) cc_final: 0.8682 (tpp)
REVERT: F  396 MET cc_start: 0.8994 (mtm) cc_final: 0.8623 (mtt)
REVERT: F  403 ARG cc_start: 0.9548 (mtp180) cc_final: 0.9188 (mtp-110)
  outliers start: 8
  outliers final: 7
  residues processed: 92
  average time/residue: 1.5457
  time to fit residues: 152.1370
Evaluate side-chains
  97 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain B residue    2 HIS
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain D residue    2 HIS
Chi-restraints excluded: chain D residue   52 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 55 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 57 optimal weight:    0.4980
   chunk 118 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.059631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.037629 restraints weight = 239884.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.2655 rms_B_bonded: 7.44
r_work: 0.2375 rms_B_bonded: 6.95 restraints_weight: 2.0000
r_work (final): 0.2375
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2390 r_free = 0.2390    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2390 r_free = 0.2390    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8995
moved from start:          0.3726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10564  Z= 0.109
  Angle     :  0.567  11.984  14344  Z= 0.279
  Chirality :  0.039   0.125   1542
  Planarity :  0.004   0.049   1818
  Dihedral  :  7.044  89.878   1400
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.39 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.24), residues: 1284
  helix:  3.06 (0.21), residues: 618
  sheet:  0.43 (0.39), residues: 186
  loop :  0.23 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.003   0.000   HIS D 146 
 PHE   0.009   0.001   PHE F 418 
 TYR   0.011   0.001   TYR F 444 
 ARG   0.010   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02827 (  600)
  hydrogen bonds       : angle       4.31710 ( 1714)
  covalent geometry    : bond        0.00293 (10560)
  covalent geometry    : angle       0.56714 (14344)
  Misc. bond           : bond        0.04792 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9155 (m-30) cc_final: 0.8756 (p0)
REVERT: A   78 ASN cc_start: 0.9543 (t0) cc_final: 0.9249 (t0)
REVERT: B   21 ASP cc_start: 0.9337 (m-30) cc_final: 0.8785 (p0)
REVERT: B   22 GLU cc_start: 0.9158 (pm20) cc_final: 0.8886 (pm20)
REVERT: B   90 GLU cc_start: 0.9262 (tt0) cc_final: 0.8973 (tm-30)
REVERT: E  180 ASP cc_start: 0.9281 (m-30) cc_final: 0.8896 (p0)
REVERT: E  276 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8937 (tm-30)
REVERT: E  375 MET cc_start: 0.9073 (tpp) cc_final: 0.8660 (tpp)
REVERT: E  396 MET cc_start: 0.8983 (mtm) cc_final: 0.8604 (mtt)
REVERT: E  403 ARG cc_start: 0.9545 (mtp180) cc_final: 0.9154 (mtp-110)
REVERT: C    6 ASP cc_start: 0.9154 (m-30) cc_final: 0.8757 (p0)
REVERT: C   78 ASN cc_start: 0.9540 (t0) cc_final: 0.9244 (t0)
REVERT: D   21 ASP cc_start: 0.9283 (m-30) cc_final: 0.8672 (p0)
REVERT: D   22 GLU cc_start: 0.9140 (pm20) cc_final: 0.8896 (pm20)
REVERT: D   90 GLU cc_start: 0.9257 (tt0) cc_final: 0.8970 (tm-30)
REVERT: F  180 ASP cc_start: 0.9276 (m-30) cc_final: 0.8896 (p0)
REVERT: F  276 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8879 (tm-30)
REVERT: F  375 MET cc_start: 0.9075 (tpp) cc_final: 0.8780 (tpp)
REVERT: F  396 MET cc_start: 0.8978 (mtm) cc_final: 0.8598 (mtt)
REVERT: F  403 ARG cc_start: 0.9546 (mtp180) cc_final: 0.9159 (mtp-110)
  outliers start: 7
  outliers final: 6
  residues processed: 92
  average time/residue: 1.5975
  time to fit residues: 157.5198
Evaluate side-chains
  96 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain B residue    2 HIS
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain D residue    2 HIS
Chi-restraints excluded: chain D residue   50 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0870
   chunk 41 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0970
   chunk 78 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.5356

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.060347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.038542 restraints weight = 204612.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.2685 rms_B_bonded: 7.16
r_work: 0.2411 rms_B_bonded: 6.87 restraints_weight: 2.0000
r_work (final): 0.2411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8980
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10564  Z= 0.102
  Angle     :  0.569  12.322  14344  Z= 0.279
  Chirality :  0.039   0.125   1542
  Planarity :  0.004   0.043   1818
  Dihedral  :  6.904  87.930   1400
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 13.93 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.24), residues: 1284
  helix:  3.12 (0.21), residues: 616
  sheet:  0.34 (0.39), residues: 190
  loop :  0.19 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.003   0.000   HIS D 146 
 PHE   0.009   0.001   PHE F 418 
 TYR   0.009   0.001   TYR F 310 
 ARG   0.010   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02620 (  600)
  hydrogen bonds       : angle       4.15155 ( 1714)
  covalent geometry    : bond        0.00271 (10560)
  covalent geometry    : angle       0.56905 (14344)
  Misc. bond           : bond        0.04610 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 1.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9126 (m-30) cc_final: 0.8748 (p0)
REVERT: A   78 ASN cc_start: 0.9541 (t0) cc_final: 0.9282 (t0)
REVERT: B   21 ASP cc_start: 0.9282 (m-30) cc_final: 0.8691 (p0)
REVERT: B   22 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8866 (pm20)
REVERT: B   90 GLU cc_start: 0.9244 (tt0) cc_final: 0.8974 (tm-30)
REVERT: E  124 MET cc_start: 0.8098 (ppp) cc_final: 0.7880 (ppp)
REVERT: E  180 ASP cc_start: 0.9264 (m-30) cc_final: 0.8871 (p0)
REVERT: E  276 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8927 (tm-30)
REVERT: E  375 MET cc_start: 0.9061 (tpp) cc_final: 0.8772 (tpp)
REVERT: E  396 MET cc_start: 0.8982 (mtm) cc_final: 0.8597 (mtt)
REVERT: E  403 ARG cc_start: 0.9535 (mtp180) cc_final: 0.9182 (mtp-110)
REVERT: C    6 ASP cc_start: 0.9128 (m-30) cc_final: 0.8749 (p0)
REVERT: C   78 ASN cc_start: 0.9542 (t0) cc_final: 0.9282 (t0)
REVERT: D   21 ASP cc_start: 0.9195 (m-30) cc_final: 0.8598 (p0)
REVERT: D   90 GLU cc_start: 0.9244 (tt0) cc_final: 0.8976 (tm-30)
REVERT: F  124 MET cc_start: 0.8103 (ppp) cc_final: 0.7887 (ppp)
REVERT: F  180 ASP cc_start: 0.9263 (m-30) cc_final: 0.8872 (p0)
REVERT: F  276 GLU cc_start: 0.9298 (tm-30) cc_final: 0.8872 (tm-30)
REVERT: F  375 MET cc_start: 0.9050 (tpp) cc_final: 0.8760 (tpp)
REVERT: F  396 MET cc_start: 0.8977 (mtm) cc_final: 0.8591 (mtt)
REVERT: F  403 ARG cc_start: 0.9529 (mtp180) cc_final: 0.9180 (mtp-110)
  outliers start: 3
  outliers final: 4
  residues processed: 93
  average time/residue: 1.6652
  time to fit residues: 165.3638
Evaluate side-chains
  97 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain D residue   52 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0770
   chunk 17 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   chunk 25 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   overall best weight:    0.6138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.058556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.037920 restraints weight = 214492.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.2678 rms_B_bonded: 7.24
r_work: 0.2404 rms_B_bonded: 6.90 restraints_weight: 2.0000
r_work (final): 0.2404
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2422
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2422 r_free = 0.2422    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2422 r_free = 0.2422    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2422
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8978
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10564  Z= 0.106
  Angle     :  0.573  11.892  14344  Z= 0.281
  Chirality :  0.039   0.128   1542
  Planarity :  0.004   0.043   1818
  Dihedral  :  6.872  87.860   1400
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 14.30 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.24), residues: 1284
  helix:  3.13 (0.21), residues: 616
  sheet:  0.34 (0.39), residues: 186
  loop :  0.19 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.003   0.000   HIS D 146 
 PHE   0.009   0.001   PHE F 418 
 TYR   0.010   0.001   TYR F 444 
 ARG   0.009   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02650 (  600)
  hydrogen bonds       : angle       4.13658 ( 1714)
  covalent geometry    : bond        0.00282 (10560)
  covalent geometry    : angle       0.57277 (14344)
  Misc. bond           : bond        0.04387 (    4)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ASP cc_start: 0.9132 (m-30) cc_final: 0.8752 (p0)
REVERT: A   78 ASN cc_start: 0.9540 (t0) cc_final: 0.9291 (t0)
REVERT: B   21 ASP cc_start: 0.9265 (m-30) cc_final: 0.8688 (p0)
REVERT: B   22 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8876 (pm20)
REVERT: B   90 GLU cc_start: 0.9240 (tt0) cc_final: 0.8982 (tm-30)
REVERT: E  124 MET cc_start: 0.8119 (ppp) cc_final: 0.7899 (ppp)
REVERT: E  180 ASP cc_start: 0.9265 (m-30) cc_final: 0.8866 (p0)
REVERT: E  276 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8918 (tm-30)
REVERT: E  375 MET cc_start: 0.9050 (tpp) cc_final: 0.8768 (tpp)
REVERT: E  396 MET cc_start: 0.8993 (mtm) cc_final: 0.8607 (mtt)
REVERT: E  403 ARG cc_start: 0.9532 (mtp180) cc_final: 0.9180 (mtp-110)
REVERT: C    6 ASP cc_start: 0.9135 (m-30) cc_final: 0.8752 (p0)
REVERT: C   78 ASN cc_start: 0.9542 (t0) cc_final: 0.9294 (t0)
REVERT: D   90 GLU cc_start: 0.9241 (tt0) cc_final: 0.8985 (tm-30)
REVERT: F  124 MET cc_start: 0.8127 (ppp) cc_final: 0.7908 (ppp)
REVERT: F  180 ASP cc_start: 0.9261 (m-30) cc_final: 0.8870 (p0)
REVERT: F  276 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8870 (tm-30)
REVERT: F  375 MET cc_start: 0.9052 (tpp) cc_final: 0.8770 (tpp)
REVERT: F  396 MET cc_start: 0.8994 (mtm) cc_final: 0.8608 (mtt)
REVERT: F  403 ARG cc_start: 0.9527 (mtp180) cc_final: 0.9181 (mtp-110)
  outliers start: 3
  outliers final: 2
  residues processed: 93
  average time/residue: 1.6324
  time to fit residues: 162.0514
Evaluate side-chains
  95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain C residue   74 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0670
   chunk 29 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0770
   chunk 85 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5276

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.058688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.037963 restraints weight = 238948.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2680 rms_B_bonded: 7.53
r_work: 0.2401 rms_B_bonded: 7.03 restraints_weight: 2.0000
r_work (final): 0.2401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2420 r_free = 0.2420    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2420 r_free = 0.2420    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.2420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8980
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10564  Z= 0.103
  Angle     :  0.568  11.931  14344  Z= 0.278
  Chirality :  0.039   0.128   1542
  Planarity :  0.004   0.041   1818
  Dihedral  :  6.783  86.793   1400
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 14.30 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.24), residues: 1284
  helix:  3.17 (0.21), residues: 616
  sheet:  0.30 (0.39), residues: 188
  loop :  0.17 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.003   0.000   HIS D 146 
 PHE   0.009   0.001   PHE E 418 
 TYR   0.010   0.001   TYR E 444 
 ARG   0.009   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02616 (  600)
  hydrogen bonds       : angle       4.08042 ( 1714)
  covalent geometry    : bond        0.00274 (10560)
  covalent geometry    : angle       0.56802 (14344)
  Misc. bond           : bond        0.04049 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8478.30 seconds
wall clock time: 148 minutes 4.73 seconds (8884.73 seconds total)