Starting phenix.real_space_refine
on Thu Sep 18 01:10:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ngf_49383/09_2025/9ngf_49383_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ngf_49383/09_2025/9ngf_49383.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ngf_49383/09_2025/9ngf_49383_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ngf_49383/09_2025/9ngf_49383_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ngf_49383/09_2025/9ngf_49383.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ngf_49383/09_2025/9ngf_49383.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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
     S      30      5.16       5
     Na      5      4.78       5
     C    8210      2.51       5
     N    2085      2.21       5
     O    2255      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12585
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2516
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2560
    Chain: "B"
      Number of atoms: 2516
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2560
    Chain: "C"
      Number of atoms: 2516
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2560
    Chain: "D"
      Number of atoms: 2516
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2560
    Chain: "E"
      Number of atoms: 2516
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2560
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' NA': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  APHE A 247 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 247 " occ=0.50
    residue:
      pdb=" N  APHE B 247 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE B 247 " occ=0.50
    residue:
      pdb=" N  APHE C 247 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE C 247 " occ=0.50
    residue:
      pdb=" N  APHE D 247 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE D 247 " occ=0.50
    residue:
      pdb=" N  APHE E 247 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE E 247 " occ=0.50
  Time building chain proxies: 5.48, per 1000 atoms: 0.44
  Number of scatterers: 12585
  At special positions: 0
  Unit cell: (92.008, 91.14, 123.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     Na      5     11.00
     O    2255      8.00
     N    2085      7.00
     C    8210      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 993.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2920

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 20 sheets defined
      38.4% alpha, 40.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 70
      removed outlier: 3.650A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'A' and resid 176 through 181
      removed outlier: 3.652A  pdb=" N   SER A 179 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 227 through 251
      removed outlier: 3.651A  pdb=" N   ASN A 251 " --> pdb=" O  APHE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 285
    Processing helix  chain 'A' and resid 296 through 302
      removed outlier: 3.680A  pdb=" N   ARG A 299 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   CYS A 300 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ARG A 301 " --> pdb=" O   GLN A 298 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU A 302 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 296 through 302'
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'B' and resid 62 through 70
      removed outlier: 3.649A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'B' and resid 176 through 181
      removed outlier: 3.652A  pdb=" N   SER B 179 " --> pdb=" O   ASP B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 227 through 251
      removed outlier: 3.650A  pdb=" N   ASN B 251 " --> pdb=" O  APHE B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 285
    Processing helix  chain 'B' and resid 296 through 302
      removed outlier: 3.680A  pdb=" N   ARG B 299 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS B 300 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ARG B 301 " --> pdb=" O   GLN B 298 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU B 302 " --> pdb=" O   ARG B 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 296 through 302'
    Processing helix  chain 'B' and resid 303 through 317
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.650A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'C' and resid 176 through 181
      removed outlier: 3.652A  pdb=" N   SER C 179 " --> pdb=" O   ASP C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 227 through 251
      removed outlier: 3.651A  pdb=" N   ASN C 251 " --> pdb=" O  APHE C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 285
    Processing helix  chain 'C' and resid 296 through 302
      removed outlier: 3.680A  pdb=" N   ARG C 299 " --> pdb=" O   LEU C 296 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS C 300 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ARG C 301 " --> pdb=" O   GLN C 298 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU C 302 " --> pdb=" O   ARG C 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 296 through 302'
    Processing helix  chain 'C' and resid 303 through 317
    Processing helix  chain 'D' and resid 62 through 70
      removed outlier: 3.650A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 121
    Processing helix  chain 'D' and resid 176 through 181
      removed outlier: 3.652A  pdb=" N   SER D 179 " --> pdb=" O   ASP D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 227 through 251
      removed outlier: 3.650A  pdb=" N   ASN D 251 " --> pdb=" O  APHE D 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 285
    Processing helix  chain 'D' and resid 296 through 302
      removed outlier: 3.681A  pdb=" N   ARG D 299 " --> pdb=" O   LEU D 296 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   CYS D 300 " --> pdb=" O   ILE D 297 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ARG D 301 " --> pdb=" O   GLN D 298 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU D 302 " --> pdb=" O   ARG D 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 296 through 302'
    Processing helix  chain 'D' and resid 303 through 317
    Processing helix  chain 'E' and resid 62 through 70
      removed outlier: 3.649A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 121
    Processing helix  chain 'E' and resid 176 through 181
      removed outlier: 3.652A  pdb=" N   SER E 179 " --> pdb=" O   ASP E 176 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
    Processing helix  chain 'E' and resid 222 through 225
    Processing helix  chain 'E' and resid 227 through 251
      removed outlier: 3.651A  pdb=" N   ASN E 251 " --> pdb=" O  APHE E 247 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 285
    Processing helix  chain 'E' and resid 296 through 302
      removed outlier: 3.680A  pdb=" N   ARG E 299 " --> pdb=" O   LEU E 296 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   CYS E 300 " --> pdb=" O   ILE E 297 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ARG E 301 " --> pdb=" O   GLN E 298 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU E 302 " --> pdb=" O   ARG E 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 296 through 302'
    Processing helix  chain 'E' and resid 303 through 317
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.578A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58
      removed outlier: 3.575A  pdb=" N   GLY A 108 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   VAL A  14 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 8.757A  pdb=" N   GLN A 146 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   VAL A  16 " --> pdb=" O   GLN A 146 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   TYR A 148 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ILE A  18 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.801A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.801A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58
      removed outlier: 4.578A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58
      removed outlier: 3.575A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   VAL B  14 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
      removed outlier: 8.757A  pdb=" N   GLN B 146 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   VAL B  16 " --> pdb=" O   GLN B 146 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   TYR B 148 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ILE B  18 " --> pdb=" O   TYR B 148 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.801A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.801A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58
      removed outlier: 4.578A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58
      removed outlier: 3.575A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   VAL C  14 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
      removed outlier: 8.757A  pdb=" N   GLN C 146 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   VAL C  16 " --> pdb=" O   GLN C 146 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   TYR C 148 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE C  18 " --> pdb=" O   TYR C 148 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.802A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.802A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58
      removed outlier: 4.578A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58
      removed outlier: 3.574A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   VAL D  14 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
      removed outlier: 8.757A  pdb=" N   GLN D 146 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   VAL D  16 " --> pdb=" O   GLN D 146 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   TYR D 148 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE D  18 " --> pdb=" O   TYR D 148 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.801A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.801A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58
      removed outlier: 4.578A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58
      removed outlier: 3.575A  pdb=" N   GLY E 108 " --> pdb=" O   VAL E  35 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   VAL E  14 " --> pdb=" O   ASP E 144 " (cutoff:3.500A)
      removed outlier: 8.757A  pdb=" N   GLN E 146 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   VAL E  16 " --> pdb=" O   GLN E 146 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   TYR E 148 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ILE E  18 " --> pdb=" O   TYR E 148 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.801A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.801A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    705 hydrogen bonds defined for protein.
    2015 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3971
        1.34 -     1.46: 2521
        1.46 -     1.57: 6388
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 12930
  Sorted by residual:
  bond pdb=" CA  ASN E 186 "
       pdb=" CB  ASN E 186 "
    ideal  model  delta    sigma   weight residual
    1.531  1.557 -0.027 1.51e-02 4.39e+03 3.09e+00
  bond pdb=" CA  ASN A 186 "
       pdb=" CB  ASN A 186 "
    ideal  model  delta    sigma   weight residual
    1.531  1.557 -0.026 1.51e-02 4.39e+03 2.99e+00
  bond pdb=" CA  ASN D 186 "
       pdb=" CB  ASN D 186 "
    ideal  model  delta    sigma   weight residual
    1.531  1.556 -0.026 1.51e-02 4.39e+03 2.86e+00
  bond pdb=" CB  ASN E 186 "
       pdb=" CG  ASN E 186 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.86e+00
  bond pdb=" CB  ASN C 186 "
       pdb=" CG  ASN C 186 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.82e+00
  ... (remaining 12925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 16994
        1.64 -     3.28: 530
        3.28 -     4.92: 61
        4.92 -     6.56: 30
        6.56 -     8.20: 15
  Bond angle restraints: 17630
  Sorted by residual:
  angle pdb=" C   ASN E  60 "
        pdb=" N   THR E  61 "
        pdb=" CA  THR E  61 "
      ideal   model   delta    sigma   weight residual
     122.61  129.43   -6.82 1.56e+00 4.11e-01 1.91e+01
  angle pdb=" C   ASN D  60 "
        pdb=" N   THR D  61 "
        pdb=" CA  THR D  61 "
      ideal   model   delta    sigma   weight residual
     122.61  129.41   -6.80 1.56e+00 4.11e-01 1.90e+01
  angle pdb=" C   ASN B  60 "
        pdb=" N   THR B  61 "
        pdb=" CA  THR B  61 "
      ideal   model   delta    sigma   weight residual
     122.61  129.41   -6.80 1.56e+00 4.11e-01 1.90e+01
  angle pdb=" C   ASN A  60 "
        pdb=" N   THR A  61 "
        pdb=" CA  THR A  61 "
      ideal   model   delta    sigma   weight residual
     122.61  129.40   -6.79 1.56e+00 4.11e-01 1.90e+01
  angle pdb=" C   ASN C  60 "
        pdb=" N   THR C  61 "
        pdb=" CA  THR C  61 "
      ideal   model   delta    sigma   weight residual
     122.61  129.38   -6.77 1.56e+00 4.11e-01 1.88e+01
  ... (remaining 17625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.11: 6546
       14.11 -    28.22: 759
       28.22 -    42.33: 180
       42.33 -    56.45: 50
       56.45 -    70.56: 20
  Dihedral angle restraints: 7555
    sinusoidal: 3030
      harmonic: 4525
  Sorted by residual:
  dihedral pdb=" CA  ASP D 196 "
           pdb=" CB  ASP D 196 "
           pdb=" CG  ASP D 196 "
           pdb=" OD1 ASP D 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.07   59.07     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CA  ASP A 196 "
           pdb=" CB  ASP A 196 "
           pdb=" CG  ASP A 196 "
           pdb=" OD1 ASP A 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.06   59.06     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CA  ASP E 196 "
           pdb=" CB  ASP E 196 "
           pdb=" CG  ASP E 196 "
           pdb=" OD1 ASP E 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.04   59.04     1      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 7552 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1250
       0.040 -    0.079: 454
       0.079 -    0.119: 173
       0.119 -    0.158: 63
       0.158 -    0.198: 15
  Chirality restraints: 1955
  Sorted by residual:
  chirality pdb=" CA BPHE C 247 "
            pdb=" N  BPHE C 247 "
            pdb=" C  BPHE C 247 "
            pdb=" CB BPHE C 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.81e-01
  chirality pdb=" CA BPHE A 247 "
            pdb=" N  BPHE A 247 "
            pdb=" C  BPHE A 247 "
            pdb=" CB BPHE A 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.68e-01
  chirality pdb=" CA BPHE E 247 "
            pdb=" N  BPHE E 247 "
            pdb=" C  BPHE E 247 "
            pdb=" CB BPHE E 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.67e-01
  ... (remaining 1952 not shown)

  Planarity restraints: 2250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB BPHE D 247 "   -0.018 2.00e-02 2.50e+03   1.70e-02 5.06e+00
        pdb=" CG BPHE D 247 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1BPHE D 247 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2BPHE D 247 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1BPHE D 247 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2BPHE D 247 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ BPHE D 247 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB BPHE B 247 "    0.018 2.00e-02 2.50e+03   1.70e-02 5.05e+00
        pdb=" CG BPHE B 247 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1BPHE B 247 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2BPHE B 247 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1BPHE B 247 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2BPHE B 247 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ BPHE B 247 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB BPHE A 247 "   -0.018 2.00e-02 2.50e+03   1.69e-02 5.01e+00
        pdb=" CG BPHE A 247 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1BPHE A 247 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2BPHE A 247 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1BPHE A 247 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2BPHE A 247 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ BPHE A 247 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2247 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3774
        2.83 -     3.35: 10914
        3.35 -     3.86: 20616
        3.86 -     4.38: 23780
        4.38 -     4.90: 41949
  Nonbonded interactions: 101033
  Sorted by model distance:
  nonbonded pdb=" O   SER C 221 "
            pdb=" OG  SER C 221 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   SER A 221 "
            pdb=" OG  SER A 221 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   SER B 221 "
            pdb=" OG  SER B 221 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   SER D 221 "
            pdb=" OG  SER D 221 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   SER E 221 "
            pdb=" OG  SER E 221 "
     model   vdw
     2.312 3.040
  ... (remaining 101028 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 11 through 246 or resid 248 through 317))
  selection = (chain 'B' and (resid 11 through 246 or resid 248 through 317))
  selection = (chain 'C' and (resid 11 through 246 or resid 248 through 317))
  selection = (chain 'D' and (resid 11 through 246 or resid 248 through 317))
  selection = (chain 'E' and (resid 11 through 246 or resid 248 through 317))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.260
  Find NCS groups from input model:        0.300
  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:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
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      :  0.004   0.051  12930  Z= 0.191
  Angle     :  0.720   8.198  17630  Z= 0.382
  Chirality :  0.052   0.198   1955
  Planarity :  0.005   0.033   2250
  Dihedral  : 13.594  70.556   4635
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.21), residues: 1540
  helix: -0.23 (0.19), residues: 550
  sheet:  1.15 (0.26), residues: 475
  loop : -2.16 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 123 
 TYR   0.009   0.001   TYR B 270 
 PHE   0.017   0.002   PHE B 236 
 TRP   0.010   0.001   TRP E 220 
 HIS   0.004   0.002   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (12930)
  covalent geometry    : angle       0.72039 (17630)
  hydrogen bonds       : bond        0.18078 (  615)
  hydrogen bonds       : angle       7.14861 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A  128 LEU cc_start: 0.8667 (mp) cc_final: 0.8454 (mp)
REVERT: B   95 PHE cc_start: 0.8170 (m-80) cc_final: 0.7709 (m-80)
REVERT: B  270 TYR cc_start: 0.8287 (m-80) cc_final: 0.8005 (m-80)
REVERT: D  251 ASN cc_start: 0.8044 (t0) cc_final: 0.7705 (t0)
REVERT: E  223 PHE cc_start: 0.8596 (m-80) cc_final: 0.8368 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0864
  time to fit residues: 30.0085
Evaluate side-chains
  186 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.0170
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
A 285 HIS
A 298 GLN
B 251 ASN
C 177 HIS
C 251 ASN
** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 177 HIS
E 285 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.150981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.123309 restraints weight = 31672.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.13
r_work: 0.3146 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12930  Z= 0.112
  Angle     :  0.520   5.751  17630  Z= 0.275
  Chirality :  0.046   0.154   1955
  Planarity :  0.004   0.028   2250
  Dihedral  :  4.299  15.878   1695
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.57 %
    Favored  : 94.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.22), residues: 1540
  helix:  0.80 (0.21), residues: 580
  sheet:  1.28 (0.26), residues: 450
  loop : -2.09 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 123 
 TYR   0.008   0.001   TYR D 245 
 PHE   0.012   0.001   PHE A 223 
 TRP   0.007   0.001   TRP C  43 
 HIS   0.003   0.001   HIS E 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12930)
  covalent geometry    : angle       0.52019 (17630)
  hydrogen bonds       : bond        0.03961 (  615)
  hydrogen bonds       : angle       4.58248 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 181
  time to evaluate  : 0.470 
Fit side-chains
REVERT: B   95 PHE cc_start: 0.7807 (m-80) cc_final: 0.7444 (m-80)
REVERT: B  177 HIS cc_start: 0.6989 (p-80) cc_final: 0.6743 (p-80)
REVERT: C  177 HIS cc_start: 0.6655 (p-80) cc_final: 0.6448 (p-80)
REVERT: C  270 TYR cc_start: 0.8511 (m-80) cc_final: 0.8234 (m-80)
REVERT: D  177 HIS cc_start: 0.6655 (p-80) cc_final: 0.6171 (p-80)
REVERT: D  251 ASN cc_start: 0.8542 (t0) cc_final: 0.8097 (t0)
REVERT: E  248 TYR cc_start: 0.8715 (t80) cc_final: 0.8454 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 183
  average time/residue: 0.0890
  time to fit residues: 25.8175
Evaluate side-chains
  159 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue  256 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 74 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 113 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 127 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 298 GLN
C 285 HIS
** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 298 GLN
E 177 HIS
E 285 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.145822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.119508 restraints weight = 29823.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.99
r_work: 0.3099 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12930  Z= 0.153
  Angle     :  0.558   5.946  17630  Z= 0.294
  Chirality :  0.047   0.163   1955
  Planarity :  0.004   0.031   2250
  Dihedral  :  4.439  17.158   1695
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  6.45 %
    Favored  : 91.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.22), residues: 1540
  helix:  1.26 (0.21), residues: 580
  sheet:  1.07 (0.25), residues: 450
  loop : -1.97 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 123 
 TYR   0.013   0.001   TYR D 248 
 PHE   0.012   0.002   PHE B 236 
 TRP   0.008   0.001   TRP D 161 
 HIS   0.005   0.001   HIS E 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (12930)
  covalent geometry    : angle       0.55801 (17630)
  hydrogen bonds       : bond        0.04444 (  615)
  hydrogen bonds       : angle       4.52797 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.8000 (t0) cc_final: 0.7758 (t0)
REVERT: A  140 LEU cc_start: 0.8574 (tp) cc_final: 0.8335 (tt)
REVERT: B  177 HIS cc_start: 0.7307 (p-80) cc_final: 0.7029 (p-80)
REVERT: B  255 ARG cc_start: 0.7179 (mmp-170) cc_final: 0.6878 (mmm-85)
REVERT: C  205 LEU cc_start: 0.8824 (tp) cc_final: 0.8589 (tp)
REVERT: D  155 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6789 (mm-30)
REVERT: D  177 HIS cc_start: 0.6994 (p-80) cc_final: 0.6382 (p-80)
REVERT: D  205 LEU cc_start: 0.8743 (tp) cc_final: 0.8528 (tp)
REVERT: D  251 ASN cc_start: 0.8550 (t0) cc_final: 0.8142 (t0)
REVERT: D  255 ARG cc_start: 0.7325 (mmp-170) cc_final: 0.6983 (mmm-85)
REVERT: E  140 LEU cc_start: 0.8449 (tp) cc_final: 0.8227 (tt)
REVERT: E  255 ARG cc_start: 0.7119 (mmp-170) cc_final: 0.6902 (mmm-85)
  outliers start: 25
  outliers final: 21
  residues processed: 188
  average time/residue: 0.1249
  time to fit residues: 33.4686
Evaluate side-chains
  191 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  250 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  250 SER
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  306 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 139 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   chunk 130 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 120 optimal weight:    0.0060
   chunk 104 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
B  42 GLN
B 251 ASN
C 177 HIS
C 285 HIS
D  42 GLN
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  42 GLN
E 177 HIS
E 251 ASN
E 285 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.149993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.123455 restraints weight = 31870.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.16
r_work: 0.3145 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12930  Z= 0.100
  Angle     :  0.484   5.481  17630  Z= 0.255
  Chirality :  0.045   0.146   1955
  Planarity :  0.003   0.029   2250
  Dihedral  :  4.041  15.587   1695
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  8.04 %
    Favored  : 90.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.22), residues: 1540
  helix:  1.53 (0.21), residues: 580
  sheet:  1.05 (0.25), residues: 455
  loop : -1.81 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  99 
 TYR   0.008   0.001   TYR D 245 
 PHE   0.010   0.001   PHE A 308 
 TRP   0.007   0.001   TRP C  43 
 HIS   0.002   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (12930)
  covalent geometry    : angle       0.48406 (17630)
  hydrogen bonds       : bond        0.03357 (  615)
  hydrogen bonds       : angle       4.11776 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 166
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.7894 (t0) cc_final: 0.7647 (t0)
REVERT: B   84 SER cc_start: 0.8605 (m) cc_final: 0.8295 (p)
REVERT: B  177 HIS cc_start: 0.7284 (p-80) cc_final: 0.7007 (p-80)
REVERT: C  177 HIS cc_start: 0.6783 (p-80) cc_final: 0.6182 (p-80)
REVERT: C  270 TYR cc_start: 0.8493 (m-80) cc_final: 0.8201 (m-80)
REVERT: D  155 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6741 (mm-30)
REVERT: D  177 HIS cc_start: 0.6950 (p-80) cc_final: 0.6332 (p-80)
REVERT: D  251 ASN cc_start: 0.8578 (t0) cc_final: 0.8222 (t0)
REVERT: E  140 LEU cc_start: 0.8462 (tp) cc_final: 0.8245 (tt)
REVERT: E  248 TYR cc_start: 0.8726 (t80) cc_final: 0.8523 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 176
  average time/residue: 0.0856
  time to fit residues: 24.2154
Evaluate side-chains
  176 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  250 SER
Chi-restraints excluded: chain E residue  256 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 120 optimal weight:    0.0980
   chunk 123 optimal weight:    7.9990
   chunk 121 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
C  42 GLN
C 285 HIS
** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 177 HIS
E 251 ASN
E 285 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.144241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.118301 restraints weight = 28759.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.01
r_work: 0.3075 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12930  Z= 0.174
  Angle     :  0.572   6.178  17630  Z= 0.301
  Chirality :  0.048   0.169   1955
  Planarity :  0.004   0.034   2250
  Dihedral  :  4.476  18.034   1695
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  8.33 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.22), residues: 1540
  helix:  1.88 (0.22), residues: 550
  sheet:  0.94 (0.25), residues: 470
  loop : -1.90 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 255 
 TYR   0.013   0.002   TYR A 248 
 PHE   0.012   0.002   PHE E  95 
 TRP   0.009   0.001   TRP D 161 
 HIS   0.004   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (12930)
  covalent geometry    : angle       0.57179 (17630)
  hydrogen bonds       : bond        0.04517 (  615)
  hydrogen bonds       : angle       4.43925 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.8102 (t0) cc_final: 0.7818 (t0)
REVERT: A  140 LEU cc_start: 0.8646 (tp) cc_final: 0.8421 (tt)
REVERT: B  255 ARG cc_start: 0.7360 (mmp-170) cc_final: 0.6914 (mmm-85)
REVERT: C  251 ASN cc_start: 0.8694 (t0) cc_final: 0.8460 (t0)
REVERT: D  177 HIS cc_start: 0.7013 (p-80) cc_final: 0.6341 (p-80)
REVERT: D  206 TRP cc_start: 0.8163 (m100) cc_final: 0.7960 (m100)
REVERT: D  251 ASN cc_start: 0.8590 (t0) cc_final: 0.8206 (t0)
REVERT: D  255 ARG cc_start: 0.7395 (mmp-170) cc_final: 0.7053 (mmm-85)
REVERT: E  255 ARG cc_start: 0.7191 (mmp-170) cc_final: 0.6925 (mmm-85)
  outliers start: 25
  outliers final: 24
  residues processed: 188
  average time/residue: 0.1293
  time to fit residues: 34.7239
Evaluate side-chains
  191 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  250 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  250 SER
Chi-restraints excluded: chain E residue  256 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 59 optimal weight:    0.3980
   chunk 22 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 177 HIS
E 251 ASN
E 285 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.148305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.123104 restraints weight = 26973.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.94
r_work: 0.3139 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12930  Z= 0.105
  Angle     :  0.493   5.628  17630  Z= 0.259
  Chirality :  0.046   0.146   1955
  Planarity :  0.003   0.031   2250
  Dihedral  :  4.093  16.269   1695
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.84 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.22), residues: 1540
  helix:  2.03 (0.22), residues: 550
  sheet:  0.75 (0.24), residues: 500
  loop : -1.77 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.007   0.001   TYR D 245 
 PHE   0.010   0.001   PHE E  95 
 TRP   0.007   0.001   TRP C  43 
 HIS   0.003   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (12930)
  covalent geometry    : angle       0.49255 (17630)
  hydrogen bonds       : bond        0.03446 (  615)
  hydrogen bonds       : angle       4.10620 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 167
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.7876 (t0) cc_final: 0.7589 (t0)
REVERT: A  140 LEU cc_start: 0.8606 (tp) cc_final: 0.8371 (tt)
REVERT: B   84 SER cc_start: 0.8619 (m) cc_final: 0.8307 (p)
REVERT: B  177 HIS cc_start: 0.7324 (p-80) cc_final: 0.7015 (p-80)
REVERT: B  255 ARG cc_start: 0.7259 (mmp-170) cc_final: 0.6905 (mmm-85)
REVERT: C  177 HIS cc_start: 0.6851 (p-80) cc_final: 0.6188 (p-80)
REVERT: C  251 ASN cc_start: 0.8727 (t0) cc_final: 0.8497 (t0)
REVERT: C  270 TYR cc_start: 0.8492 (m-80) cc_final: 0.8186 (m-80)
REVERT: D  177 HIS cc_start: 0.6948 (p-80) cc_final: 0.6268 (p-80)
REVERT: D  251 ASN cc_start: 0.8546 (t0) cc_final: 0.8213 (t0)
REVERT: D  255 ARG cc_start: 0.7412 (mmp-170) cc_final: 0.6994 (mmm-85)
REVERT: E  248 TYR cc_start: 0.8728 (t80) cc_final: 0.8489 (t80)
REVERT: E  255 ARG cc_start: 0.7145 (mmp-170) cc_final: 0.6884 (mmm-85)
  outliers start: 21
  outliers final: 20
  residues processed: 182
  average time/residue: 0.1234
  time to fit residues: 32.4448
Evaluate side-chains
  191 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 171
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  250 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  250 SER
Chi-restraints excluded: chain E residue  256 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9980
   chunk 132 optimal weight:    0.6980
   chunk 6 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
C 285 HIS
** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 177 HIS
E 251 ASN
E 285 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.147480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.120789 restraints weight = 31797.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.22
r_work: 0.3106 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12930  Z= 0.115
  Angle     :  0.502   5.679  17630  Z= 0.263
  Chirality :  0.046   0.151   1955
  Planarity :  0.004   0.032   2250
  Dihedral  :  4.100  16.337   1695
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.57 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.22), residues: 1540
  helix:  2.07 (0.22), residues: 550
  sheet:  0.75 (0.24), residues: 500
  loop : -1.73 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 163 
 TYR   0.008   0.001   TYR A 248 
 PHE   0.009   0.001   PHE A 308 
 TRP   0.005   0.001   TRP C  43 
 HIS   0.003   0.001   HIS E 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (12930)
  covalent geometry    : angle       0.50155 (17630)
  hydrogen bonds       : bond        0.03620 (  615)
  hydrogen bonds       : angle       4.11249 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.7762 (t0) cc_final: 0.7465 (t0)
REVERT: A  140 LEU cc_start: 0.8641 (tp) cc_final: 0.8423 (tt)
REVERT: B   84 SER cc_start: 0.8559 (m) cc_final: 0.8261 (p)
REVERT: B  177 HIS cc_start: 0.7333 (p-80) cc_final: 0.7010 (p-80)
REVERT: B  255 ARG cc_start: 0.7160 (mmp-170) cc_final: 0.6946 (mmm-85)
REVERT: C  251 ASN cc_start: 0.8620 (t0) cc_final: 0.8396 (t0)
REVERT: C  270 TYR cc_start: 0.8436 (m-80) cc_final: 0.8121 (m-80)
REVERT: D  177 HIS cc_start: 0.7005 (p-80) cc_final: 0.6262 (p-80)
REVERT: D  251 ASN cc_start: 0.8429 (t0) cc_final: 0.8086 (t0)
REVERT: D  255 ARG cc_start: 0.7395 (mmp-170) cc_final: 0.7013 (mmm-85)
REVERT: E  255 ARG cc_start: 0.7104 (mmp-170) cc_final: 0.6881 (mmm-85)
  outliers start: 23
  outliers final: 22
  residues processed: 182
  average time/residue: 0.1199
  time to fit residues: 31.7114
Evaluate side-chains
  181 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  250 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  250 SER
Chi-restraints excluded: chain E residue  256 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 99 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 138 optimal weight:    5.9990
   chunk 81 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
C 285 HIS
** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 177 HIS
E 251 ASN
E 285 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.144600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.117496 restraints weight = 24728.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.08
r_work: 0.3053 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12930  Z= 0.161
  Angle     :  0.557   5.991  17630  Z= 0.292
  Chirality :  0.048   0.162   1955
  Planarity :  0.004   0.034   2250
  Dihedral  :  4.409  17.085   1695
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  9.42 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.22), residues: 1540
  helix:  1.99 (0.22), residues: 550
  sheet:  0.81 (0.25), residues: 475
  loop : -1.72 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 163 
 TYR   0.013   0.002   TYR A 248 
 PHE   0.011   0.002   PHE C 304 
 TRP   0.008   0.001   TRP C 161 
 HIS   0.005   0.001   HIS C 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (12930)
  covalent geometry    : angle       0.55681 (17630)
  hydrogen bonds       : bond        0.04336 (  615)
  hydrogen bonds       : angle       4.34503 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.7923 (t0) cc_final: 0.7607 (t0)
REVERT: A  140 LEU cc_start: 0.8612 (tp) cc_final: 0.8397 (tt)
REVERT: B  255 ARG cc_start: 0.7258 (mmp-170) cc_final: 0.6897 (mmm-85)
REVERT: C  251 ASN cc_start: 0.8665 (t0) cc_final: 0.8418 (t0)
REVERT: C  255 ARG cc_start: 0.7069 (mmp-170) cc_final: 0.6855 (mmm-85)
REVERT: D  177 HIS cc_start: 0.7141 (p-80) cc_final: 0.6236 (p-80)
REVERT: D  251 ASN cc_start: 0.8531 (t0) cc_final: 0.8133 (t0)
REVERT: D  255 ARG cc_start: 0.7347 (mmp-170) cc_final: 0.6994 (mmm-85)
REVERT: E  255 ARG cc_start: 0.7159 (mmp-170) cc_final: 0.6891 (mmm-85)
  outliers start: 26
  outliers final: 24
  residues processed: 186
  average time/residue: 0.1448
  time to fit residues: 36.9759
Evaluate side-chains
  186 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  250 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  250 SER
Chi-restraints excluded: chain E residue  256 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 120 optimal weight:    7.9990
   chunk 134 optimal weight:    6.9990
   chunk 113 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
C 285 HIS
D 251 ASN
** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 177 HIS
E 251 ASN
E 285 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.141197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 105)---------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.114771 restraints weight = 30491.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.12
r_work: 0.3048 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  12930  Z= 0.232
  Angle     :  0.640   6.457  17630  Z= 0.337
  Chirality :  0.050   0.178   1955
  Planarity :  0.004   0.036   2250
  Dihedral  :  4.857  19.291   1695
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  9.57 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.22), residues: 1540
  helix:  1.71 (0.22), residues: 550
  sheet:  0.59 (0.25), residues: 470
  loop : -1.94 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 163 
 TYR   0.019   0.002   TYR E 248 
 PHE   0.019   0.002   PHE E  95 
 TRP   0.012   0.002   TRP C 161 
 HIS   0.005   0.001   HIS E 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 (12930)
  covalent geometry    : angle       0.63993 (17630)
  hydrogen bonds       : bond        0.05109 (  615)
  hydrogen bonds       : angle       4.62702 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.8150 (t0) cc_final: 0.7843 (t0)
REVERT: A  140 LEU cc_start: 0.8653 (tp) cc_final: 0.8416 (tt)
REVERT: B  255 ARG cc_start: 0.7352 (mmp-170) cc_final: 0.6959 (mmm-85)
REVERT: C  251 ASN cc_start: 0.8730 (t0) cc_final: 0.8499 (t0)
REVERT: D  177 HIS cc_start: 0.7242 (p-80) cc_final: 0.6422 (p-80)
REVERT: D  251 ASN cc_start: 0.8655 (t0) cc_final: 0.8163 (t0)
REVERT: D  255 ARG cc_start: 0.7396 (mmp-170) cc_final: 0.7028 (mmm-85)
REVERT: E  255 ARG cc_start: 0.7277 (mmp-170) cc_final: 0.6942 (mmm-85)
  outliers start: 25
  outliers final: 24
  residues processed: 179
  average time/residue: 0.1353
  time to fit residues: 33.9777
Evaluate side-chains
  179 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  250 SER
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  250 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  250 SER
Chi-restraints excluded: chain E residue  256 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 80 optimal weight:    0.7980
   chunk 17 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0570
   chunk 109 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 135 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0170
   chunk 53 optimal weight:    0.9980
   chunk 73 optimal weight:    0.1980
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
C 251 ASN
C 285 HIS
D 251 ASN
E 177 HIS
E 251 ASN
E 285 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.148751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.121604 restraints weight = 32880.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.39
r_work: 0.3092 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12930  Z= 0.099
  Angle     :  0.494   5.434  17630  Z= 0.261
  Chirality :  0.045   0.139   1955
  Planarity :  0.004   0.031   2250
  Dihedral  :  4.174  15.496   1695
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 10.14 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.22), residues: 1540
  helix:  2.05 (0.22), residues: 550
  sheet:  0.75 (0.25), residues: 475
  loop : -1.69 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 163 
 TYR   0.007   0.001   TYR D 245 
 PHE   0.010   0.001   PHE E  95 
 TRP   0.010   0.001   TRP C  43 
 HIS   0.003   0.001   HIS C 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (12930)
  covalent geometry    : angle       0.49372 (17630)
  hydrogen bonds       : bond        0.03317 (  615)
  hydrogen bonds       : angle       4.06930 ( 2015)

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

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

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3080 Ramachandran restraints generated.
    1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.7729 (t0) cc_final: 0.7442 (t0)
REVERT: A  140 LEU cc_start: 0.8602 (tp) cc_final: 0.8350 (tt)
REVERT: B   84 SER cc_start: 0.8596 (m) cc_final: 0.8331 (p)
REVERT: B  255 ARG cc_start: 0.7231 (mmp-170) cc_final: 0.6863 (mmm-85)
REVERT: C  177 HIS cc_start: 0.6814 (p-80) cc_final: 0.6150 (p-80)
REVERT: C  255 ARG cc_start: 0.7092 (mmp-170) cc_final: 0.6822 (mmm-85)
REVERT: C  270 TYR cc_start: 0.8458 (m-80) cc_final: 0.8158 (m-80)
REVERT: D  177 HIS cc_start: 0.7190 (p-80) cc_final: 0.6415 (p-80)
REVERT: D  251 ASN cc_start: 0.8531 (t0) cc_final: 0.8159 (t0)
REVERT: E  206 TRP cc_start: 0.7995 (m100) cc_final: 0.7781 (m100)
  outliers start: 16
  outliers final: 15
  residues processed: 174
  average time/residue: 0.1220
  time to fit residues: 30.5915
Evaluate side-chains
  175 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue   73 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  250 SER
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  134 SER
Chi-restraints excluded: chain E residue  256 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 134 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 109 optimal weight:    0.7980
   chunk 14 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 118 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 177 HIS
E 251 ASN
E 285 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.145745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.117743 restraints weight = 30568.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.50
r_work: 0.3039 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12930  Z= 0.129
  Angle     :  0.519   5.844  17630  Z= 0.273
  Chirality :  0.046   0.155   1955
  Planarity :  0.004   0.032   2250
  Dihedral  :  4.232  16.123   1695
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.29 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.22), residues: 1540
  helix:  2.08 (0.22), residues: 550
  sheet:  0.57 (0.25), residues: 495
  loop : -1.79 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 163 
 TYR   0.010   0.001   TYR A 248 
 PHE   0.010   0.001   PHE A 308 
 TRP   0.006   0.001   TRP E 206 
 HIS   0.003   0.001   HIS E 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12930)
  covalent geometry    : angle       0.51920 (17630)
  hydrogen bonds       : bond        0.03758 (  615)
  hydrogen bonds       : angle       4.17534 ( 2015)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3130.91 seconds
wall clock time: 54 minutes 17.08 seconds (3257.08 seconds total)