Starting phenix.real_space_refine
on Sat Aug 23 11:07:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8go8_34173/08_2025/8go8_34173.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8go8_34173/08_2025/8go8_34173.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8go8_34173/08_2025/8go8_34173.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8go8_34173/08_2025/8go8_34173.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8go8_34173/08_2025/8go8_34173.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8go8_34173/08_2025/8go8_34173.map"
  }
  resolution = 3.41
  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=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 74 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      38      5.16       5
     C    7280      2.51       5
     N    1938      2.21       5
     O    2239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11505
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2803
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 49
    Chain: "V"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 90
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'TPO:plan-1': 3}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2808
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 42
    Chain: "U"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 90
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'TPO:plan-1': 3}
          Unresolved non-hydrogen planarities: 3
    Chain: "H"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1496
          Classifications: {'peptide': 204}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "I"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1496
          Classifications: {'peptide': 204}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "L"
      Number of atoms: 1363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1363
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "M"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1359
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 26
  Time building chain proxies: 2.60, per 1000 atoms: 0.23
  Number of scatterers: 11505
  At special positions: 0
  Unit cell: (112.238, 201.413, 99.9375, 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      38     16.00
     P      10     15.00
     O    2239      8.00
     N    1938      7.00
     C    7280      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  25 " - pdb=" SG  CYS I  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 150 " - pdb=" SG  CYS I 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  24 " - pdb=" SG  CYS M  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 427.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2860

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 32 sheets defined
      5.3% alpha, 46.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 109
      removed outlier: 3.849A  pdb=" N   ARG A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 161
      No H-bonds generated for 'chain 'A' and resid 159 through 161'
    Processing helix  chain 'B' and resid 98 through 109
      removed outlier: 3.850A  pdb=" N   ARG B 103 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'H' and resid 166 through 168
      No H-bonds generated for 'chain 'H' and resid 166 through 168'
    Processing helix  chain 'I' and resid 90 through 94
    Processing helix  chain 'I' and resid 166 through 168
      No H-bonds generated for 'chain 'I' and resid 166 through 168'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.059A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 123 through 129
      removed outlier: 4.241A  pdb=" N   LYS L 127 " --> pdb=" O   ASP L 123 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 188
    Processing helix  chain 'M' and resid 80 through 84
      removed outlier: 4.060A  pdb=" N   PHE M  84 " --> pdb=" O   PRO M  81 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 123 through 129
      removed outlier: 4.241A  pdb=" N   LYS M 127 " --> pdb=" O   ASP M 123 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 184 through 188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28
    Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75
      removed outlier: 3.830A  pdb=" N   ALA A  60 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP A 143 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 85
      removed outlier: 6.511A  pdb=" N   CYS A  59 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   ASN A  83 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL A  55 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLN A  85 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   VAL A  53 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA A  60 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP A 143 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   CYS A 140 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 189
    Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 209
      removed outlier: 3.560A  pdb=" N   PHE A 349 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   LEU A 351 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 9.344A  pdb=" N   VAL A 319 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLY A 316 " --> pdb=" O   CYS A 242 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS A 230 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   GLN A 237 " --> pdb=" O   PRO A 252 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ALA A 239 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   LYS A 250 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   ILE A 241 " --> pdb=" O   GLN A 248 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   GLN A 248 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 117
    Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28
    Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 75
      removed outlier: 3.830A  pdb=" N   ALA B  60 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP B 143 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 78 through 85
      removed outlier: 6.510A  pdb=" N   CYS B  59 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ASN B  83 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL B  55 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLN B  85 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   VAL B  53 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA B  60 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP B 143 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   CYS B 140 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 183 through 189
    Processing sheet with id=AB3, first strand: chain 'B' and resid 207 through 209
      removed outlier: 3.560A  pdb=" N   PHE B 349 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 9.344A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLY B 316 " --> pdb=" O   CYS B 242 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LYS B 230 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   GLN B 237 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ALA B 239 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   LYS B 250 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ILE B 241 " --> pdb=" O   GLN B 248 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   GLN B 248 " --> pdb=" O   ILE B 241 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 6 through 10
      removed outlier: 3.868A  pdb=" N   VAL H   8 " --> pdb=" O   ALA H  26 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 14 through 15
      removed outlier: 8.804A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 14 through 15
      removed outlier: 3.770A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 134
      removed outlier: 4.014A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 130 through 134
      removed outlier: 4.014A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 161 through 164
    Processing sheet with id=AC1, first strand: chain 'I' and resid 6 through 10
      removed outlier: 3.868A  pdb=" N   VAL I   8 " --> pdb=" O   ALA I  26 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'I' and resid 14 through 15
      removed outlier: 8.803A  pdb=" N   SER I  35 " --> pdb=" O   SER I  55 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   SER I  55 " --> pdb=" O   SER I  35 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ILE I  37 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   SER I  53 " --> pdb=" O   ILE I  37 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   TRP I  39 " --> pdb=" O   VAL I  51 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'I' and resid 14 through 15
      removed outlier: 3.771A  pdb=" N   TYR I 112 " --> pdb=" O   ARG I 101 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'I' and resid 130 through 134
      removed outlier: 4.014A  pdb=" N   GLY I 149 " --> pdb=" O   LEU I 134 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   TYR I 186 " --> pdb=" O   ASP I 154 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'I' and resid 130 through 134
      removed outlier: 4.014A  pdb=" N   GLY I 149 " --> pdb=" O   LEU I 134 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   TYR I 186 " --> pdb=" O   ASP I 154 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'I' and resid 161 through 164
    Processing sheet with id=AC7, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AC8, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.529A  pdb=" N   GLU L 106 " --> pdb=" O   LEU L  12 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.529A  pdb=" N   GLU L 106 " --> pdb=" O   LEU L  12 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'L' and resid 115 through 119
      removed outlier: 3.636A  pdb=" N   SER L 115 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   VAL L 134 " --> pdb=" O   PHE L 119 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER L 177 " --> pdb=" O   SER L 163 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'M' and resid 5 through 8
    Processing sheet with id=AD3, first strand: chain 'M' and resid 11 through 13
      removed outlier: 3.528A  pdb=" N   GLU M 106 " --> pdb=" O   LEU M  12 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL M  34 " --> pdb=" O   TYR M  50 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   TYR M  50 " --> pdb=" O   VAL M  34 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   TRP M  36 " --> pdb=" O   LEU M  48 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'M' and resid 11 through 13
      removed outlier: 3.528A  pdb=" N   GLU M 106 " --> pdb=" O   LEU M  12 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR M  98 " --> pdb=" O   GLN M  91 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'M' and resid 115 through 119
      removed outlier: 3.635A  pdb=" N   SER M 115 " --> pdb=" O   ASN M 138 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL M 134 " --> pdb=" O   PHE M 119 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   TYR M 174 " --> pdb=" O   ASN M 139 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER M 177 " --> pdb=" O   SER M 163 " (cutoff:3.500A)

    480 hydrogen bonds defined for protein.
    1254 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3708
        1.34 -     1.46: 2688
        1.46 -     1.58: 5291
        1.58 -     1.69: 34
        1.69 -     1.81: 48
  Bond restraints: 11769
  Sorted by residual:
  bond pdb=" OG1 TPO U 342 "
       pdb=" P   TPO U 342 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" OG1 TPO U 336 "
       pdb=" P   TPO U 336 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" OG1 TPO V 342 "
       pdb=" P   TPO V 342 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.93e+01
  bond pdb=" OG1 TPO V 339 "
       pdb=" P   TPO V 339 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.93e+01
  bond pdb=" OG1 TPO V 336 "
       pdb=" P   TPO V 336 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.92e+01
  ... (remaining 11764 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 15894
        2.48 -     4.96: 131
        4.96 -     7.44: 18
        7.44 -     9.92: 6
        9.92 -    12.40: 8
  Bond angle restraints: 16057
  Sorted by residual:
  angle pdb=" CB  TPO V 339 "
        pdb=" OG1 TPO V 339 "
        pdb=" P   TPO V 339 "
      ideal   model   delta    sigma   weight residual
     119.31  106.91   12.40 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" CB  TPO U 339 "
        pdb=" OG1 TPO U 339 "
        pdb=" P   TPO U 339 "
      ideal   model   delta    sigma   weight residual
     119.31  106.94   12.37 3.00e+00 1.11e-01 1.70e+01
  angle pdb=" CB  TPO U 342 "
        pdb=" OG1 TPO U 342 "
        pdb=" P   TPO U 342 "
      ideal   model   delta    sigma   weight residual
     119.31  107.10   12.21 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" CB  TPO V 336 "
        pdb=" OG1 TPO V 336 "
        pdb=" P   TPO V 336 "
      ideal   model   delta    sigma   weight residual
     119.31  107.10   12.21 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" CB  TPO U 336 "
        pdb=" OG1 TPO U 336 "
        pdb=" P   TPO U 336 "
      ideal   model   delta    sigma   weight residual
     119.31  107.12   12.19 3.00e+00 1.11e-01 1.65e+01
  ... (remaining 16052 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 6481
       16.85 -    33.70: 458
       33.70 -    50.54: 104
       50.54 -    67.39: 14
       67.39 -    84.24: 12
  Dihedral angle restraints: 7069
    sinusoidal: 2631
      harmonic: 4438
  Sorted by residual:
  dihedral pdb=" CB  LYS A 226 "
           pdb=" CG  LYS A 226 "
           pdb=" CD  LYS A 226 "
           pdb=" CE  LYS A 226 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.52  -56.52     3      1.50e+01 4.44e-03 9.40e+00
  dihedral pdb=" CB  LYS B 226 "
           pdb=" CG  LYS B 226 "
           pdb=" CD  LYS B 226 "
           pdb=" CE  LYS B 226 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.45  -56.45     3      1.50e+01 4.44e-03 9.40e+00
  dihedral pdb=" CG  ARG B  65 "
           pdb=" CD  ARG B  65 "
           pdb=" NE  ARG B  65 "
           pdb=" CZ  ARG B  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.48   40.52     2      1.50e+01 4.44e-03 9.00e+00
  ... (remaining 7066 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1026
       0.026 -    0.052: 516
       0.052 -    0.079: 102
       0.079 -    0.105: 119
       0.105 -    0.131: 73
  Chirality restraints: 1836
  Sorted by residual:
  chirality pdb=" CA  VAL L  95 "
            pdb=" N   VAL L  95 "
            pdb=" C   VAL L  95 "
            pdb=" CB  VAL L  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CA  PHE U 335 "
            pdb=" N   PHE U 335 "
            pdb=" C   PHE U 335 "
            pdb=" CB  PHE U 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  ILE B 233 "
            pdb=" N   ILE B 233 "
            pdb=" C   ILE B 233 "
            pdb=" CB  ILE B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 1833 not shown)

  Planarity restraints: 2058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 158 "    0.022 5.00e-02 4.00e+02   3.36e-02 1.80e+00
        pdb=" N   PRO H 159 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO H 159 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO H 159 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 358 "    0.006 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   GLU B 358 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   GLU B 358 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLU B 359 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU I 158 "   -0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO I 159 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO I 159 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO I 159 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 2055 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2149
        2.78 -     3.31: 9782
        3.31 -     3.84: 17768
        3.84 -     4.37: 20063
        4.37 -     4.90: 37084
  Nonbonded interactions: 86846
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN L 125 "
            pdb=" O   THR L 130 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NE2 GLN M 125 "
            pdb=" O   THR M 130 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   ALA B 301 "
            pdb=" OH  TYR B 321 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   ALA A 301 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   ALA B 263 "
            pdb=" OG  SER B 266 "
     model   vdw
     2.290 3.040
  ... (remaining 86841 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 7 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 68 or (resid 69 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 135 through 368))
  selection = (chain 'B' and (resid 7 through 176 or (resid 177 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 178 through 311 or (resid 312 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 313 through 358 or (resid 35 \ 
9 and (name N or name CA or name C or name O or name CB )) or resid 360 through  \ 
368))
}
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 5 through 190))
  selection = chain 'M'
}
ncs_group {
  reference = chain 'U'
  selection = chain 'V'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.65 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.580
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
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   0.109  11775  Z= 0.213
  Angle     :  0.607  12.405  16069  Z= 0.270
  Chirality :  0.042   0.131   1836
  Planarity :  0.003   0.034   2058
  Dihedral  : 12.950  84.237   4191
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  1.03 (0.23), residues: 1478
  helix:  0.56 (0.84), residues: 34
  sheet:  1.29 (0.21), residues: 644
  loop :  0.25 (0.23), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 331 
 TYR   0.008   0.001   TYR M  50 
 PHE   0.008   0.001   PHE V 335 
 TRP   0.008   0.001   TRP H  39 
 HIS   0.002   0.000   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (11769)
  covalent geometry    : angle       0.60672 (16057)
  SS BOND              : bond        0.00158 (    6)
  SS BOND              : angle       0.19994 (   12)
  hydrogen bonds       : bond        0.24428 (  424)
  hydrogen bonds       : angle       9.52906 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8525 (ttmt)
REVERT: A  294 LYS cc_start: 0.8092 (mttp) cc_final: 0.7793 (mtpp)
REVERT: B  147 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8411 (ttmt)
REVERT: B  294 LYS cc_start: 0.8154 (mttp) cc_final: 0.7880 (mtpp)
REVERT: H   86 MET cc_start: 0.7239 (mtm) cc_final: 0.7013 (mtp)
REVERT: H  210 HIS cc_start: 0.5789 (t-90) cc_final: 0.5149 (t-90)
REVERT: I  210 HIS cc_start: 0.6173 (t-90) cc_final: 0.5274 (t-90)
REVERT: L  161 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7373 (mm110)
REVERT: M    5 MET cc_start: 0.8295 (mmm) cc_final: 0.8080 (mmt)
REVERT: M   82 GLU cc_start: 0.7357 (pt0) cc_final: 0.7045 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1399
  time to fit residues: 37.7491
Evaluate side-chains
  127 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
I   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.166291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.115651 restraints weight = 16204.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 3.26
r_work: 0.3183 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11775  Z= 0.160
  Angle     :  0.585  14.597  16069  Z= 0.296
  Chirality :  0.045   0.143   1836
  Planarity :  0.004   0.040   2058
  Dihedral  :  4.356  39.899   1658
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  7.55 %
    Favored  : 91.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.98 (0.23), residues: 1478
  helix:  0.55 (0.69), residues: 50
  sheet:  1.07 (0.20), residues: 708
  loop :  0.32 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 312 
 TYR   0.025   0.002   TYR H 155 
 PHE   0.016   0.002   PHE M 117 
 TRP   0.021   0.002   TRP H 164 
 HIS   0.004   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (11769)
  covalent geometry    : angle       0.58476 (16057)
  SS BOND              : bond        0.00456 (    6)
  SS BOND              : angle       0.79491 (   12)
  hydrogen bonds       : bond        0.04379 (  424)
  hydrogen bonds       : angle       6.25324 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.7298 (mt) cc_final: 0.7065 (mp)
REVERT: A  161 ARG cc_start: 0.7479 (ptt-90) cc_final: 0.6738 (ptp90)
REVERT: A  294 LYS cc_start: 0.8361 (mttp) cc_final: 0.8155 (mtpp)
REVERT: A  352 MET cc_start: 0.8576 (mtm) cc_final: 0.8345 (mtm)
REVERT: B  104 LEU cc_start: 0.7319 (mt) cc_final: 0.7107 (mp)
REVERT: B  294 LYS cc_start: 0.8422 (mttp) cc_final: 0.8143 (mtpp)
REVERT: B  295 HIS cc_start: 0.8660 (m-70) cc_final: 0.8418 (m-70)
REVERT: B  352 MET cc_start: 0.8495 (mtm) cc_final: 0.8199 (mtm)
REVERT: H   92 GLU cc_start: 0.8055 (pm20) cc_final: 0.7831 (pm20)
REVERT: H  164 TRP cc_start: 0.6368 (m100) cc_final: 0.6166 (m100)
REVERT: H  210 HIS cc_start: 0.5726 (t-90) cc_final: 0.5281 (t-90)
REVERT: I   92 GLU cc_start: 0.8095 (pm20) cc_final: 0.7856 (pm20)
REVERT: I  210 HIS cc_start: 0.5687 (t-90) cc_final: 0.5284 (t-90)
REVERT: L   82 GLU cc_start: 0.7855 (pt0) cc_final: 0.7173 (pm20)
REVERT: L  119 PHE cc_start: 0.5362 (m-80) cc_final: 0.5047 (m-80)
REVERT: L  161 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7398 (mm110)
REVERT: M    5 MET cc_start: 0.8853 (mmm) cc_final: 0.8461 (mmt)
REVERT: M   82 GLU cc_start: 0.7843 (pt0) cc_final: 0.7175 (pm20)
REVERT: M  119 PHE cc_start: 0.5485 (m-80) cc_final: 0.5194 (m-80)
REVERT: M  161 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7519 (mm110)
  outliers start: 17
  outliers final: 8
  residues processed: 144
  average time/residue: 0.1248
  time to fit residues: 25.0916
Evaluate side-chains
  127 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain L residue  177 SER
Chi-restraints excluded: chain M residue  107 ILE
Chi-restraints excluded: chain M residue  177 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 145 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 127 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
L 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.163784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.111080 restraints weight = 16467.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.94
r_work: 0.3191 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11775  Z= 0.196
  Angle     :  0.583  14.151  16069  Z= 0.296
  Chirality :  0.045   0.153   1836
  Planarity :  0.004   0.034   2058
  Dihedral  :  4.519  37.700   1658
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.43 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.83 (0.22), residues: 1478
  helix:  0.60 (0.78), residues: 48
  sheet:  1.09 (0.20), residues: 696
  loop :  0.10 (0.24), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 312 
 TYR   0.026   0.002   TYR A 249 
 PHE   0.017   0.002   PHE B 277 
 TRP   0.019   0.002   TRP I 164 
 HIS   0.003   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (11769)
  covalent geometry    : angle       0.58303 (16057)
  SS BOND              : bond        0.00423 (    6)
  SS BOND              : angle       0.59171 (   12)
  hydrogen bonds       : bond        0.04119 (  424)
  hydrogen bonds       : angle       5.67211 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ARG cc_start: 0.7492 (ptt-90) cc_final: 0.6606 (ptp90)
REVERT: A  195 LYS cc_start: 0.8564 (mmmt) cc_final: 0.7659 (mtmt)
REVERT: A  206 GLU cc_start: 0.8075 (tt0) cc_final: 0.7857 (tt0)
REVERT: A  294 LYS cc_start: 0.8512 (mttp) cc_final: 0.8309 (mtpp)
REVERT: B  144 TYR cc_start: 0.9064 (m-80) cc_final: 0.8640 (m-80)
REVERT: B  195 LYS cc_start: 0.8468 (mmmt) cc_final: 0.7586 (mtmt)
REVERT: B  206 GLU cc_start: 0.8042 (tt0) cc_final: 0.7822 (tt0)
REVERT: B  294 LYS cc_start: 0.8548 (mttp) cc_final: 0.8331 (mtpp)
REVERT: H  210 HIS cc_start: 0.5815 (t-170) cc_final: 0.5334 (t-90)
REVERT: I  210 HIS cc_start: 0.5813 (t-170) cc_final: 0.5198 (t-90)
REVERT: L   82 GLU cc_start: 0.7866 (pt0) cc_final: 0.7189 (pm20)
REVERT: L  119 PHE cc_start: 0.5609 (m-80) cc_final: 0.5165 (m-80)
REVERT: L  161 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7357 (mm110)
REVERT: M    5 MET cc_start: 0.8647 (mmm) cc_final: 0.8345 (mmm)
REVERT: M   82 GLU cc_start: 0.7867 (pt0) cc_final: 0.7132 (pm20)
REVERT: M  119 PHE cc_start: 0.5520 (m-80) cc_final: 0.5068 (m-80)
REVERT: M  161 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7647 (mm110)
  outliers start: 12
  outliers final: 7
  residues processed: 132
  average time/residue: 0.1380
  time to fit residues: 24.9202
Evaluate side-chains
  116 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain M residue  135 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 42 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 120 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0010
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.163830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.113562 restraints weight = 16111.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 3.17
r_work: 0.3212 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11775  Z= 0.109
  Angle     :  0.518  14.130  16069  Z= 0.256
  Chirality :  0.043   0.132   1836
  Planarity :  0.003   0.033   2058
  Dihedral  :  4.366  41.467   1658
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.01 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.90 (0.22), residues: 1478
  helix:  0.73 (0.76), residues: 48
  sheet:  1.04 (0.19), residues: 716
  loop :  0.22 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 312 
 TYR   0.012   0.001   TYR B 249 
 PHE   0.011   0.001   PHE A  75 
 TRP   0.020   0.001   TRP H 164 
 HIS   0.001   0.000   HIS I 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (11769)
  covalent geometry    : angle       0.51774 (16057)
  SS BOND              : bond        0.00368 (    6)
  SS BOND              : angle       0.52764 (   12)
  hydrogen bonds       : bond        0.03209 (  424)
  hydrogen bonds       : angle       5.17742 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TYR cc_start: 0.9013 (m-80) cc_final: 0.8628 (m-80)
REVERT: A  161 ARG cc_start: 0.7443 (ptt-90) cc_final: 0.6560 (ptp90)
REVERT: A  195 LYS cc_start: 0.8505 (mmmt) cc_final: 0.7616 (mtmt)
REVERT: A  294 LYS cc_start: 0.8491 (mttp) cc_final: 0.8247 (mtpp)
REVERT: B  144 TYR cc_start: 0.9068 (m-80) cc_final: 0.8744 (m-80)
REVERT: B  195 LYS cc_start: 0.8508 (mmmt) cc_final: 0.7620 (mtmt)
REVERT: B  294 LYS cc_start: 0.8452 (mttp) cc_final: 0.8201 (mtpp)
REVERT: H   92 GLU cc_start: 0.8069 (pm20) cc_final: 0.7857 (pm20)
REVERT: H  210 HIS cc_start: 0.5778 (t-170) cc_final: 0.5263 (t-90)
REVERT: I  210 HIS cc_start: 0.5752 (t-170) cc_final: 0.5276 (t-90)
REVERT: L   82 GLU cc_start: 0.7910 (pt0) cc_final: 0.7144 (pm20)
REVERT: L  119 PHE cc_start: 0.5655 (m-80) cc_final: 0.5100 (m-80)
REVERT: L  161 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7452 (mm110)
REVERT: L  184 LYS cc_start: 0.7217 (mmtt) cc_final: 0.7010 (mmtt)
REVERT: M   82 GLU cc_start: 0.7899 (pt0) cc_final: 0.7141 (pm20)
REVERT: M  117 PHE cc_start: 0.6394 (m-10) cc_final: 0.6191 (m-10)
REVERT: M  119 PHE cc_start: 0.5556 (m-80) cc_final: 0.4992 (m-80)
  outliers start: 15
  outliers final: 6
  residues processed: 130
  average time/residue: 0.1222
  time to fit residues: 22.7064
Evaluate side-chains
  122 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  176 LEU
Chi-restraints excluded: chain M residue  107 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 137 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 135 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
B  15 ASN
B 181 GLN
I  85 GLN
** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.159381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108524 restraints weight = 16293.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.80
r_work: 0.3152 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.088  11775  Z= 0.389
  Angle     :  0.721  13.462  16069  Z= 0.373
  Chirality :  0.051   0.166   1836
  Planarity :  0.005   0.034   2058
  Dihedral  :  5.031  39.371   1658
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.47 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.33 (0.22), residues: 1478
  helix:  0.56 (0.76), residues: 44
  sheet:  0.70 (0.19), residues: 696
  loop : -0.19 (0.23), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 282 
 TYR   0.028   0.003   TYR M  92 
 PHE   0.019   0.003   PHE I 105 
 TRP   0.019   0.003   TRP I  50 
 HIS   0.008   0.002   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00939 (11769)
  covalent geometry    : angle       0.72132 (16057)
  SS BOND              : bond        0.00698 (    6)
  SS BOND              : angle       0.67451 (   12)
  hydrogen bonds       : bond        0.04373 (  424)
  hydrogen bonds       : angle       5.83228 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7185 (pt)
REVERT: A  161 ARG cc_start: 0.7467 (ptt-90) cc_final: 0.6644 (ptp90)
REVERT: A  195 LYS cc_start: 0.8598 (mmmt) cc_final: 0.7760 (mtmt)
REVERT: A  245 ASN cc_start: 0.8426 (m-40) cc_final: 0.8186 (p0)
REVERT: B   33 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7185 (pt)
REVERT: B  161 ARG cc_start: 0.7478 (ptt-90) cc_final: 0.6638 (ptp90)
REVERT: B  195 LYS cc_start: 0.8608 (mmmt) cc_final: 0.7768 (mtmt)
REVERT: B  245 ASN cc_start: 0.8368 (m-40) cc_final: 0.8131 (p0)
REVERT: H   92 GLU cc_start: 0.8078 (pm20) cc_final: 0.7846 (pm20)
REVERT: H  210 HIS cc_start: 0.6127 (t-170) cc_final: 0.5583 (t-90)
REVERT: L   19 ARG cc_start: 0.8950 (ttt-90) cc_final: 0.8706 (mtp-110)
REVERT: L   82 GLU cc_start: 0.7937 (pt0) cc_final: 0.7177 (pm20)
REVERT: L  119 PHE cc_start: 0.5477 (m-80) cc_final: 0.4831 (m-80)
REVERT: L  161 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7352 (mm110)
REVERT: M   82 GLU cc_start: 0.7994 (pt0) cc_final: 0.7189 (pm20)
REVERT: M  119 PHE cc_start: 0.5511 (m-80) cc_final: 0.4835 (m-80)
  outliers start: 22
  outliers final: 9
  residues processed: 132
  average time/residue: 0.1296
  time to fit residues: 24.2701
Evaluate side-chains
  115 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue  149 TRP
Chi-restraints excluded: chain M residue   21 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 133 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 138 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.4980
   chunk 121 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.162915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.110646 restraints weight = 16332.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.91
r_work: 0.3187 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11775  Z= 0.143
  Angle     :  0.549  13.341  16069  Z= 0.277
  Chirality :  0.044   0.137   1836
  Planarity :  0.003   0.032   2058
  Dihedral  :  4.657  42.403   1658
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.52 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.42 (0.22), residues: 1478
  helix:  0.92 (0.74), residues: 48
  sheet:  0.74 (0.20), residues: 704
  loop : -0.15 (0.24), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 312 
 TYR   0.012   0.001   TYR M  92 
 PHE   0.012   0.001   PHE A 349 
 TRP   0.011   0.001   TRP H 164 
 HIS   0.002   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (11769)
  covalent geometry    : angle       0.54856 (16057)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       0.62642 (   12)
  hydrogen bonds       : bond        0.03393 (  424)
  hydrogen bonds       : angle       5.35211 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7164 (pt)
REVERT: A  161 ARG cc_start: 0.7392 (ptt-90) cc_final: 0.6547 (ptp90)
REVERT: A  195 LYS cc_start: 0.8561 (mmmt) cc_final: 0.7772 (mtmt)
REVERT: A  245 ASN cc_start: 0.8667 (m-40) cc_final: 0.8173 (p0)
REVERT: B   33 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7160 (pt)
REVERT: B  195 LYS cc_start: 0.8584 (mmmt) cc_final: 0.7806 (mtmt)
REVERT: B  245 ASN cc_start: 0.8414 (m-40) cc_final: 0.8160 (p0)
REVERT: H   92 GLU cc_start: 0.8075 (pm20) cc_final: 0.7837 (pm20)
REVERT: H  210 HIS cc_start: 0.6010 (t-170) cc_final: 0.5460 (t-90)
REVERT: L   82 GLU cc_start: 0.7931 (pt0) cc_final: 0.7177 (pm20)
REVERT: L  117 PHE cc_start: 0.6679 (m-10) cc_final: 0.6439 (m-10)
REVERT: L  119 PHE cc_start: 0.5437 (m-80) cc_final: 0.4736 (m-80)
REVERT: L  161 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7341 (mm110)
REVERT: M   82 GLU cc_start: 0.7909 (pt0) cc_final: 0.7168 (pm20)
REVERT: M  117 PHE cc_start: 0.6506 (m-10) cc_final: 0.6255 (m-10)
REVERT: M  119 PHE cc_start: 0.5476 (m-80) cc_final: 0.4793 (m-80)
  outliers start: 18
  outliers final: 9
  residues processed: 123
  average time/residue: 0.1231
  time to fit residues: 21.4327
Evaluate side-chains
  118 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  149 TRP
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   79 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 73 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.161389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.108870 restraints weight = 16348.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.91
r_work: 0.3162 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074  11775  Z= 0.243
  Angle     :  0.600  13.121  16069  Z= 0.306
  Chirality :  0.046   0.148   1836
  Planarity :  0.004   0.032   2058
  Dihedral  :  4.741  41.527   1658
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.50 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.30 (0.22), residues: 1478
  helix:  0.96 (0.73), residues: 48
  sheet:  0.61 (0.20), residues: 710
  loop : -0.20 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  19 
 TYR   0.022   0.002   TYR M  92 
 PHE   0.014   0.002   PHE H 105 
 TRP   0.013   0.002   TRP I  50 
 HIS   0.005   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 (11769)
  covalent geometry    : angle       0.60052 (16057)
  SS BOND              : bond        0.00587 (    6)
  SS BOND              : angle       0.56282 (   12)
  hydrogen bonds       : bond        0.03655 (  424)
  hydrogen bonds       : angle       5.43392 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7160 (pt)
REVERT: A  161 ARG cc_start: 0.7424 (ptt-90) cc_final: 0.6561 (ptp90)
REVERT: A  195 LYS cc_start: 0.8612 (mmmt) cc_final: 0.7841 (mtmt)
REVERT: A  245 ASN cc_start: 0.8415 (m-40) cc_final: 0.8162 (p0)
REVERT: B  195 LYS cc_start: 0.8606 (mmmt) cc_final: 0.7837 (mtmt)
REVERT: B  245 ASN cc_start: 0.8629 (m-40) cc_final: 0.8129 (p0)
REVERT: B  359 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6933 (mt-10)
REVERT: H   92 GLU cc_start: 0.8101 (pm20) cc_final: 0.7858 (pm20)
REVERT: L   82 GLU cc_start: 0.7949 (pt0) cc_final: 0.7185 (pm20)
REVERT: L  117 PHE cc_start: 0.6703 (m-10) cc_final: 0.6462 (m-10)
REVERT: L  119 PHE cc_start: 0.5457 (m-80) cc_final: 0.4739 (m-80)
REVERT: L  161 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7377 (mm110)
REVERT: M   19 ARG cc_start: 0.8965 (ttt-90) cc_final: 0.8730 (mtp-110)
REVERT: M   82 GLU cc_start: 0.7926 (pt0) cc_final: 0.7178 (pm20)
  outliers start: 22
  outliers final: 16
  residues processed: 123
  average time/residue: 0.1287
  time to fit residues: 22.2944
Evaluate side-chains
  124 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  359 GLU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  147 VAL
Chi-restraints excluded: chain L residue  149 TRP
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue  107 ILE
Chi-restraints excluded: chain M residue  147 VAL
Chi-restraints excluded: chain M residue  149 TRP
Chi-restraints excluded: chain M residue  179 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 121 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 82 optimal weight:    0.2980
   chunk 29 optimal weight:    0.1980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.163846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111635 restraints weight = 16251.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.92
r_work: 0.3206 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3227
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11775  Z= 0.118
  Angle     :  0.529  13.222  16069  Z= 0.264
  Chirality :  0.043   0.134   1836
  Planarity :  0.003   0.033   2058
  Dihedral  :  4.505  44.555   1658
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 16.65 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.53 (0.22), residues: 1478
  helix:  1.24 (0.75), residues: 48
  sheet:  0.82 (0.20), residues: 704
  loop : -0.10 (0.24), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  19 
 TYR   0.017   0.001   TYR I 155 
 PHE   0.012   0.001   PHE B 349 
 TRP   0.014   0.001   TRP H 164 
 HIS   0.002   0.000   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11769)
  covalent geometry    : angle       0.52904 (16057)
  SS BOND              : bond        0.00392 (    6)
  SS BOND              : angle       0.46887 (   12)
  hydrogen bonds       : bond        0.03110 (  424)
  hydrogen bonds       : angle       5.06775 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ARG cc_start: 0.7311 (ptt-90) cc_final: 0.6501 (ptp90)
REVERT: A  195 LYS cc_start: 0.8565 (mmmt) cc_final: 0.7760 (mtmt)
REVERT: A  245 ASN cc_start: 0.8396 (m-40) cc_final: 0.8156 (p0)
REVERT: B  111 HIS cc_start: 0.7936 (m-70) cc_final: 0.7418 (m-70)
REVERT: B  195 LYS cc_start: 0.8561 (mmmt) cc_final: 0.7777 (mtmt)
REVERT: H   92 GLU cc_start: 0.8078 (pm20) cc_final: 0.7833 (pm20)
REVERT: L   82 GLU cc_start: 0.7959 (pt0) cc_final: 0.7211 (pm20)
REVERT: L  119 PHE cc_start: 0.5411 (m-80) cc_final: 0.4647 (m-80)
REVERT: L  161 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7382 (mm110)
REVERT: M   82 GLU cc_start: 0.7932 (pt0) cc_final: 0.7203 (pm20)
  outliers start: 13
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1188
  time to fit residues: 20.6456
Evaluate side-chains
  119 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  149 TRP
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue  107 ILE
Chi-restraints excluded: chain M residue  147 VAL
Chi-restraints excluded: chain M residue  149 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0970
   chunk 46 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 125 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 127 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0270
   overall best weight:    1.2242

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

Flipped N/Q/H residues before XYZ refinement:
** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.160414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.109946 restraints weight = 15908.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 3.20
r_work: 0.3161 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  11775  Z= 0.198
  Angle     :  0.577  12.982  16069  Z= 0.289
  Chirality :  0.045   0.141   1836
  Planarity :  0.004   0.032   2058
  Dihedral  :  4.607  43.186   1658
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 16.49 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.45 (0.22), residues: 1478
  helix:  1.14 (0.73), residues: 48
  sheet:  0.73 (0.20), residues: 706
  loop : -0.11 (0.24), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG M  19 
 TYR   0.017   0.002   TYR M  92 
 PHE   0.013   0.002   PHE H 105 
 TRP   0.013   0.002   TRP H 164 
 HIS   0.004   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (11769)
  covalent geometry    : angle       0.57661 (16057)
  SS BOND              : bond        0.00489 (    6)
  SS BOND              : angle       0.47265 (   12)
  hydrogen bonds       : bond        0.03363 (  424)
  hydrogen bonds       : angle       5.17438 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ARG cc_start: 0.7408 (ptt-90) cc_final: 0.6584 (ptp90)
REVERT: A  195 LYS cc_start: 0.8588 (mmmt) cc_final: 0.7797 (mtmt)
REVERT: A  245 ASN cc_start: 0.8408 (m-40) cc_final: 0.8142 (p0)
REVERT: B  195 LYS cc_start: 0.8589 (mmmt) cc_final: 0.7805 (mtmt)
REVERT: B  245 ASN cc_start: 0.8453 (m-40) cc_final: 0.8178 (p0)
REVERT: B  359 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6937 (mt-10)
REVERT: H   92 GLU cc_start: 0.8094 (pm20) cc_final: 0.7844 (pm20)
REVERT: L   82 GLU cc_start: 0.7974 (pt0) cc_final: 0.7219 (pm20)
REVERT: L  117 PHE cc_start: 0.6871 (m-10) cc_final: 0.6650 (m-10)
REVERT: L  119 PHE cc_start: 0.5490 (m-80) cc_final: 0.4666 (m-80)
REVERT: L  161 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7376 (mm110)
REVERT: M    3 ILE cc_start: 0.8927 (mt) cc_final: 0.8722 (mt)
REVERT: M   82 GLU cc_start: 0.7959 (pt0) cc_final: 0.7217 (pm20)
  outliers start: 14
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1222
  time to fit residues: 20.5600
Evaluate side-chains
  117 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue  359 GLU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  147 VAL
Chi-restraints excluded: chain L residue  149 TRP
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue  107 ILE
Chi-restraints excluded: chain M residue  147 VAL
Chi-restraints excluded: chain M residue  149 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 123 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 114 optimal weight:    3.9990
   chunk 141 optimal weight:    7.9990
   chunk 139 optimal weight:    0.1980
   chunk 109 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B  85 GLN
I  85 GLN
** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.160668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111758 restraints weight = 16042.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 3.20
r_work: 0.3159 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  11775  Z= 0.170
  Angle     :  0.562  12.868  16069  Z= 0.280
  Chirality :  0.045   0.173   1836
  Planarity :  0.003   0.033   2058
  Dihedral  :  4.609  43.969   1658
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 16.74 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.47 (0.22), residues: 1478
  helix:  1.19 (0.74), residues: 48
  sheet:  0.74 (0.20), residues: 706
  loop : -0.09 (0.24), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG M  19 
 TYR   0.015   0.001   TYR I 155 
 PHE   0.012   0.002   PHE A  75 
 TRP   0.013   0.002   TRP I 164 
 HIS   0.003   0.001   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (11769)
  covalent geometry    : angle       0.56259 (16057)
  SS BOND              : bond        0.00439 (    6)
  SS BOND              : angle       0.41931 (   12)
  hydrogen bonds       : bond        0.03224 (  424)
  hydrogen bonds       : angle       5.04689 ( 1254)

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

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

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2956 Ramachandran restraints generated.
    1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ARG cc_start: 0.7371 (ptt-90) cc_final: 0.6563 (ptp90)
REVERT: A  195 LYS cc_start: 0.8581 (mmmt) cc_final: 0.7788 (mtmt)
REVERT: A  245 ASN cc_start: 0.8417 (m-40) cc_final: 0.8170 (p0)
REVERT: B  195 LYS cc_start: 0.8586 (mmmt) cc_final: 0.7795 (mtmt)
REVERT: B  245 ASN cc_start: 0.8674 (m-40) cc_final: 0.8129 (p0)
REVERT: B  359 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6947 (mt-10)
REVERT: H   92 GLU cc_start: 0.8106 (pm20) cc_final: 0.7858 (pm20)
REVERT: L   82 GLU cc_start: 0.7997 (pt0) cc_final: 0.7242 (pm20)
REVERT: L  161 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7515 (mm110)
REVERT: M    3 ILE cc_start: 0.8975 (mt) cc_final: 0.8468 (mt)
REVERT: M   82 GLU cc_start: 0.7979 (pt0) cc_final: 0.7233 (pm20)
  outliers start: 14
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1155
  time to fit residues: 19.2785
Evaluate side-chains
  118 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue  359 GLU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  147 VAL
Chi-restraints excluded: chain L residue  149 TRP
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue  107 ILE
Chi-restraints excluded: chain M residue  147 VAL
Chi-restraints excluded: chain M residue  149 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 110 optimal weight:    7.9990
   chunk 95 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0270
   chunk 125 optimal weight:    7.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
M 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.161505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.111344 restraints weight = 16086.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.12
r_work: 0.3203 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11775  Z= 0.121
  Angle     :  0.541  13.243  16069  Z= 0.270
  Chirality :  0.044   0.138   1836
  Planarity :  0.003   0.035   2058
  Dihedral  :  4.575  44.988   1658
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 16.98 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    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:  0.59 (0.22), residues: 1478
  helix:  1.84 (0.75), residues: 48
  sheet:  0.87 (0.20), residues: 702
  loop : -0.11 (0.24), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 312 
 TYR   0.015   0.001   TYR I 155 
 PHE   0.036   0.002   PHE L 119 
 TRP   0.013   0.001   TRP H 164 
 HIS   0.002   0.000   HIS B 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (11769)
  covalent geometry    : angle       0.54101 (16057)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       0.42496 (   12)
  hydrogen bonds       : bond        0.03061 (  424)
  hydrogen bonds       : angle       4.94896 ( 1254)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3000.91 seconds
wall clock time: 52 minutes 22.52 seconds (3142.52 seconds total)