Starting phenix.real_space_refine
on Thu Jul 31 08:26:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zui_60484/07_2025/8zui_60484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zui_60484/07_2025/8zui_60484.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zui_60484/07_2025/8zui_60484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zui_60484/07_2025/8zui_60484.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zui_60484/07_2025/8zui_60484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zui_60484/07_2025/8zui_60484.cif"
  }
  resolution = 2.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     144      5.16       5
     C    8318      2.51       5
     N    2392      2.21       5
     O    2524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13378
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1145
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 9, 'TRANS': 136}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1145
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 9, 'TRANS': 136}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1145
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 9, 'TRANS': 136}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1080
          Classifications: {'peptide': 141}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "E"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1080
          Classifications: {'peptide': 141}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "F"
      Number of atoms: 1094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1094
          Classifications: {'peptide': 141}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1145
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 9, 'TRANS': 136}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1145
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 9, 'TRANS': 136}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1145
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 9, 'TRANS': 136}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1080
          Classifications: {'peptide': 141}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "K"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1080
          Classifications: {'peptide': 141}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "L"
      Number of atoms: 1094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1094
          Classifications: {'peptide': 141}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 9.16, per 1000 atoms: 0.68
  Number of scatterers: 13378
  At special positions: 0
  Unit cell: (148.42, 117.26, 100.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     144     16.00
     O    2524      8.00
     N    2392      7.00
     C    8318      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=66, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 145 " - pdb=" SG  CYS A 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 145 " - pdb=" SG  CYS B 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 145 " - pdb=" SG  CYS C 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  44 " - pdb=" SG  CYS D  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  59 " - pdb=" SG  CYS D  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  62 " - pdb=" SG  CYS D  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  84 " - pdb=" SG  CYS D  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 102 " - pdb=" SG  CYS D 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 105 " - pdb=" SG  CYS D 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 127 " - pdb=" SG  CYS D 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 146 " - pdb=" SG  CYS D 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 149 " - pdb=" SG  CYS D 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 168 " - pdb=" SG  CYS D 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  44 " - pdb=" SG  CYS E  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  59 " - pdb=" SG  CYS E  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  62 " - pdb=" SG  CYS E  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 102 " - pdb=" SG  CYS E 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 105 " - pdb=" SG  CYS E 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 127 " - pdb=" SG  CYS E 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 146 " - pdb=" SG  CYS E 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 149 " - pdb=" SG  CYS E 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 168 " - pdb=" SG  CYS E 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  44 " - pdb=" SG  CYS F  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  59 " - pdb=" SG  CYS F  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  62 " - pdb=" SG  CYS F  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  84 " - pdb=" SG  CYS F  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 102 " - pdb=" SG  CYS F 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 105 " - pdb=" SG  CYS F 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 127 " - pdb=" SG  CYS F 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 146 " - pdb=" SG  CYS F 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 149 " - pdb=" SG  CYS F 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 168 " - pdb=" SG  CYS F 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 145 " - pdb=" SG  CYS G 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 145 " - pdb=" SG  CYS H 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 145 " - pdb=" SG  CYS I 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  44 " - pdb=" SG  CYS J  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  59 " - pdb=" SG  CYS J  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  62 " - pdb=" SG  CYS J  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  84 " - pdb=" SG  CYS J  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 102 " - pdb=" SG  CYS J 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 105 " - pdb=" SG  CYS J 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 127 " - pdb=" SG  CYS J 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 146 " - pdb=" SG  CYS J 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 149 " - pdb=" SG  CYS J 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 168 " - pdb=" SG  CYS J 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  44 " - pdb=" SG  CYS K  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  59 " - pdb=" SG  CYS K  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  62 " - pdb=" SG  CYS K  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  84 " - pdb=" SG  CYS K  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 102 " - pdb=" SG  CYS K 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 105 " - pdb=" SG  CYS K 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 127 " - pdb=" SG  CYS K 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 146 " - pdb=" SG  CYS K 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 149 " - pdb=" SG  CYS K 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 168 " - pdb=" SG  CYS K 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  44 " - pdb=" SG  CYS L  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  59 " - pdb=" SG  CYS L  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  62 " - pdb=" SG  CYS L  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  84 " - pdb=" SG  CYS L  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 102 " - pdb=" SG  CYS L 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 105 " - pdb=" SG  CYS L 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 127 " - pdb=" SG  CYS L 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 146 " - pdb=" SG  CYS L 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 149 " - pdb=" SG  CYS L 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 168 " - pdb=" SG  CYS L 179 " 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: 3.01
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3216

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 60 sheets defined
      1.7% alpha, 37.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'B' and resid 214 through 218
    Processing helix  chain 'C' and resid 214 through 218
    Processing helix  chain 'G' and resid 214 through 218
    Processing helix  chain 'H' and resid 214 through 218
    Processing helix  chain 'I' and resid 214 through 218
    Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 105
    Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 105
    Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 120
      removed outlier: 6.550A  pdb=" N   LEU A 152 " --> pdb=" O   ILE A 173 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE A 173 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   HIS A 154 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER A 171 " --> pdb=" O   HIS A 154 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE A 156 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
    Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105
    Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 120
      removed outlier: 6.550A  pdb=" N   LEU B 152 " --> pdb=" O   ILE B 173 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE B 173 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   HIS B 154 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   SER B 171 " --> pdb=" O   HIS B 154 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE B 156 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 104 through 105
    Processing sheet with id=AA8, first strand: chain 'C' and resid 104 through 105
    Processing sheet with id=AA9, first strand: chain 'C' and resid 118 through 120
      removed outlier: 6.550A  pdb=" N   LEU C 152 " --> pdb=" O   ILE C 173 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE C 173 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   HIS C 154 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   SER C 171 " --> pdb=" O   HIS C 154 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE C 156 " --> pdb=" O   LEU C 169 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 50
    Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 70
      removed outlier: 7.249A  pdb=" N   ASP D  80 " --> pdb=" O   TYR D  69 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AB4, first strand: chain 'D' and resid 112 through 115
      removed outlier: 6.623A  pdb=" N   VAL D 124 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 131 through 135
    Processing sheet with id=AB6, first strand: chain 'D' and resid 152 through 156
      removed outlier: 6.809A  pdb=" N   VAL D 165 " --> pdb=" O   HIS D 155 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 172 through 175
    Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 50
    Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 70
      removed outlier: 7.241A  pdb=" N   ASP E  80 " --> pdb=" O   TYR E  69 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 88 through 89
    Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 115
      removed outlier: 6.640A  pdb=" N   VAL E 124 " --> pdb=" O   ILE E 114 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 131 through 135
    Processing sheet with id=AC4, first strand: chain 'E' and resid 152 through 156
      removed outlier: 6.795A  pdb=" N   VAL E 165 " --> pdb=" O   HIS E 155 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 172 through 175
    Processing sheet with id=AC6, first strand: chain 'F' and resid 48 through 50
    Processing sheet with id=AC7, first strand: chain 'F' and resid 66 through 70
      removed outlier: 7.211A  pdb=" N   ASP F  80 " --> pdb=" O   TYR F  69 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 88 through 89
    Processing sheet with id=AC9, first strand: chain 'F' and resid 112 through 115
      removed outlier: 6.627A  pdb=" N   VAL F 124 " --> pdb=" O   ILE F 114 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'F' and resid 131 through 135
    Processing sheet with id=AD2, first strand: chain 'F' and resid 152 through 156
      removed outlier: 6.802A  pdb=" N   VAL F 165 " --> pdb=" O   HIS F 155 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 172 through 175
    Processing sheet with id=AD4, first strand: chain 'G' and resid 104 through 105
    Processing sheet with id=AD5, first strand: chain 'G' and resid 104 through 105
    Processing sheet with id=AD6, first strand: chain 'G' and resid 118 through 120
      removed outlier: 6.550A  pdb=" N   LEU G 152 " --> pdb=" O   ILE G 173 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE G 173 " --> pdb=" O   LEU G 152 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   HIS G 154 " --> pdb=" O   SER G 171 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER G 171 " --> pdb=" O   HIS G 154 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE G 156 " --> pdb=" O   LEU G 169 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'H' and resid 104 through 105
    Processing sheet with id=AD8, first strand: chain 'H' and resid 104 through 105
    Processing sheet with id=AD9, first strand: chain 'H' and resid 118 through 120
      removed outlier: 6.550A  pdb=" N   LEU H 152 " --> pdb=" O   ILE H 173 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE H 173 " --> pdb=" O   LEU H 152 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   HIS H 154 " --> pdb=" O   SER H 171 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   SER H 171 " --> pdb=" O   HIS H 154 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE H 156 " --> pdb=" O   LEU H 169 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'I' and resid 104 through 105
    Processing sheet with id=AE2, first strand: chain 'I' and resid 104 through 105
    Processing sheet with id=AE3, first strand: chain 'I' and resid 118 through 120
      removed outlier: 6.550A  pdb=" N   LEU I 152 " --> pdb=" O   ILE I 173 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ILE I 173 " --> pdb=" O   LEU I 152 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   HIS I 154 " --> pdb=" O   SER I 171 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   SER I 171 " --> pdb=" O   HIS I 154 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE I 156 " --> pdb=" O   LEU I 169 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'J' and resid 48 through 50
    Processing sheet with id=AE5, first strand: chain 'J' and resid 66 through 70
      removed outlier: 7.249A  pdb=" N   ASP J  80 " --> pdb=" O   TYR J  69 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'J' and resid 88 through 89
    Processing sheet with id=AE7, first strand: chain 'J' and resid 112 through 115
      removed outlier: 6.623A  pdb=" N   VAL J 124 " --> pdb=" O   ILE J 114 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'J' and resid 131 through 135
    Processing sheet with id=AE9, first strand: chain 'J' and resid 152 through 156
      removed outlier: 6.819A  pdb=" N   VAL J 165 " --> pdb=" O   HIS J 155 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'J' and resid 172 through 175
    Processing sheet with id=AF2, first strand: chain 'K' and resid 48 through 50
    Processing sheet with id=AF3, first strand: chain 'K' and resid 66 through 70
      removed outlier: 7.244A  pdb=" N   ASP K  80 " --> pdb=" O   TYR K  69 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'K' and resid 88 through 89
    Processing sheet with id=AF5, first strand: chain 'K' and resid 112 through 115
      removed outlier: 6.641A  pdb=" N   VAL K 124 " --> pdb=" O   ILE K 114 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'K' and resid 131 through 135
    Processing sheet with id=AF7, first strand: chain 'K' and resid 152 through 156
      removed outlier: 6.794A  pdb=" N   VAL K 165 " --> pdb=" O   HIS K 155 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'K' and resid 172 through 175
    Processing sheet with id=AF9, first strand: chain 'L' and resid 48 through 50
    Processing sheet with id=AG1, first strand: chain 'L' and resid 66 through 70
      removed outlier: 7.208A  pdb=" N   ASP L  80 " --> pdb=" O   TYR L  69 " (cutoff:3.500A)
    Processing sheet with id=AG2, first strand: chain 'L' and resid 88 through 89
    Processing sheet with id=AG3, first strand: chain 'L' and resid 112 through 115
      removed outlier: 6.635A  pdb=" N   VAL L 124 " --> pdb=" O   ILE L 114 " (cutoff:3.500A)
    Processing sheet with id=AG4, first strand: chain 'L' and resid 131 through 135
    Processing sheet with id=AG5, first strand: chain 'L' and resid 152 through 156
      removed outlier: 6.807A  pdb=" N   VAL L 165 " --> pdb=" O   HIS L 155 " (cutoff:3.500A)
    Processing sheet with id=AG6, first strand: chain 'L' and resid 172 through 175

    420 hydrogen bonds defined for protein.
    1044 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.99

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 4517
        1.35 -     1.46: 3061
        1.46 -     1.58: 5932
        1.58 -     1.70: 0
        1.70 -     1.81: 150
  Bond restraints: 13660
  Sorted by residual:
  bond pdb=" C   CYS L  44 "
       pdb=" N   PRO L  45 "
    ideal  model  delta    sigma   weight residual
    1.331  1.346 -0.015 1.21e-02 6.83e+03 1.48e+00
  bond pdb=" C   CYS F  44 "
       pdb=" N   PRO F  45 "
    ideal  model  delta    sigma   weight residual
    1.331  1.345 -0.014 1.21e-02 6.83e+03 1.31e+00
  bond pdb=" CB  PRO I 193 "
       pdb=" CG  PRO I 193 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 5.00e-02 4.00e+02 5.95e-01
  bond pdb=" CB  PRO C 193 "
       pdb=" CG  PRO C 193 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 5.00e-02 4.00e+02 5.95e-01
  bond pdb=" CB  PRO A 193 "
       pdb=" CG  PRO A 193 "
    ideal  model  delta    sigma   weight residual
    1.492  1.530 -0.038 5.00e-02 4.00e+02 5.74e-01
  ... (remaining 13655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.72: 16937
        0.72 -     1.44: 1271
        1.44 -     2.17: 212
        2.17 -     2.89: 66
        2.89 -     3.61: 18
  Bond angle restraints: 18504
  Sorted by residual:
  angle pdb=" C   ALA H 114 "
        pdb=" N   ASN H 115 "
        pdb=" CA  ASN H 115 "
      ideal   model   delta    sigma   weight residual
     122.63  124.80   -2.17 1.44e+00 4.82e-01 2.27e+00
  angle pdb=" C   ALA B 114 "
        pdb=" N   ASN B 115 "
        pdb=" CA  ASN B 115 "
      ideal   model   delta    sigma   weight residual
     122.63  124.80   -2.17 1.44e+00 4.82e-01 2.27e+00
  angle pdb=" C   ALA I 114 "
        pdb=" N   ASN I 115 "
        pdb=" CA  ASN I 115 "
      ideal   model   delta    sigma   weight residual
     122.63  124.78   -2.15 1.44e+00 4.82e-01 2.22e+00
  angle pdb=" C   ALA C 114 "
        pdb=" N   ASN C 115 "
        pdb=" CA  ASN C 115 "
      ideal   model   delta    sigma   weight residual
     122.63  124.78   -2.15 1.44e+00 4.82e-01 2.22e+00
  angle pdb=" C   ALA G 114 "
        pdb=" N   ASN G 115 "
        pdb=" CA  ASN G 115 "
      ideal   model   delta    sigma   weight residual
     122.63  124.77   -2.14 1.44e+00 4.82e-01 2.20e+00
  ... (remaining 18499 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 7834
       16.97 -    33.93: 416
       33.93 -    50.90: 122
       50.90 -    67.86: 30
       67.86 -    84.83: 6
  Dihedral angle restraints: 8408
    sinusoidal: 3416
      harmonic: 4992
  Sorted by residual:
  dihedral pdb=" CB  CYS F 149 "
           pdb=" SG  CYS F 149 "
           pdb=" SG  CYS F 166 "
           pdb=" CB  CYS F 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.93  -57.93     1      1.00e+01 1.00e-02 4.50e+01
  dihedral pdb=" CB  CYS L 149 "
           pdb=" SG  CYS L 149 "
           pdb=" SG  CYS L 166 "
           pdb=" CB  CYS L 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.90  -57.90     1      1.00e+01 1.00e-02 4.50e+01
  dihedral pdb=" CB  CYS D 149 "
           pdb=" SG  CYS D 149 "
           pdb=" SG  CYS D 166 "
           pdb=" CB  CYS D 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.21  -55.21     1      1.00e+01 1.00e-02 4.12e+01
  ... (remaining 8405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1312
       0.027 -    0.054: 373
       0.054 -    0.080: 173
       0.080 -    0.107: 97
       0.107 -    0.134: 69
  Chirality restraints: 2024
  Sorted by residual:
  chirality pdb=" CA  ILE L  57 "
            pdb=" N   ILE L  57 "
            pdb=" C   ILE L  57 "
            pdb=" CB  ILE L  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE B 156 "
            pdb=" N   ILE B 156 "
            pdb=" C   ILE B 156 "
            pdb=" CB  ILE B 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  ILE H 156 "
            pdb=" N   ILE H 156 "
            pdb=" C   ILE H 156 "
            pdb=" CB  ILE H 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.33e-01
  ... (remaining 2021 not shown)

  Planarity restraints: 2430
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS E  44 "   -0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO E  45 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO E  45 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E  45 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS K  44 "    0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO K  45 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO K  45 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO K  45 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS D  44 "    0.018 5.00e-02 4.00e+02   2.81e-02 1.26e+00
        pdb=" N   PRO D  45 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO D  45 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D  45 "    0.016 5.00e-02 4.00e+02
  ... (remaining 2427 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 865
        2.74 -     3.28: 12076
        3.28 -     3.82: 22130
        3.82 -     4.36: 26447
        4.36 -     4.90: 45647
  Nonbonded interactions: 107165
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 191 "
            pdb=" OE2 GLU E 108 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OH  TYR H 191 "
            pdb=" OE2 GLU K 108 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OH  TYR C 191 "
            pdb=" OE2 GLU D 108 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OH  TYR G 191 "
            pdb=" OE2 GLU L 108 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OH  TYR I 191 "
            pdb=" OE2 GLU J 108 "
     model   vdw
     2.235 3.040
  ... (remaining 107160 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'D'
  selection = chain 'K'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'L'
}

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=1.00 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:             5.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     32.930
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.070
  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:15.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
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      :  0.002   0.039  13726  Z= 0.087
  Angle     :  0.439   3.612  18636  Z= 0.241
  Chirality :  0.041   0.134   2024
  Planarity :  0.003   0.028   2430
  Dihedral  : 11.317  84.828   4994
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  7.04 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.21), residues: 1686
  helix:  None (None), residues: 0
  sheet:  1.17 (0.24), residues: 468
  loop :  0.43 (0.18), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 190 
 HIS   0.002   0.001   HIS H 154 
 PHE   0.006   0.001   PHE L 141 
 TYR   0.006   0.001   TYR F  67 
 ARG   0.002   0.000   ARG E 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10956 (  408)
  hydrogen bonds       : angle       4.93191 ( 1044)
  SS BOND              : bond        0.00118 (   66)
  SS BOND              : angle       0.30047 (  132)
  covalent geometry    : bond        0.00193 (13660)
  covalent geometry    : angle       0.43972 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 207
  time to evaluate  : 1.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 TYR cc_start: 0.8070 (m-10) cc_final: 0.7850 (m-10)
REVERT: J  105 CYS cc_start: 0.5962 (m) cc_final: 0.5574 (m)
  outliers start: 12
  outliers final: 2
  residues processed: 216
  average time/residue: 0.7552
  time to fit residues: 187.5013
Evaluate side-chains
  188 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain G residue  139 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.9980
   chunk 127 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 85 optimal weight:    0.2980
   chunk 68 optimal weight:    7.9990
   chunk 131 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0970
   chunk 98 optimal weight:    2.9990
   chunk 152 optimal weight:    5.9990
   overall best weight:    1.0380

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

Flipped N/Q/H residues before XYZ refinement:
A  91 HIS
A 101 GLN
A 103 GLN
A 123 GLN
A 137 GLN
A 149 HIS
B 101 GLN
B 103 GLN
B 115 ASN
B 123 GLN
B 149 HIS
B 168 ASN
C 103 GLN
C 115 ASN
C 123 GLN
C 149 HIS
D 111 GLN
D 162 GLN
D 177 ASN
E 111 GLN
E 162 GLN
E 177 ASN
F  46 GLN
F 111 GLN
F 134 HIS
F 169 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 101 GLN
G 103 GLN
G 123 GLN
G 149 HIS
H 101 GLN
H 103 GLN
** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 115 ASN
H 123 GLN
H 149 HIS
H 168 ASN
I 101 GLN
I 103 GLN
I 115 ASN
I 123 GLN
I 149 HIS
J 111 GLN
J 162 GLN
J 177 ASN
K 111 GLN
K 162 GLN
K 177 ASN
L  46 GLN
L 111 GLN
L 177 ASN

Total number of N/Q/H flips: 50

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.178876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.148295 restraints weight = 16383.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.42
r_work: 0.3876 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  13726  Z= 0.228
  Angle     :  0.592   7.855  18636  Z= 0.313
  Chirality :  0.044   0.162   2024
  Planarity :  0.004   0.041   2430
  Dihedral  :  4.615  36.326   1864
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.33 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.20), residues: 1686
  helix:  None (None), residues: 0
  sheet:  1.01 (0.23), residues: 522
  loop :  0.03 (0.18), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 190 
 HIS   0.007   0.001   HIS L 134 
 PHE   0.018   0.002   PHE L 141 
 TYR   0.015   0.002   TYR C 191 
 ARG   0.004   0.000   ARG H 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  408)
  hydrogen bonds       : angle       5.06652 ( 1044)
  SS BOND              : bond        0.00401 (   66)
  SS BOND              : angle       1.57842 (  132)
  covalent geometry    : bond        0.00515 (13660)
  covalent geometry    : angle       0.57884 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 214
  time to evaluate  : 1.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8389 (m)
REVERT: B  222 GLU cc_start: 0.7608 (mp0) cc_final: 0.7284 (mp0)
REVERT: C  129 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6825 (tm-30)
REVERT: C  137 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7975 (tm-30)
REVERT: D  177 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5761 (t0)
REVERT: E  159 GLN cc_start: 0.8521 (mt0) cc_final: 0.8084 (mt0)
REVERT: E  162 GLN cc_start: 0.8346 (tt0) cc_final: 0.8011 (tt0)
REVERT: E  177 ASN cc_start: 0.6930 (OUTLIER) cc_final: 0.6350 (t0)
REVERT: F   90 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7813 (p)
REVERT: G  105 LEU cc_start: 0.8234 (mt) cc_final: 0.7926 (mp)
REVERT: H   93 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8377 (m)
REVERT: H  129 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6835 (tm-30)
REVERT: I  129 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6654 (tm-30)
REVERT: J  177 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6671 (t160)
REVERT: K   44 CYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6499 (t)
REVERT: L  103 SER cc_start: 0.8328 (m) cc_final: 0.8058 (p)
REVERT: L  133 ARG cc_start: 0.8186 (ptp-170) cc_final: 0.7921 (ptp-170)
  outliers start: 39
  outliers final: 12
  residues processed: 239
  average time/residue: 1.0297
  time to fit residues: 282.5760
Evaluate side-chains
  217 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 1.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain D residue  177 ASN
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain E residue  177 ASN
Chi-restraints excluded: chain F residue   90 THR
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  129 GLU
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain J residue  177 ASN
Chi-restraints excluded: chain K residue   44 CYS
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue  159 GLN
Chi-restraints excluded: chain L residue  167 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   chunk 94 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 161 optimal weight:    5.9990
   chunk 130 optimal weight:    0.7980
   chunk 166 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
B 149 HIS
B 168 ASN
C 164 GLN
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  91 HIS
G 115 ASN
H 149 HIS
H 168 ASN
I 149 HIS
L 162 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.178796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.148393 restraints weight = 16395.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 2.40
r_work: 0.3878 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  13726  Z= 0.170
  Angle     :  0.544   6.569  18636  Z= 0.290
  Chirality :  0.043   0.167   2024
  Planarity :  0.004   0.042   2430
  Dihedral  :  4.449  19.553   1860
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 13.67 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.20), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.90 (0.24), residues: 498
  loop :  0.05 (0.18), residues: 1188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 190 
 HIS   0.005   0.001   HIS L 134 
 PHE   0.016   0.002   PHE L 141 
 TYR   0.011   0.001   TYR C 191 
 ARG   0.008   0.000   ARG H 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02972 (  408)
  hydrogen bonds       : angle       5.03537 ( 1044)
  SS BOND              : bond        0.00308 (   66)
  SS BOND              : angle       1.48638 (  132)
  covalent geometry    : bond        0.00385 (13660)
  covalent geometry    : angle       0.53119 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 185
  time to evaluate  : 1.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8393 (m)
REVERT: B  129 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6769 (tm-30)
REVERT: B  222 GLU cc_start: 0.7639 (mp0) cc_final: 0.7288 (mp0)
REVERT: C  129 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6791 (tm-30)
REVERT: E  159 GLN cc_start: 0.8553 (mt0) cc_final: 0.8008 (mt0)
REVERT: E  162 GLN cc_start: 0.8383 (tt0) cc_final: 0.8012 (tt0)
REVERT: F   46 GLN cc_start: 0.8723 (tt0) cc_final: 0.8506 (tp40)
REVERT: G  105 LEU cc_start: 0.8289 (mt) cc_final: 0.7988 (mp)
REVERT: H  179 ARG cc_start: 0.7636 (ttm-80) cc_final: 0.7419 (ttm-80)
REVERT: I  129 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6642 (tm-30)
REVERT: L  103 SER cc_start: 0.8238 (m) cc_final: 0.7943 (p)
REVERT: L  128 ARG cc_start: 0.8381 (ptp90) cc_final: 0.8148 (mtt90)
  outliers start: 42
  outliers final: 14
  residues processed: 208
  average time/residue: 1.0463
  time to fit residues: 249.7920
Evaluate side-chains
  201 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain I residue   93 VAL
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   99 CYS
Chi-restraints excluded: chain L residue  167 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 143 optimal weight:    1.9990
   chunk 167 optimal weight:    2.9990
   chunk 164 optimal weight:    1.9990
   chunk 152 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 136 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
B 137 GLN
B 149 HIS
C 137 GLN
C 164 GLN
D 177 ASN
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 149 HIS
H 149 HIS
H 168 ASN
I 149 HIS
J 177 ASN
K 177 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.175918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.145481 restraints weight = 16296.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 2.35
r_work: 0.3842 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3683 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  13726  Z= 0.267
  Angle     :  0.615   8.685  18636  Z= 0.326
  Chirality :  0.045   0.200   2024
  Planarity :  0.004   0.044   2430
  Dihedral  :  4.858  21.998   1860
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.14 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.20), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.60 (0.23), residues: 534
  loop : -0.09 (0.18), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 190 
 HIS   0.009   0.001   HIS L 134 
 PHE   0.019   0.002   PHE A 228 
 TYR   0.012   0.002   TYR I 191 
 ARG   0.006   0.000   ARG H 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03375 (  408)
  hydrogen bonds       : angle       5.33140 ( 1044)
  SS BOND              : bond        0.00412 (   66)
  SS BOND              : angle       1.74423 (  132)
  covalent geometry    : bond        0.00601 (13660)
  covalent geometry    : angle       0.59902 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 205
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  129 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6877 (tm-30)
REVERT: B  222 GLU cc_start: 0.7653 (mp0) cc_final: 0.7324 (mp0)
REVERT: C  129 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6826 (tm-30)
REVERT: D  177 ASN cc_start: 0.6100 (OUTLIER) cc_final: 0.5820 (t0)
REVERT: F   90 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7799 (p)
REVERT: F  133 ARG cc_start: 0.8184 (ptp-170) cc_final: 0.7901 (mtm180)
REVERT: G  105 LEU cc_start: 0.8341 (mt) cc_final: 0.8059 (mp)
REVERT: H  167 VAL cc_start: 0.8154 (t) cc_final: 0.7922 (m)
REVERT: H  179 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7450 (ttm-80)
REVERT: H  222 GLU cc_start: 0.7578 (mp0) cc_final: 0.7105 (mp0)
REVERT: I  129 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6713 (tm-30)
REVERT: L  133 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.7898 (ptp-170)
  outliers start: 46
  outliers final: 26
  residues processed: 231
  average time/residue: 0.8493
  time to fit residues: 225.6070
Evaluate side-chains
  225 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 194
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain D residue  177 ASN
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain F residue   90 THR
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  159 GLN
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain F residue  181 SER
Chi-restraints excluded: chain G residue  102 LEU
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain I residue   93 VAL
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain J residue   72 CYS
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue   99 CYS
Chi-restraints excluded: chain L residue  159 GLN
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    0.2980
   chunk 52 optimal weight:    3.9990
   chunk 157 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 59 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:
A  91 HIS
B 137 GLN
B 149 HIS
B 201 GLN
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 HIS
I 149 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.177198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.146469 restraints weight = 16392.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 2.39
r_work: 0.3859 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3700 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  13726  Z= 0.176
  Angle     :  0.544   7.436  18636  Z= 0.290
  Chirality :  0.042   0.142   2024
  Planarity :  0.004   0.035   2430
  Dihedral  :  4.673  25.150   1860
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.15 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.20), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.69 (0.23), residues: 522
  loop : -0.09 (0.18), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 190 
 HIS   0.005   0.001   HIS L 134 
 PHE   0.015   0.001   PHE L 141 
 TYR   0.009   0.001   TYR B 191 
 ARG   0.005   0.000   ARG H 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03015 (  408)
  hydrogen bonds       : angle       5.15880 ( 1044)
  SS BOND              : bond        0.00305 (   66)
  SS BOND              : angle       1.45460 (  132)
  covalent geometry    : bond        0.00400 (13660)
  covalent geometry    : angle       0.53218 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 187
  time to evaluate  : 1.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 TYR cc_start: 0.8555 (m-80) cc_final: 0.8224 (m-80)
REVERT: B  141 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8376 (ptmt)
REVERT: B  222 GLU cc_start: 0.7669 (mp0) cc_final: 0.7350 (mp0)
REVERT: C  129 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6826 (tm-30)
REVERT: E  109 MET cc_start: 0.7894 (mmm) cc_final: 0.7626 (mtt)
REVERT: E  141 PHE cc_start: 0.8667 (p90) cc_final: 0.8442 (p90)
REVERT: F   90 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7813 (p)
REVERT: F  133 ARG cc_start: 0.8168 (ptp-170) cc_final: 0.7918 (mtm180)
REVERT: G  105 LEU cc_start: 0.8321 (mt) cc_final: 0.8044 (mp)
REVERT: H  129 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6862 (tm-30)
REVERT: H  167 VAL cc_start: 0.8145 (t) cc_final: 0.7915 (m)
REVERT: H  179 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7445 (ttm-80)
REVERT: H  222 GLU cc_start: 0.7592 (mp0) cc_final: 0.7127 (mp0)
REVERT: I  129 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6717 (tm-30)
REVERT: L  133 ARG cc_start: 0.8159 (ptp-170) cc_final: 0.7827 (mtm180)
  outliers start: 44
  outliers final: 26
  residues processed: 210
  average time/residue: 0.7866
  time to fit residues: 189.4589
Evaluate side-chains
  215 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain F residue   79 THR
Chi-restraints excluded: chain F residue   90 THR
Chi-restraints excluded: chain F residue   92 SER
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain F residue  181 SER
Chi-restraints excluded: chain G residue  102 LEU
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  129 GLU
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain I residue   93 VAL
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain J residue   72 CYS
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue   99 CYS
Chi-restraints excluded: chain L residue  127 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 137 optimal weight:    4.9990
   chunk 151 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0010
   chunk 3 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9980
   chunk 160 optimal weight:    0.7980
   chunk 108 optimal weight:    0.6980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
B 101 GLN
B 137 GLN
B 149 HIS
B 201 GLN
D 177 ASN
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 101 GLN
H 149 HIS
I 149 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.174732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.144632 restraints weight = 16572.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.33
r_work: 0.3879 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13726  Z= 0.150
  Angle     :  0.519   7.292  18636  Z= 0.276
  Chirality :  0.042   0.138   2024
  Planarity :  0.004   0.036   2430
  Dihedral  :  4.507  25.467   1860
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.68 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.20), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.72 (0.25), residues: 468
  loop :  0.04 (0.18), residues: 1218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 190 
 HIS   0.004   0.001   HIS L 134 
 PHE   0.012   0.001   PHE L 141 
 TYR   0.008   0.001   TYR B 191 
 ARG   0.005   0.000   ARG L 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02902 (  408)
  hydrogen bonds       : angle       5.03491 ( 1044)
  SS BOND              : bond        0.00266 (   66)
  SS BOND              : angle       1.28112 (  132)
  covalent geometry    : bond        0.00343 (13660)
  covalent geometry    : angle       0.50955 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 192
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 TYR cc_start: 0.8553 (m-80) cc_final: 0.8141 (m-80)
REVERT: B  222 GLU cc_start: 0.7665 (mp0) cc_final: 0.7342 (mp0)
REVERT: C  129 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6804 (tm-30)
REVERT: F   90 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7851 (p)
REVERT: G  105 LEU cc_start: 0.8334 (mt) cc_final: 0.8071 (mp)
REVERT: H  129 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6788 (tm-30)
REVERT: H  150 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8687 (t)
REVERT: H  167 VAL cc_start: 0.8112 (t) cc_final: 0.7893 (m)
REVERT: H  179 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7417 (ttm-80)
  outliers start: 45
  outliers final: 26
  residues processed: 217
  average time/residue: 0.7525
  time to fit residues: 189.2779
Evaluate side-chains
  215 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain F residue   79 THR
Chi-restraints excluded: chain F residue   90 THR
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain F residue  181 SER
Chi-restraints excluded: chain G residue  102 LEU
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  129 GLU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain I residue   93 VAL
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain J residue   72 CYS
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   99 CYS
Chi-restraints excluded: chain L residue  127 CYS
Chi-restraints excluded: chain L residue  148 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 120 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 160 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 149 HIS
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 HIS
H 168 ASN
I 149 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.173023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.144060 restraints weight = 16470.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.26
r_work: 0.3878 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13726  Z= 0.181
  Angle     :  0.542   6.790  18636  Z= 0.290
  Chirality :  0.042   0.139   2024
  Planarity :  0.004   0.037   2430
  Dihedral  :  4.697  33.239   1860
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.02 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.21), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.64 (0.24), residues: 498
  loop :  0.02 (0.18), residues: 1188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 190 
 HIS   0.005   0.001   HIS L 134 
 PHE   0.013   0.002   PHE L 141 
 TYR   0.009   0.001   TYR H 191 
 ARG   0.010   0.000   ARG L 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02956 (  408)
  hydrogen bonds       : angle       5.06221 ( 1044)
  SS BOND              : bond        0.00302 (   66)
  SS BOND              : angle       1.42466 (  132)
  covalent geometry    : bond        0.00413 (13660)
  covalent geometry    : angle       0.53097 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 193
  time to evaluate  : 1.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 TYR cc_start: 0.8563 (m-80) cc_final: 0.8251 (m-80)
REVERT: B  222 GLU cc_start: 0.7654 (mp0) cc_final: 0.7332 (mp0)
REVERT: F   90 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7868 (p)
REVERT: G  105 LEU cc_start: 0.8331 (mt) cc_final: 0.8068 (mp)
REVERT: H  102 LEU cc_start: 0.8338 (tt) cc_final: 0.8136 (tp)
REVERT: H  129 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6816 (tm-30)
REVERT: H  150 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8685 (t)
REVERT: H  167 VAL cc_start: 0.8128 (t) cc_final: 0.7904 (m)
REVERT: H  222 GLU cc_start: 0.7603 (mp0) cc_final: 0.7153 (mp0)
REVERT: L  133 ARG cc_start: 0.8165 (ptp-170) cc_final: 0.7823 (mtm180)
  outliers start: 47
  outliers final: 34
  residues processed: 218
  average time/residue: 0.9071
  time to fit residues: 227.4864
Evaluate side-chains
  227 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 190
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain C residue  151 LEU
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain F residue   79 THR
Chi-restraints excluded: chain F residue   90 THR
Chi-restraints excluded: chain F residue   92 SER
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain F residue  181 SER
Chi-restraints excluded: chain G residue  102 LEU
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  129 GLU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain H residue  174 LYS
Chi-restraints excluded: chain I residue   93 VAL
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain J residue   72 CYS
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue   99 CYS
Chi-restraints excluded: chain L residue  127 CYS
Chi-restraints excluded: chain L residue  148 LEU
Chi-restraints excluded: chain L residue  159 GLN
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 108 optimal weight:    0.4980
   chunk 115 optimal weight:    3.9990
   chunk 129 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 48 optimal weight:    0.4980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 149 HIS
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 149 HIS
** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 HIS
I 149 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.173143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.143130 restraints weight = 16521.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 2.31
r_work: 0.3864 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13726  Z= 0.214
  Angle     :  0.582   8.501  18636  Z= 0.306
  Chirality :  0.043   0.175   2024
  Planarity :  0.004   0.037   2430
  Dihedral  :  4.822  30.215   1860
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.09 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.28 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.21), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.48 (0.23), residues: 534
  loop : -0.03 (0.19), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 190 
 HIS   0.007   0.001   HIS L 134 
 PHE   0.012   0.002   PHE L 141 
 TYR   0.010   0.001   TYR I 191 
 ARG   0.009   0.000   ARG L 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  408)
  hydrogen bonds       : angle       5.19143 ( 1044)
  SS BOND              : bond        0.00325 (   66)
  SS BOND              : angle       1.61581 (  132)
  covalent geometry    : bond        0.00486 (13660)
  covalent geometry    : angle       0.56766 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 196
  time to evaluate  : 1.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  129 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6871 (tm-30)
REVERT: B  143 GLN cc_start: 0.7938 (tp40) cc_final: 0.7707 (tp40)
REVERT: B  192 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7497 (mm-30)
REVERT: B  222 GLU cc_start: 0.7708 (mp0) cc_final: 0.7372 (mp0)
REVERT: F   90 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7876 (p)
REVERT: G  105 LEU cc_start: 0.8347 (mt) cc_final: 0.8090 (mp)
REVERT: H  129 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6866 (tm-30)
REVERT: H  150 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8708 (t)
REVERT: H  167 VAL cc_start: 0.8129 (t) cc_final: 0.7906 (m)
REVERT: H  222 GLU cc_start: 0.7629 (mp0) cc_final: 0.7183 (mp0)
REVERT: I  222 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7296 (mp0)
REVERT: L  133 ARG cc_start: 0.8173 (ptp-170) cc_final: 0.7836 (ptp-170)
  outliers start: 49
  outliers final: 31
  residues processed: 221
  average time/residue: 0.8294
  time to fit residues: 209.0697
Evaluate side-chains
  232 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 197
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 LYS
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain F residue   90 THR
Chi-restraints excluded: chain F residue   92 SER
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain F residue  181 SER
Chi-restraints excluded: chain G residue  102 LEU
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  129 GLU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain I residue   93 VAL
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain J residue   72 CYS
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue   99 CYS
Chi-restraints excluded: chain L residue  127 CYS
Chi-restraints excluded: chain L residue  148 LEU
Chi-restraints excluded: chain L residue  159 GLN
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 101 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0270
   chunk 133 optimal weight:    5.9990
   chunk 126 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 165 optimal weight:    2.9990
   overall best weight:    1.0242

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

Flipped N/Q/H residues before XYZ refinement:
B 149 HIS
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 HIS
I 149 HIS
** L 177 ASN ** 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 = 0.4317 r_free = 0.4317 target = 0.172950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.143083 restraints weight = 16334.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 2.29
r_work: 0.3863 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  13726  Z= 0.224
  Angle     :  0.587   7.929  18636  Z= 0.310
  Chirality :  0.043   0.147   2024
  Planarity :  0.004   0.041   2430
  Dihedral  :  4.913  30.424   1860
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.49 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.28 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.21), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.36 (0.23), residues: 534
  loop : -0.03 (0.19), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 190 
 HIS   0.007   0.001   HIS L 134 
 PHE   0.014   0.002   PHE A 228 
 TYR   0.010   0.001   TYR I 191 
 ARG   0.013   0.000   ARG L 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03137 (  408)
  hydrogen bonds       : angle       5.32122 ( 1044)
  SS BOND              : bond        0.00342 (   66)
  SS BOND              : angle       1.59262 (  132)
  covalent geometry    : bond        0.00508 (13660)
  covalent geometry    : angle       0.57359 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 LEU cc_start: 0.8354 (tt) cc_final: 0.8147 (tp)
REVERT: B  129 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6852 (tm-30)
REVERT: B  141 LYS cc_start: 0.8588 (ptmt) cc_final: 0.8357 (ptmt)
REVERT: B  222 GLU cc_start: 0.7690 (mp0) cc_final: 0.7363 (mp0)
REVERT: F   90 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7876 (p)
REVERT: G  105 LEU cc_start: 0.8348 (mt) cc_final: 0.8095 (mp)
REVERT: H  129 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6792 (tm-30)
REVERT: H  167 VAL cc_start: 0.8139 (t) cc_final: 0.7922 (m)
REVERT: H  222 GLU cc_start: 0.7624 (mp0) cc_final: 0.7203 (mp0)
REVERT: L  133 ARG cc_start: 0.8171 (ptp-170) cc_final: 0.7854 (ptp-170)
  outliers start: 41
  outliers final: 33
  residues processed: 214
  average time/residue: 0.7721
  time to fit residues: 189.3511
Evaluate side-chains
  227 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 191
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 LYS
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain F residue   90 THR
Chi-restraints excluded: chain F residue   92 SER
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain F residue  181 SER
Chi-restraints excluded: chain G residue  102 LEU
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  129 GLU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain I residue   93 VAL
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain I residue  150 VAL
Chi-restraints excluded: chain J residue   72 CYS
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue   99 CYS
Chi-restraints excluded: chain L residue  127 CYS
Chi-restraints excluded: chain L residue  148 LEU
Chi-restraints excluded: chain L residue  159 GLN
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 143 optimal weight:    0.4980
   chunk 16 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 161 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 166 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 150 optimal weight:    0.9980
   chunk 128 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 101 GLN
B 149 HIS
B 201 GLN
D 145 ASN
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 HIS
H 168 ASN
I 149 HIS
** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.174397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.144284 restraints weight = 16415.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.30
r_work: 0.3878 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13726  Z= 0.163
  Angle     :  0.555   6.672  18636  Z= 0.294
  Chirality :  0.042   0.139   2024
  Planarity :  0.004   0.035   2430
  Dihedral  :  4.795  28.712   1860
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.89 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.21), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.43 (0.24), residues: 498
  loop :  0.04 (0.18), residues: 1188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 190 
 HIS   0.006   0.001   HIS A 149 
 PHE   0.013   0.001   PHE A 228 
 TYR   0.008   0.001   TYR I 191 
 ARG   0.008   0.000   ARG L 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02937 (  408)
  hydrogen bonds       : angle       5.25423 ( 1044)
  SS BOND              : bond        0.00290 (   66)
  SS BOND              : angle       1.39044 (  132)
  covalent geometry    : bond        0.00377 (13660)
  covalent geometry    : angle       0.54398 (18504)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 188
  time to evaluate  : 1.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 TYR cc_start: 0.8564 (m-80) cc_final: 0.8130 (m-80)
REVERT: B  141 LYS cc_start: 0.8591 (ptmt) cc_final: 0.8379 (ptmt)
REVERT: B  222 GLU cc_start: 0.7717 (mp0) cc_final: 0.7379 (mp0)
REVERT: F   90 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7870 (p)
REVERT: G  105 LEU cc_start: 0.8330 (mt) cc_final: 0.8087 (mp)
REVERT: H  129 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6813 (tm-30)
REVERT: H  150 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8708 (t)
REVERT: H  167 VAL cc_start: 0.8129 (t) cc_final: 0.7909 (m)
REVERT: H  174 LYS cc_start: 0.8418 (tttt) cc_final: 0.8148 (ttpt)
REVERT: H  222 GLU cc_start: 0.7623 (mp0) cc_final: 0.7185 (mp0)
REVERT: L  133 ARG cc_start: 0.8151 (ptp-170) cc_final: 0.7822 (ptp-170)
  outliers start: 42
  outliers final: 35
  residues processed: 208
  average time/residue: 1.1241
  time to fit residues: 267.2095
Evaluate side-chains
  224 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 186
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue  129 GLU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 LYS
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain E residue   44 CYS
Chi-restraints excluded: chain F residue   79 THR
Chi-restraints excluded: chain F residue   90 THR
Chi-restraints excluded: chain F residue   92 SER
Chi-restraints excluded: chain F residue   99 CYS
Chi-restraints excluded: chain F residue  127 CYS
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  167 THR
Chi-restraints excluded: chain F residue  181 SER
Chi-restraints excluded: chain G residue  102 LEU
Chi-restraints excluded: chain G residue  139 LEU
Chi-restraints excluded: chain G residue  150 VAL
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  129 GLU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain H residue  157 SER
Chi-restraints excluded: chain I residue   93 VAL
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  129 GLU
Chi-restraints excluded: chain I residue  150 VAL
Chi-restraints excluded: chain J residue   72 CYS
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue   99 CYS
Chi-restraints excluded: chain L residue  127 CYS
Chi-restraints excluded: chain L residue  148 LEU
Chi-restraints excluded: chain L residue  159 GLN
Chi-restraints excluded: chain L residue  165 VAL
Chi-restraints excluded: chain L residue  167 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 148 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 162 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 152 optimal weight:   10.0000
   chunk 102 optimal weight:    0.5980
   chunk 137 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 121 optimal weight:    0.0770
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
B 149 HIS
B 201 GLN
F 134 HIS
** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 HIS
** L 177 ASN ** 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 = 0.4332 r_free = 0.4332 target = 0.174295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.144577 restraints weight = 16458.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 2.29
r_work: 0.3879 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3721 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13726  Z= 0.152
  Angle     :  0.543   6.537  18636  Z= 0.288
  Chirality :  0.042   0.137   2024
  Planarity :  0.004   0.035   2430
  Dihedral  :  4.702  28.343   1860
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.96 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.21), residues: 1686
  helix:  None (None), residues: 0
  sheet:  0.43 (0.24), residues: 498
  loop :  0.08 (0.18), residues: 1188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 190 
 HIS   0.007   0.001   HIS A 149 
 PHE   0.012   0.001   PHE A 228 
 TYR   0.008   0.001   TYR L 132 
 ARG   0.008   0.000   ARG L 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02884 (  408)
  hydrogen bonds       : angle       5.16210 ( 1044)
  SS BOND              : bond        0.00242 (   66)
  SS BOND              : angle       1.31355 (  132)
  covalent geometry    : bond        0.00351 (13660)
  covalent geometry    : angle       0.53388 (18504)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13046.86 seconds
wall clock time: 232 minutes 19.17 seconds (13939.17 seconds total)