Starting phenix.real_space_refine
on Mon Jul 28 16:47:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x2c_32964/07_2025/7x2c_32964.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x2c_32964/07_2025/7x2c_32964.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2025/7x2c_32964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2025/7x2c_32964.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2025/7x2c_32964.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2025/7x2c_32964.cif"
  }
  resolution = 3.2
  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=  -0.005 sd=   0.086
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2939 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     Cl      2      4.86       5
     C    5071      2.51       5
     N    1341      2.21       5
     O    1483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7953
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 2167
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 279, 2156
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 9, 'TRANS': 269}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 65
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 47
      Conformer: "B"
        Number of residues, atoms: 279, 2156
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 9, 'TRANS': 269}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 65
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 47
          bond proxies already assigned to first conformer: 2197
    Chain: "A"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1824
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 52
    Chain: "B"
      Number of atoms: 2538
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 339, 2526
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 67
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 9, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 64
      Conformer: "B"
        Number of residues, atoms: 339, 2526
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 67
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 9, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 64
          bond proxies already assigned to first conformer: 2559
    Chain: "D"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 401
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "E"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 953
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "F"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 70
          Unusual residues: {'CLR': 1, 'G3C': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ACYS B 233 " occ=0.50
      ... (10 atoms not shown)
      pdb=" SG BCYS B 233 " occ=0.50
    residue:
      pdb=" N  ACYS B 271 " occ=0.50
      ... (10 atoms not shown)
      pdb=" SG BCYS B 271 " occ=0.50
  Time building chain proxies: 7.59, per 1000 atoms: 0.95
  Number of scatterers: 7953
  At special positions: 0
  Unit cell: (77.177, 101.091, 123.918, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      56     16.00
     O    1483      8.00
     N    1341      7.00
     C    5071      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  96 " - pdb=" SG  CYS F 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " 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: 2.72
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1958

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      44.2% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'F' and resid 20 through 51
      removed outlier: 3.522A  pdb=" N   VAL F  48 " --> pdb=" O   VAL F  44 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 53 through 57
      removed outlier: 3.620A  pdb=" N   LYS F  57 " --> pdb=" O   LEU F  54 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 58 through 88
      removed outlier: 3.815A  pdb=" N   PHE F  62 " --> pdb=" O   VAL F  58 " (cutoff:3.500A)
      Proline residue:  F  79  - end of helix
    Processing helix  chain 'F' and resid 94 through 127
      removed outlier: 4.444A  pdb=" N   ILE F  98 " --> pdb=" O   SER F  94 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   MET F 105 " --> pdb=" O   ALA F 101 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   CYS F 106 " --> pdb=" O   PHE F 102 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
    Processing helix  chain 'F' and resid 136 through 161
      removed outlier: 3.527A  pdb=" N   SER F 155 " --> pdb=" O   SER F 151 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   ILE F 157 " --> pdb=" O   LEU F 153 " (cutoff:3.500A)
      Proline residue:  F 158  - end of helix
    Processing helix  chain 'F' and resid 191 through 203
    Processing helix  chain 'F' and resid 203 through 241
    Processing helix  chain 'F' and resid 265 through 298
      removed outlier: 3.883A  pdb=" N   PHE F 281 " --> pdb=" O   ILE F 277 " (cutoff:3.500A)
      Proline residue:  F 287  - end of helix
      Proline residue:  F 296  - end of helix
    Processing helix  chain 'F' and resid 309 through 332
      removed outlier: 3.637A  pdb=" N   PHE F 313 " --> pdb=" O   ASP F 309 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   SER F 324 " --> pdb=" O   GLY F 320 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER F 325 " --> pdb=" O   TRP F 321 " (cutoff:3.500A)
      Proline residue:  F 328  - end of helix
    Processing helix  chain 'F' and resid 334 through 344
      removed outlier: 3.580A  pdb=" N   LYS F 339 " --> pdb=" O   ALA F 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.675A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.879A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.556A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.862A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.636A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.559A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.635A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 9 through 23
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.552A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
      removed outlier: 3.595A  pdb=" N   ASP D  48 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 48'
    Processing helix  chain 'D' and resid 55 through 59
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.159A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 6.241A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.394A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.821A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.028A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.615A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.595A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.526A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.983A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 7.055A  pdb=" N   MET E  34 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ASP E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)

    427 hydrogen bonds defined for protein.
    1232 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 3.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2575
        1.34 -     1.46: 2028
        1.46 -     1.58: 3444
        1.58 -     1.70: 6
        1.70 -     1.82: 77
  Bond restraints: 8130
  Sorted by residual:
  bond pdb=" C06 G3C F 503 "
       pdb=" C07 G3C F 503 "
    ideal  model  delta    sigma   weight residual
    1.523  1.650 -0.127 2.00e-02 2.50e+03 4.06e+01
  bond pdb=" C07 G3C F 502 "
       pdb=" C08 G3C F 502 "
    ideal  model  delta    sigma   weight residual
    1.510  1.637 -0.127 2.00e-02 2.50e+03 4.03e+01
  bond pdb=" C07 G3C F 503 "
       pdb=" C08 G3C F 503 "
    ideal  model  delta    sigma   weight residual
    1.510  1.632 -0.122 2.00e-02 2.50e+03 3.72e+01
  bond pdb=" C06 G3C F 502 "
       pdb=" C07 G3C F 502 "
    ideal  model  delta    sigma   weight residual
    1.523  1.639 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" C13 CLR F 501 "
       pdb=" C17 CLR F 501 "
    ideal  model  delta    sigma   weight residual
    1.550  1.438  0.112 2.00e-02 2.50e+03 3.13e+01
  ... (remaining 8125 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 10910
        2.40 -     4.80: 136
        4.80 -     7.20: 26
        7.20 -     9.59: 6
        9.59 -    11.99: 2
  Bond angle restraints: 11080
  Sorted by residual:
  angle pdb=" C23 CLR F 501 "
        pdb=" C24 CLR F 501 "
        pdb=" C25 CLR F 501 "
      ideal   model   delta    sigma   weight residual
     115.14  103.15   11.99 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" C   GLY A 353 "
        pdb=" N   ASP A 354 "
        pdb=" CA  ASP A 354 "
      ideal   model   delta    sigma   weight residual
     122.61  128.39   -5.78 1.56e+00 4.11e-01 1.37e+01
  angle pdb=" N   GLY B 319 "
        pdb=" CA  GLY B 319 "
        pdb=" C   GLY B 319 "
      ideal   model   delta    sigma   weight residual
     110.87  116.55   -5.68 1.54e+00 4.22e-01 1.36e+01
  angle pdb=" C   TYR F 204 "
        pdb=" N   ILE F 205 "
        pdb=" CA  ILE F 205 "
      ideal   model   delta    sigma   weight residual
     122.13  116.03    6.10 1.85e+00 2.92e-01 1.09e+01
  angle pdb=" C17 CLR F 501 "
        pdb=" C20 CLR F 501 "
        pdb=" C22 CLR F 501 "
      ideal   model   delta    sigma   weight residual
     109.45   99.78    9.67 3.00e+00 1.11e-01 1.04e+01
  ... (remaining 11075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4409
       17.95 -    35.90: 350
       35.90 -    53.85: 62
       53.85 -    71.80: 13
       71.80 -    89.75: 3
  Dihedral angle restraints: 4837
    sinusoidal: 1820
      harmonic: 3017
  Sorted by residual:
  dihedral pdb=" CB  CYS F  96 "
           pdb=" SG  CYS F  96 "
           pdb=" SG  CYS F 186 "
           pdb=" CB  CYS F 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  139.20  -46.20     1      1.00e+01 1.00e-02 2.96e+01
  dihedral pdb=" CA  ILE F 201 "
           pdb=" C   ILE F 201 "
           pdb=" N   SER F 202 "
           pdb=" CA  SER F 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.95  -21.05     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  MET F 135 "
           pdb=" C   MET F 135 "
           pdb=" N   THR F 136 "
           pdb=" CA  THR F 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.11   17.89     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 4834 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 1271
       0.135 -    0.270: 2
       0.270 -    0.405: 2
       0.405 -    0.540: 0
       0.540 -    0.675: 2
  Chirality restraints: 1277
  Sorted by residual:
  chirality pdb=" C13 CLR F 501 "
            pdb=" C12 CLR F 501 "
            pdb=" C14 CLR F 501 "
            pdb=" C17 CLR F 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.26   -0.67 2.00e-01 2.50e+01 1.14e+01
  chirality pdb=" C10 CLR F 501 "
            pdb=" C1  CLR F 501 "
            pdb=" C5  CLR F 501 "
            pdb=" C9  CLR F 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.23   -0.62 2.00e-01 2.50e+01 9.64e+00
  chirality pdb=" C07 G3C F 502 "
            pdb=" C06 G3C F 502 "
            pdb=" C08 G3C F 502 "
            pdb=" C15 G3C F 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.44   -2.75    0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 1274 not shown)

  Planarity restraints: 1403
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE F 205 "    0.052 5.00e-02 4.00e+02   7.88e-02 9.92e+00
        pdb=" N   PRO F 206 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO F 206 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO F 206 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 201 "   -0.015 2.00e-02 2.50e+03   2.98e-02 8.86e+00
        pdb=" C   ILE F 201 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ILE F 201 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER F 202 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN F 327 "    0.047 5.00e-02 4.00e+02   7.08e-02 8.02e+00
        pdb=" N   PRO F 328 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO F 328 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO F 328 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1400 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 122
        2.66 -     3.22: 7579
        3.22 -     3.78: 12542
        3.78 -     4.34: 16750
        4.34 -     4.90: 28139
  Nonbonded interactions: 65132
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OD1 ASP A 229 "
            pdb=" OG1 THR E 111 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" N   GLY B 324 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG  SER F 198 "
            pdb=" O01 G3C F 503 "
     model   vdw
     2.255 3.040
  ... (remaining 65127 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.550
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
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      :  0.006   0.127   8133  Z= 0.293
  Angle     :  0.706  11.992  11086  Z= 0.358
  Chirality :  0.051   0.675   1277
  Planarity :  0.005   0.079   1403
  Dihedral  : 13.490  89.746   2870
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.24 %
    Favored  : 99.27 %
  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:  0.97 (0.26), residues: 1020
  helix:  1.81 (0.26), residues: 406
  sheet:  0.52 (0.33), residues: 224
  loop : -0.48 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B  63 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.020   0.001   PHE A 212 
 TYR   0.021   0.001   TYR B  59 
 ARG   0.005   0.000   ARG F 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15181 (  427)
  hydrogen bonds       : angle       6.37957 ( 1232)
  SS BOND              : bond        0.00122 (    3)
  SS BOND              : angle       1.13817 (    6)
  covalent geometry    : bond        0.00588 ( 8130)
  covalent geometry    : angle       0.70545 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6845 (mt-10)
REVERT: A   29 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7120 (tm-30)
REVERT: A  386 MET cc_start: 0.7988 (ttm) cc_final: 0.7455 (tpp)
REVERT: B  137 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7337 (mmm160)
REVERT: B  148 CYS cc_start: 0.8391 (t) cc_final: 0.8171 (t)
REVERT: B  217 MET cc_start: 0.6838 (tmm) cc_final: 0.6290 (tmm)
REVERT: D   41 CYS cc_start: 0.7902 (m) cc_final: 0.7668 (m)
REVERT: D   47 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6891 (mp0)
REVERT: E   82 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7407 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1890
  time to fit residues: 41.0365
Evaluate side-chains
  139 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:   20.0000
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0970
   chunk 57 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    2.7384

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 160 GLN
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
A 213 GLN
B 119 ASN
B 237 ASN
B 259 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.164476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.112808 restraints weight = 29002.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 5.35
r_work: 0.3269 rms_B_bonded: 5.34 restraints_weight: 2.0000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3293
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3293 r_free = 0.3293    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8133  Z= 0.237
  Angle     :  0.632   6.714  11086  Z= 0.343
  Chirality :  0.045   0.153   1277
  Planarity :  0.005   0.077   1403
  Dihedral  :  4.635  28.194   1203
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  8.95 %
    Favored  : 89.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1020
  helix:  1.94 (0.25), residues: 405
  sheet:  0.43 (0.35), residues: 198
  loop : -0.40 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP B  63 
 HIS   0.006   0.002   HIS A 220 
 PHE   0.016   0.002   PHE F 289 
 TYR   0.031   0.002   TYR B  59 
 ARG   0.004   0.001   ARG D  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04747 (  427)
  hydrogen bonds       : angle       4.97310 ( 1232)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       1.75897 (    6)
  covalent geometry    : bond        0.00549 ( 8130)
  covalent geometry    : angle       0.63077 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.7786 (tpt-90)
REVERT: A  294 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7778 (mm-40)
REVERT: A  386 MET cc_start: 0.8558 (ttm) cc_final: 0.7818 (tpp)
REVERT: B   68 ARG cc_start: 0.8349 (mtp180) cc_final: 0.7498 (mtp180)
REVERT: B  137 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7136 (mmm160)
REVERT: B  217 MET cc_start: 0.6474 (tmm) cc_final: 0.5988 (tmm)
REVERT: B  220 GLN cc_start: 0.7738 (tt0) cc_final: 0.7478 (tt0)
REVERT: B  254 ASP cc_start: 0.7854 (t70) cc_final: 0.7607 (t70)
REVERT: D   47 GLU cc_start: 0.7746 (mt-10) cc_final: 0.6925 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 150
  average time/residue: 0.1960
  time to fit residues: 40.1251
Evaluate side-chains
  143 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 43 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.168637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.114538 restraints weight = 35422.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 6.09
r_work: 0.3304 rms_B_bonded: 5.90 restraints_weight: 2.0000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8133  Z= 0.131
  Angle     :  0.543   7.158  11086  Z= 0.289
  Chirality :  0.042   0.200   1277
  Planarity :  0.004   0.067   1403
  Dihedral  :  4.413  31.649   1203
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.49 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1020
  helix:  2.20 (0.25), residues: 406
  sheet:  0.45 (0.35), residues: 192
  loop : -0.28 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  63 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.017   0.001   PHE F 288 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.003   0.000   ARG F 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04140 (  427)
  hydrogen bonds       : angle       4.64145 ( 1232)
  SS BOND              : bond        0.00150 (    3)
  SS BOND              : angle       1.21921 (    6)
  covalent geometry    : bond        0.00290 ( 8130)
  covalent geometry    : angle       0.54272 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7895 (mm-40)
REVERT: A  317 ARG cc_start: 0.8700 (ttp80) cc_final: 0.8454 (ttp80)
REVERT: A  368 ASP cc_start: 0.7152 (m-30) cc_final: 0.6811 (m-30)
REVERT: A  386 MET cc_start: 0.8649 (ttm) cc_final: 0.7926 (tpp)
REVERT: B  137 ARG cc_start: 0.7830 (mmm160) cc_final: 0.7402 (mmm160)
REVERT: B  217 MET cc_start: 0.6241 (tmm) cc_final: 0.5786 (tmm)
REVERT: B  220 GLN cc_start: 0.7694 (tt0) cc_final: 0.7459 (tt0)
REVERT: B  254 ASP cc_start: 0.7942 (t70) cc_final: 0.7635 (t70)
REVERT: B  298 ASP cc_start: 0.7976 (t70) cc_final: 0.7183 (t0)
REVERT: D   47 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7027 (mp0)
REVERT: E   32 TYR cc_start: 0.8444 (m-80) cc_final: 0.8131 (m-80)
REVERT: E   49 SER cc_start: 0.8799 (m) cc_final: 0.8439 (t)
  outliers start: 11
  outliers final: 8
  residues processed: 152
  average time/residue: 0.2580
  time to fit residues: 53.0597
Evaluate side-chains
  149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  146 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 92 optimal weight:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0470
   chunk 95 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 29 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.7484

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
A 278 ASN
E  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.166327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.114118 restraints weight = 29512.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 5.49
r_work: 0.3284 rms_B_bonded: 5.42 restraints_weight: 2.0000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8133  Z= 0.169
  Angle     :  0.561   6.482  11086  Z= 0.301
  Chirality :  0.043   0.165   1277
  Planarity :  0.004   0.066   1403
  Dihedral  :  4.443  34.090   1203
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.91 %
    Favored  : 84.16 %
  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:  1.23 (0.26), residues: 1020
  helix:  2.15 (0.25), residues: 406
  sheet:  0.42 (0.35), residues: 192
  loop : -0.28 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B  63 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.015   0.002   PHE F 289 
 TYR   0.009   0.001   TYR F 194 
 ARG   0.006   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04200 (  427)
  hydrogen bonds       : angle       4.58047 ( 1232)
  SS BOND              : bond        0.00157 (    3)
  SS BOND              : angle       1.35703 (    6)
  covalent geometry    : bond        0.00390 ( 8130)
  covalent geometry    : angle       0.56074 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  226 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7420 (mtm-85)
REVERT: A  294 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7654 (mm110)
REVERT: A  317 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8454 (ttp80)
REVERT: A  368 ASP cc_start: 0.6987 (m-30) cc_final: 0.6668 (m-30)
REVERT: A  386 MET cc_start: 0.8526 (ttm) cc_final: 0.7772 (tpp)
REVERT: B   68 ARG cc_start: 0.8319 (mtp180) cc_final: 0.7899 (mtp180)
REVERT: B  137 ARG cc_start: 0.7702 (mmm160) cc_final: 0.7312 (mmm160)
REVERT: B  217 MET cc_start: 0.5962 (tmm) cc_final: 0.5541 (tmm)
REVERT: B  254 ASP cc_start: 0.7860 (t70) cc_final: 0.7593 (t70)
REVERT: B  298 ASP cc_start: 0.7809 (t70) cc_final: 0.7011 (t0)
REVERT: D   47 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6922 (mp0)
REVERT: E   49 SER cc_start: 0.8680 (m) cc_final: 0.8279 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 157
  average time/residue: 0.2684
  time to fit residues: 57.8296
Evaluate side-chains
  153 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 ILE
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain E residue   31 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0870
   chunk 76 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.168206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.117401 restraints weight = 24689.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 5.00
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3550
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3550
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8133  Z= 0.127
  Angle     :  0.527   6.679  11086  Z= 0.282
  Chirality :  0.042   0.168   1277
  Planarity :  0.004   0.060   1403
  Dihedral  :  4.341  36.439   1203
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.48 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1020
  helix:  2.27 (0.25), residues: 407
  sheet:  0.44 (0.36), residues: 192
  loop : -0.24 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  63 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.016   0.001   PHE F 288 
 TYR   0.009   0.001   TYR A 253 
 ARG   0.005   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  427)
  hydrogen bonds       : angle       4.41943 ( 1232)
  SS BOND              : bond        0.00117 (    3)
  SS BOND              : angle       1.13306 (    6)
  covalent geometry    : bond        0.00283 ( 8130)
  covalent geometry    : angle       0.52676 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7356 (m100) cc_final: 0.7142 (m100)
REVERT: F  226 ARG cc_start: 0.7645 (ttm170) cc_final: 0.7402 (mtm-85)
REVERT: A  280 ARG cc_start: 0.8000 (ttt-90) cc_final: 0.7401 (tpt-90)
REVERT: A  294 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7742 (mm-40)
REVERT: A  317 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8458 (ttp80)
REVERT: A  368 ASP cc_start: 0.7203 (m-30) cc_final: 0.6888 (m-30)
REVERT: A  386 MET cc_start: 0.8219 (ttm) cc_final: 0.7543 (tpp)
REVERT: B   68 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7851 (mtp180)
REVERT: B  137 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7323 (mmm160)
REVERT: B  171 ILE cc_start: 0.7857 (mp) cc_final: 0.7394 (mp)
REVERT: B  217 MET cc_start: 0.6288 (tmm) cc_final: 0.5883 (tmm)
REVERT: B  220 GLN cc_start: 0.8070 (tt0) cc_final: 0.7839 (tt0)
REVERT: B  254 ASP cc_start: 0.7795 (t70) cc_final: 0.7549 (t70)
REVERT: D   47 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6948 (mp0)
REVERT: E   29 PHE cc_start: 0.8647 (t80) cc_final: 0.8231 (t80)
REVERT: E   49 SER cc_start: 0.8622 (m) cc_final: 0.8219 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 161
  average time/residue: 0.3060
  time to fit residues: 64.9912
Evaluate side-chains
  155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain E residue   20 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 88 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0970
   chunk 29 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 323 ASN
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.169970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.119313 restraints weight = 23722.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 4.96
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8133  Z= 0.113
  Angle     :  0.519   7.137  11086  Z= 0.276
  Chirality :  0.041   0.168   1277
  Planarity :  0.004   0.056   1403
  Dihedral  :  4.231  39.262   1203
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.60 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1020
  helix:  2.36 (0.25), residues: 408
  sheet:  0.25 (0.36), residues: 197
  loop : -0.16 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.013   0.001   PHE F 289 
 TYR   0.008   0.001   TYR A 253 
 ARG   0.008   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03733 (  427)
  hydrogen bonds       : angle       4.30385 ( 1232)
  SS BOND              : bond        0.00111 (    3)
  SS BOND              : angle       1.01149 (    6)
  covalent geometry    : bond        0.00248 ( 8130)
  covalent geometry    : angle       0.51840 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7419 (m100) cc_final: 0.7187 (m100)
REVERT: F  226 ARG cc_start: 0.7650 (ttm170) cc_final: 0.7425 (mtm-85)
REVERT: A  294 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7740 (mm-40)
REVERT: A  368 ASP cc_start: 0.7252 (m-30) cc_final: 0.6906 (m-30)
REVERT: A  386 MET cc_start: 0.8194 (ttm) cc_final: 0.7507 (tpp)
REVERT: B  101 MET cc_start: 0.8699 (mtt) cc_final: 0.8391 (mtp)
REVERT: B  137 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7309 (mmm160)
REVERT: B  171 ILE cc_start: 0.7928 (mp) cc_final: 0.7481 (mp)
REVERT: B  217 MET cc_start: 0.6323 (tmm) cc_final: 0.5930 (tmm)
REVERT: B  220 GLN cc_start: 0.8108 (tt0) cc_final: 0.7890 (tt0)
REVERT: B  254 ASP cc_start: 0.7725 (t70) cc_final: 0.7505 (t70)
REVERT: B  283 ARG cc_start: 0.7801 (tpt-90) cc_final: 0.7543 (tpt-90)
REVERT: B  298 ASP cc_start: 0.7823 (t70) cc_final: 0.7254 (t70)
REVERT: B  303 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7325 (m-30)
REVERT: D   47 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6840 (mp0)
  outliers start: 18
  outliers final: 11
  residues processed: 161
  average time/residue: 0.2335
  time to fit residues: 49.7623
Evaluate side-chains
  154 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain E residue   20 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0770
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.4146

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
B 230 ASN
E  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.167848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.114706 restraints weight = 35307.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 6.02
r_work: 0.3293 rms_B_bonded: 5.79 restraints_weight: 2.0000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8133  Z= 0.148
  Angle     :  0.550   6.494  11086  Z= 0.293
  Chirality :  0.042   0.162   1277
  Planarity :  0.004   0.058   1403
  Dihedral  :  4.290  38.180   1203
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.20 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1020
  helix:  2.21 (0.25), residues: 412
  sheet:  0.18 (0.36), residues: 197
  loop : -0.09 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 281 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.014   0.001   PHE F 289 
 TYR   0.009   0.001   TYR A 253 
 ARG   0.007   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  427)
  hydrogen bonds       : angle       4.36997 ( 1232)
  SS BOND              : bond        0.00161 (    3)
  SS BOND              : angle       1.11312 (    6)
  covalent geometry    : bond        0.00343 ( 8130)
  covalent geometry    : angle       0.54953 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7381 (m100) cc_final: 0.7070 (m100)
REVERT: F  226 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7478 (mtm-85)
REVERT: A  294 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7712 (mm-40)
REVERT: A  368 ASP cc_start: 0.7027 (m-30) cc_final: 0.6723 (m-30)
REVERT: A  386 MET cc_start: 0.8558 (ttm) cc_final: 0.7817 (tpp)
REVERT: B   68 ARG cc_start: 0.8372 (mtp180) cc_final: 0.7584 (mtp-110)
REVERT: B  137 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7311 (mmm160)
REVERT: B  171 ILE cc_start: 0.8037 (mp) cc_final: 0.7583 (mp)
REVERT: B  217 MET cc_start: 0.6407 (tmm) cc_final: 0.5921 (tmm)
REVERT: B  254 ASP cc_start: 0.7866 (t70) cc_final: 0.7618 (t0)
REVERT: B  298 ASP cc_start: 0.8213 (t70) cc_final: 0.7474 (t70)
REVERT: D   47 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6941 (mp0)
REVERT: E   49 SER cc_start: 0.8632 (m) cc_final: 0.8251 (t)
  outliers start: 19
  outliers final: 16
  residues processed: 158
  average time/residue: 0.2603
  time to fit residues: 56.3682
Evaluate side-chains
  162 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 1.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain E residue   31 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.168509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.118351 restraints weight = 27729.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 5.74
r_work: 0.3315 rms_B_bonded: 5.48 restraints_weight: 2.0000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3334
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3334
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8133  Z= 0.136
  Angle     :  0.543   6.843  11086  Z= 0.289
  Chirality :  0.042   0.158   1277
  Planarity :  0.004   0.057   1403
  Dihedral  :  4.346  38.569   1203
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.57 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.27), residues: 1020
  helix:  2.22 (0.25), residues: 412
  sheet:  0.18 (0.36), residues: 197
  loop : -0.10 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 281 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.014   0.001   PHE F 288 
 TYR   0.008   0.001   TYR A 253 
 ARG   0.008   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  427)
  hydrogen bonds       : angle       4.33306 ( 1232)
  SS BOND              : bond        0.00119 (    3)
  SS BOND              : angle       1.15255 (    6)
  covalent geometry    : bond        0.00311 ( 8130)
  covalent geometry    : angle       0.54212 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7366 (m100) cc_final: 0.7038 (m100)
REVERT: F  226 ARG cc_start: 0.7692 (ttm170) cc_final: 0.7437 (mtm-85)
REVERT: A  368 ASP cc_start: 0.7029 (m-30) cc_final: 0.6705 (m-30)
REVERT: A  386 MET cc_start: 0.8516 (ttm) cc_final: 0.7768 (tpp)
REVERT: B   68 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7192 (mtp180)
REVERT: B  137 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7322 (mmm160)
REVERT: B  171 ILE cc_start: 0.7957 (mp) cc_final: 0.7518 (mp)
REVERT: B  217 MET cc_start: 0.6313 (tmm) cc_final: 0.5844 (tmm)
REVERT: B  254 ASP cc_start: 0.7832 (t70) cc_final: 0.7569 (t70)
REVERT: B  298 ASP cc_start: 0.8152 (t70) cc_final: 0.7356 (t70)
REVERT: D   47 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6933 (mp0)
REVERT: E   49 SER cc_start: 0.8535 (m) cc_final: 0.8142 (t)
  outliers start: 17
  outliers final: 14
  residues processed: 154
  average time/residue: 0.2345
  time to fit residues: 48.0948
Evaluate side-chains
  158 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   46 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.169620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.117426 restraints weight = 32113.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 6.14
r_work: 0.3303 rms_B_bonded: 5.80 restraints_weight: 2.0000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8133  Z= 0.127
  Angle     :  0.537   7.103  11086  Z= 0.286
  Chirality :  0.041   0.150   1277
  Planarity :  0.004   0.057   1403
  Dihedral  :  4.334  39.536   1203
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.05 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.27), residues: 1020
  helix:  2.23 (0.25), residues: 413
  sheet:  0.15 (0.36), residues: 196
  loop : -0.09 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 281 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.013   0.001   PHE F 289 
 TYR   0.008   0.001   TYR F 131 
 ARG   0.008   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  427)
  hydrogen bonds       : angle       4.29612 ( 1232)
  SS BOND              : bond        0.00101 (    3)
  SS BOND              : angle       1.08648 (    6)
  covalent geometry    : bond        0.00290 ( 8130)
  covalent geometry    : angle       0.53666 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7369 (m100) cc_final: 0.7073 (m100)
REVERT: F  226 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7440 (mtm-85)
REVERT: A  294 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7896 (mm-40)
REVERT: A  368 ASP cc_start: 0.7085 (m-30) cc_final: 0.6834 (m-30)
REVERT: A  386 MET cc_start: 0.8522 (ttm) cc_final: 0.7780 (tpp)
REVERT: B   68 ARG cc_start: 0.8325 (mtp180) cc_final: 0.7557 (mtp-110)
REVERT: B  101 MET cc_start: 0.8793 (mtt) cc_final: 0.8580 (mtp)
REVERT: B  137 ARG cc_start: 0.7723 (mmm160) cc_final: 0.7325 (mmm160)
REVERT: B  171 ILE cc_start: 0.7956 (mp) cc_final: 0.7515 (mp)
REVERT: B  217 MET cc_start: 0.6275 (tmm) cc_final: 0.5839 (tmm)
REVERT: B  254 ASP cc_start: 0.7805 (t70) cc_final: 0.7525 (t70)
REVERT: B  298 ASP cc_start: 0.8168 (t70) cc_final: 0.7367 (t70)
REVERT: D   47 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6884 (mp0)
REVERT: E   49 SER cc_start: 0.8543 (m) cc_final: 0.8165 (t)
  outliers start: 17
  outliers final: 14
  residues processed: 154
  average time/residue: 0.2316
  time to fit residues: 48.8250
Evaluate side-chains
  155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain E residue   20 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0770
   chunk 92 optimal weight:    0.0270
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.176375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122503 restraints weight = 36454.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 6.46
r_work: 0.3334 rms_B_bonded: 6.11 restraints_weight: 2.0000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8133  Z= 0.109
  Angle     :  0.533   8.987  11086  Z= 0.281
  Chirality :  0.041   0.143   1277
  Planarity :  0.004   0.055   1403
  Dihedral  :  4.256  41.859   1203
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.65 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.27), residues: 1020
  helix:  2.34 (0.25), residues: 418
  sheet:  0.10 (0.35), residues: 201
  loop : -0.05 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 281 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.013   0.001   PHE F 289 
 TYR   0.007   0.001   TYR B 124 
 ARG   0.009   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  427)
  hydrogen bonds       : angle       4.19695 ( 1232)
  SS BOND              : bond        0.00060 (    3)
  SS BOND              : angle       0.91485 (    6)
  covalent geometry    : bond        0.00239 ( 8130)
  covalent geometry    : angle       0.53236 (11080)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   78 MET cc_start: 0.7160 (mmt) cc_final: 0.6928 (mmt)
REVERT: F  163 TRP cc_start: 0.7361 (m100) cc_final: 0.7083 (m100)
REVERT: F  226 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7404 (mtm-85)
REVERT: A  253 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7532 (m-80)
REVERT: A  294 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7809 (mm-40)
REVERT: A  368 ASP cc_start: 0.7189 (m-30) cc_final: 0.6843 (m-30)
REVERT: A  386 MET cc_start: 0.8406 (ttm) cc_final: 0.7671 (tpp)
REVERT: B   68 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7506 (mtp-110)
REVERT: B  137 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7303 (mmm160)
REVERT: B  148 CYS cc_start: 0.8009 (t) cc_final: 0.7422 (m)
REVERT: B  171 ILE cc_start: 0.7865 (mp) cc_final: 0.7413 (mp)
REVERT: B  217 MET cc_start: 0.6219 (tmm) cc_final: 0.5810 (tmm)
REVERT: B  254 ASP cc_start: 0.7751 (t70) cc_final: 0.7524 (t70)
REVERT: B  298 ASP cc_start: 0.8171 (t70) cc_final: 0.7392 (t70)
REVERT: D   47 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6762 (mp0)
REVERT: E   47 TRP cc_start: 0.7456 (t60) cc_final: 0.6940 (t60)
REVERT: E   49 SER cc_start: 0.8421 (m) cc_final: 0.8212 (t)
  outliers start: 17
  outliers final: 12
  residues processed: 149
  average time/residue: 0.2651
  time to fit residues: 54.4351
Evaluate side-chains
  148 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  253 TYR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   chunk 17 optimal weight:    0.3980
   chunk 72 optimal weight:    0.0470
   chunk 33 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.8680

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

Flipped N/Q/H residues before XYZ refinement:
** F  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.176382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.124421 restraints weight = 23700.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 5.35
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.094   8133  Z= 0.150
  Angle     :  0.903  59.200  11086  Z= 0.546
  Chirality :  0.044   0.584   1277
  Planarity :  0.004   0.055   1403
  Dihedral  :  4.273  41.844   1203
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.65 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.27), residues: 1020
  helix:  2.27 (0.25), residues: 418
  sheet:  0.11 (0.35), residues: 201
  loop : -0.05 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.033   0.001   PHE E  29 
 TYR   0.007   0.001   TYR B 124 
 ARG   0.008   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  427)
  hydrogen bonds       : angle       4.22629 ( 1232)
  SS BOND              : bond        0.00053 (    3)
  SS BOND              : angle       0.91268 (    6)
  covalent geometry    : bond        0.00317 ( 8130)
  covalent geometry    : angle       0.90326 (11080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5613.48 seconds
wall clock time: 102 minutes 51.34 seconds (6171.34 seconds total)