Starting phenix.real_space_refine
on Sun May 11 04:59:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gcm_29935/05_2025/8gcm_29935_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gcm_29935/05_2025/8gcm_29935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gcm_29935/05_2025/8gcm_29935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gcm_29935/05_2025/8gcm_29935.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gcm_29935/05_2025/8gcm_29935_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gcm_29935/05_2025/8gcm_29935_neut.cif"
  }
  resolution = 3.5
  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=  -0.002 sd=   0.060
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    4769      2.51       5
     N    1295      2.21       5
     O    1389      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7508
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1430
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'TRANS': 197}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 156
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'PHE%COO:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 95
    Chain: "B"
      Number of atoms: 2384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2384
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 224
          Unresolved non-hydrogen angles: 279
          Unresolved non-hydrogen dihedrals: 171
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 156
    Chain: "C"
      Number of atoms: 352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 352
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 42
    Chain: "E"
      Number of atoms: 1672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1672
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 106
          Unresolved non-hydrogen angles: 130
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 56
    Chain: "R"
      Number of atoms: 1640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1640
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 105}
          Link IDs: {'PTRANS': 10, 'TRANS': 243}
          Chain breaks: 4
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 389
          Unresolved non-hydrogen angles: 497
          Unresolved non-hydrogen dihedrals: 321
          Unresolved non-hydrogen chiralities: 42
          Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 193
    Chain: "R"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'YX9': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.59, per 1000 atoms: 0.61
  Number of scatterers: 7508
  At special positions: 0
  Unit cell: (89.79, 119.355, 127.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      53     16.00
     F       2      9.00
     O    1389      8.00
     N    1295      7.00
     C    4769      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  92 " - pdb=" SG  CYS R 170 " distance=2.04

  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: 1.70
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      33.4% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 29
      removed outlier: 4.622A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ASP A  26 " --> pdb=" O   ASN A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 53
      removed outlier: 3.767A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.128A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ILE A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 207 through 212'
    Processing helix  chain 'A' and resid 213 through 215
      No H-bonds generated for 'chain 'A' and resid 213 through 215'
    Processing helix  chain 'A' and resid 243 through 254
    Processing helix  chain 'A' and resid 273 through 278
      removed outlier: 3.688A  pdb=" N   LYS A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.567A  pdb=" N   GLU A 308 " --> pdb=" O   GLN A 304 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP A 309 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.610A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 340 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.644A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.896A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 34'
    Processing helix  chain 'C' and resid 10 through 23
    Processing helix  chain 'C' and resid 31 through 42
      removed outlier: 4.177A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   TYR C  40 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 48
      removed outlier: 3.616A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.656A  pdb=" N   PHE E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 65
      removed outlier: 3.630A  pdb=" N   LYS E  65 " --> pdb=" O   ASP E  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 62 through 65'
    Processing helix  chain 'R' and resid 24 through 45
      removed outlier: 4.066A  pdb=" N   PHE R  28 " --> pdb=" O   PRO R  24 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE R  29 " --> pdb=" O   ALA R  25 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY R  31 " --> pdb=" O   MET R  27 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   VAL R  32 " --> pdb=" O   PHE R  28 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL R  33 " --> pdb=" O   ILE R  29 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 46 through 50
    Processing helix  chain 'R' and resid 54 through 72
      removed outlier: 3.601A  pdb=" N   LEU R  70 " --> pdb=" O   LEU R  66 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL R  72 " --> pdb=" O   GLY R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 77
      removed outlier: 3.967A  pdb=" N   THR R  76 " --> pdb=" O   SER R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 106
      removed outlier: 3.506A  pdb=" N   LEU R  99 " --> pdb=" O   SER R  95 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   LEU R 100 " --> pdb=" O   THR R  96 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU R 104 " --> pdb=" O   LEU R 100 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 107 through 114
    Processing helix  chain 'R' and resid 115 through 120
    Processing helix  chain 'R' and resid 123 through 130
    Processing helix  chain 'R' and resid 134 through 156
      removed outlier: 4.066A  pdb=" N   LEU R 138 " --> pdb=" O   ARG R 134 " (cutoff:3.500A)
      Proline residue:  R 154  - end of helix
    Processing helix  chain 'R' and resid 184 through 219
      removed outlier: 3.881A  pdb=" N   CYS R 207 " --> pdb=" O   ASN R 203 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU R 211 " --> pdb=" O   CYS R 207 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET R 218 " --> pdb=" O   HIS R 214 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ARG R 219 " --> pdb=" O   ARG R 215 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 266 through 284
      removed outlier: 3.639A  pdb=" N   VAL R 271 " --> pdb=" O   GLU R 267 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ILE R 272 " --> pdb=" O   ILE R 268 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LEU R 273 " --> pdb=" O   GLN R 269 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 285 through 298
      removed outlier: 4.112A  pdb=" N   VAL R 289 " --> pdb=" O   SER R 285 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASN R 295 " --> pdb=" O   ARG R 291 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 319
      removed outlier: 3.564A  pdb=" N   SER R 319 " --> pdb=" O   ILE R 315 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 320 through 325
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 188
      removed outlier: 3.918A  pdb=" N   ASP A 200 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.203A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 221 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 188
      removed outlier: 3.918A  pdb=" N   ASP A 200 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.203A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.017A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.005A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.687A  pdb=" N   VAL B 112 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.607A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191
      removed outlier: 3.801A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.708A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278
      removed outlier: 4.050A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 6 through 7
      removed outlier: 3.723A  pdb=" N   SER E   7 " --> pdb=" O   SER E  21 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 33 through 35
    Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47
      removed outlier: 3.820A  pdb=" N   GLU E  46 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 49 through 50
      removed outlier: 3.920A  pdb=" N   TYR E  50 " --> pdb=" O   TYR E  59 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR E  59 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'E' and resid 141 through 142
      removed outlier: 3.660A  pdb=" N   ALA E 211 " --> pdb=" O   SER E 208 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   SER E 204 " --> pdb=" O   THR E 215 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.772A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    852 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: 2.40

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1223
        1.26 -     1.40: 1952
        1.40 -     1.54: 4323
        1.54 -     1.68: 73
        1.68 -     1.82: 76
  Bond restraints: 7647
  Sorted by residual:
  bond pdb=" C14 YX9 R 501 "
       pdb=" C18 YX9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.535  1.305  0.230 2.00e-02 2.50e+03 1.33e+02
  bond pdb=" C16 YX9 R 501 "
       pdb=" C17 YX9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.515  1.330  0.185 2.00e-02 2.50e+03 8.52e+01
  bond pdb=" C14 YX9 R 501 "
       pdb=" N15 YX9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.458  1.598 -0.140 2.00e-02 2.50e+03 4.93e+01
  bond pdb=" C17 YX9 R 501 "
       pdb=" C18 YX9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.525  1.665 -0.140 2.00e-02 2.50e+03 4.87e+01
  bond pdb=" C16 YX9 R 501 "
       pdb=" N15 YX9 R 501 "
    ideal  model  delta    sigma   weight residual
    1.349  1.475 -0.126 2.00e-02 2.50e+03 3.96e+01
  ... (remaining 7642 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.44: 10161
        3.44 -     6.87: 239
        6.87 -    10.31: 38
       10.31 -    13.74: 4
       13.74 -    17.18: 1
  Bond angle restraints: 10443
  Sorted by residual:
  angle pdb=" C   SER R  73 "
        pdb=" N   PRO R  74 "
        pdb=" CA  PRO R  74 "
      ideal   model   delta    sigma   weight residual
     119.19  136.37  -17.18 1.06e+00 8.90e-01 2.63e+02
  angle pdb=" N   ILE R  29 "
        pdb=" CA  ILE R  29 "
        pdb=" C   ILE R  29 "
      ideal   model   delta    sigma   weight residual
     110.72  122.06  -11.34 1.01e+00 9.80e-01 1.26e+02
  angle pdb=" N   MET R  27 "
        pdb=" CA  MET R  27 "
        pdb=" C   MET R  27 "
      ideal   model   delta    sigma   weight residual
     111.03  120.67   -9.64 1.11e+00 8.12e-01 7.54e+01
  angle pdb=" C   ILE R  23 "
        pdb=" N   PRO R  24 "
        pdb=" CA  PRO R  24 "
      ideal   model   delta    sigma   weight residual
     119.84  130.45  -10.61 1.25e+00 6.40e-01 7.20e+01
  angle pdb=" N   ALA R  25 "
        pdb=" CA  ALA R  25 "
        pdb=" C   ALA R  25 "
      ideal   model   delta    sigma   weight residual
     111.28  120.23   -8.95 1.09e+00 8.42e-01 6.74e+01
  ... (remaining 10438 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4062
       18.00 -    36.00: 304
       36.00 -    54.00: 63
       54.00 -    71.99: 13
       71.99 -    89.99: 8
  Dihedral angle restraints: 4450
    sinusoidal: 1332
      harmonic: 3118
  Sorted by residual:
  dihedral pdb=" CA  PHE R  97 "
           pdb=" C   PHE R  97 "
           pdb=" N   ILE R  98 "
           pdb=" CA  ILE R  98 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.65  -28.35     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" CB  CYS R  92 "
           pdb=" SG  CYS R  92 "
           pdb=" SG  CYS R 170 "
           pdb=" CB  CYS R 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.83   48.17     1      1.00e+01 1.00e-02 3.20e+01
  dihedral pdb=" C   VAL R 306 "
           pdb=" N   VAL R 306 "
           pdb=" CA  VAL R 306 "
           pdb=" CB  VAL R 306 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.79   13.79     0      2.50e+00 1.60e-01 3.04e+01
  ... (remaining 4447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1106
       0.098 -    0.197: 122
       0.197 -    0.295: 21
       0.295 -    0.393: 3
       0.393 -    0.492: 3
  Chirality restraints: 1255
  Sorted by residual:
  chirality pdb=" CA  VAL R 306 "
            pdb=" N   VAL R 306 "
            pdb=" C   VAL R 306 "
            pdb=" CB  VAL R 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.95    0.49 2.00e-01 2.50e+01 6.04e+00
  chirality pdb=" CA  LYS B 280 "
            pdb=" N   LYS B 280 "
            pdb=" C   LYS B 280 "
            pdb=" CB  LYS B 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.45e+00
  chirality pdb=" CA  MET R  27 "
            pdb=" N   MET R  27 "
            pdb=" C   MET R  27 "
            pdb=" CB  MET R  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.29e+00
  ... (remaining 1252 not shown)

  Planarity restraints: 1330
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 276 "   -0.020 2.00e-02 2.50e+03   3.99e-02 1.59e+01
        pdb=" C   VAL B 276 "    0.069 2.00e-02 2.50e+03
        pdb=" O   VAL B 276 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   SER B 277 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 150 "    0.018 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   PHE R 150 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   PHE R 150 "    0.022 2.00e-02 2.50e+03
        pdb=" N   CYS R 151 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 321 "    0.047 5.00e-02 4.00e+02   7.06e-02 7.98e+00
        pdb=" N   PRO R 322 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO R 322 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO R 322 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1327 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1272
        2.76 -     3.29: 6737
        3.29 -     3.83: 11485
        3.83 -     4.36: 12412
        4.36 -     4.90: 22557
  Nonbonded interactions: 54463
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLU R  93 "
            pdb=" OG1 THR R  96 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" N   ASP B 246 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   SER R 114 "
            pdb=" OG  SER R 114 "
     model   vdw
     2.357 3.040
  ... (remaining 54458 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.040
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
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      :  0.010   0.230   7649  Z= 0.581
  Angle     :  1.248  17.178  10447  Z= 0.784
  Chirality :  0.072   0.492   1255
  Planarity :  0.007   0.071   1330
  Dihedral  : 14.656  89.992   2424
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  1.85 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.20 %
  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: -3.35 (0.24), residues: 1047
  helix: -0.78 (0.29), residues: 312
  sheet: -2.82 (0.28), residues: 271
  loop : -2.80 (0.25), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP B 339 
 HIS   0.010   0.001   HIS E  35 
 PHE   0.026   0.003   PHE B 235 
 TYR   0.020   0.002   TYR B  85 
 ARG   0.018   0.001   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16285 (  300)
  hydrogen bonds       : angle       7.53178 (  852)
  SS BOND              : bond        0.00927 (    2)
  SS BOND              : angle       1.71354 (    4)
  covalent geometry    : bond        0.00995 ( 7647)
  covalent geometry    : angle       1.24750 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.796 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8119 (tm-30)
REVERT: E  246 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7051 (mm-30)
REVERT: R  117 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7452 (mtm110)
REVERT: R  169 TRP cc_start: 0.6528 (p-90) cc_final: 0.6140 (p-90)
REVERT: R  217 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5330 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 111
  average time/residue: 0.2143
  time to fit residues: 31.2149
Evaluate side-chains
  89 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain R residue   23 ILE
Chi-restraints excluded: chain R residue  217 PHE
Chi-restraints excluded: chain R residue  315 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0670
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0270
   chunk 61 optimal weight:    0.5980
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 231 GLN
R 313 GLN
R 321 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.138696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.106747 restraints weight = 12260.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.105875 restraints weight = 8202.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.107628 restraints weight = 6997.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   7649  Z= 0.104
  Angle     :  0.582   6.956  10447  Z= 0.311
  Chirality :  0.042   0.145   1255
  Planarity :  0.004   0.057   1330
  Dihedral  :  8.432  80.746   1171
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 11.38 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.25), residues: 1047
  helix:  0.16 (0.30), residues: 322
  sheet: -2.51 (0.29), residues: 275
  loop : -2.56 (0.26), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.017   0.001   PHE R 126 
 TYR   0.015   0.001   TYR R 184 
 ARG   0.003   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03361 (  300)
  hydrogen bonds       : angle       5.18085 (  852)
  SS BOND              : bond        0.00498 (    2)
  SS BOND              : angle       1.15743 (    4)
  covalent geometry    : bond        0.00216 ( 7647)
  covalent geometry    : angle       0.58168 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7893 (tm-30)
REVERT: B  222 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7373 (m-80)
REVERT: E  246 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6896 (mm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 95
  average time/residue: 0.2294
  time to fit residues: 28.7002
Evaluate side-chains
  82 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain B residue  222 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 102 optimal weight:   20.0000
   chunk 13 optimal weight:    0.0670
   chunk 89 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 231 GLN ** 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 = 0.3905 r_free = 0.3905 target = 0.137924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.105892 restraints weight = 12498.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.105030 restraints weight = 8393.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.106874 restraints weight = 6939.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7649  Z= 0.104
  Angle     :  0.538   6.787  10447  Z= 0.286
  Chirality :  0.041   0.132   1255
  Planarity :  0.004   0.059   1330
  Dihedral  :  7.125  59.702   1165
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.31 %
    Favored  : 84.15 %
  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: -2.11 (0.26), residues: 1047
  helix:  0.71 (0.31), residues: 320
  sheet: -2.18 (0.30), residues: 267
  loop : -2.43 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.015   0.001   TYR R 184 
 ARG   0.003   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02930 (  300)
  hydrogen bonds       : angle       4.61758 (  852)
  SS BOND              : bond        0.00472 (    2)
  SS BOND              : angle       1.12337 (    4)
  covalent geometry    : bond        0.00233 ( 7647)
  covalent geometry    : angle       0.53783 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7850 (tm-30)
REVERT: B  222 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7592 (m-80)
REVERT: E  246 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6771 (mm-30)
REVERT: R  117 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7480 (mtm110)
  outliers start: 10
  outliers final: 4
  residues processed: 93
  average time/residue: 0.2154
  time to fit residues: 26.6044
Evaluate side-chains
  83 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain R residue  197 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 17 optimal weight:    0.0010
   chunk 86 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   chunk 18 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.137542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.106687 restraints weight = 12272.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.105434 restraints weight = 7787.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.108026 restraints weight = 6741.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7649  Z= 0.093
  Angle     :  0.505   6.765  10447  Z= 0.268
  Chirality :  0.041   0.129   1255
  Planarity :  0.004   0.056   1330
  Dihedral  :  5.495  56.940   1163
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.85 %
    Favored  : 82.15 %
  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: -1.74 (0.26), residues: 1047
  helix:  1.04 (0.32), residues: 319
  sheet: -1.95 (0.30), residues: 275
  loop : -2.24 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.016   0.001   TYR R 184 
 ARG   0.003   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02616 (  300)
  hydrogen bonds       : angle       4.34261 (  852)
  SS BOND              : bond        0.00457 (    2)
  SS BOND              : angle       1.14890 (    4)
  covalent geometry    : bond        0.00206 ( 7647)
  covalent geometry    : angle       0.50473 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.780 
Fit side-chains
REVERT: B   10 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5727 (tp30)
REVERT: B   17 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7838 (tm-30)
REVERT: E   38 ARG cc_start: 0.8170 (mtm180) cc_final: 0.7933 (mtp180)
REVERT: E  246 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6772 (mm-30)
REVERT: R  117 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7411 (mtm110)
  outliers start: 13
  outliers final: 6
  residues processed: 103
  average time/residue: 0.2167
  time to fit residues: 29.3086
Evaluate side-chains
  96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain E residue   80 PHE
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  184 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 49 optimal weight:    0.0010
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.137955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.106431 restraints weight = 12389.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.105517 restraints weight = 8598.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.107311 restraints weight = 6828.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7649  Z= 0.098
  Angle     :  0.518   9.343  10447  Z= 0.273
  Chirality :  0.041   0.131   1255
  Planarity :  0.004   0.058   1330
  Dihedral  :  5.171  57.877   1163
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.23 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.52 (0.27), residues: 1047
  helix:  1.29 (0.32), residues: 317
  sheet: -1.82 (0.30), residues: 274
  loop : -2.14 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.015   0.001   TYR R 184 
 ARG   0.003   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02583 (  300)
  hydrogen bonds       : angle       4.22998 (  852)
  SS BOND              : bond        0.00478 (    2)
  SS BOND              : angle       1.09770 (    4)
  covalent geometry    : bond        0.00221 ( 7647)
  covalent geometry    : angle       0.51811 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.850 
Fit side-chains
REVERT: B   10 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5792 (tp30)
REVERT: B   17 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7944 (tm-30)
REVERT: B  300 LEU cc_start: 0.7774 (tt) cc_final: 0.7527 (mm)
REVERT: E   34 MET cc_start: 0.6886 (tpp) cc_final: 0.6619 (tpp)
REVERT: E   38 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7905 (mtp180)
REVERT: E  246 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6560 (mm-30)
REVERT: R  117 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7403 (mtm110)
  outliers start: 14
  outliers final: 8
  residues processed: 97
  average time/residue: 0.2161
  time to fit residues: 27.9439
Evaluate side-chains
  91 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain E residue   80 PHE
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain R residue  315 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 331 ASN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
E 231 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.136576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.105690 restraints weight = 12451.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.104020 restraints weight = 8231.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.105978 restraints weight = 7317.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7649  Z= 0.111
  Angle     :  0.516   8.207  10447  Z= 0.274
  Chirality :  0.041   0.129   1255
  Planarity :  0.004   0.057   1330
  Dihedral  :  5.138  56.611   1163
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 18.15 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.43 (0.27), residues: 1047
  helix:  1.42 (0.31), residues: 317
  sheet: -1.89 (0.31), residues: 270
  loop : -2.06 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP R 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.011   0.001   PHE B 235 
 TYR   0.015   0.001   TYR R 184 
 ARG   0.003   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02687 (  300)
  hydrogen bonds       : angle       4.23123 (  852)
  SS BOND              : bond        0.00509 (    2)
  SS BOND              : angle       1.19719 (    4)
  covalent geometry    : bond        0.00255 ( 7647)
  covalent geometry    : angle       0.51554 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8076 (pp)
REVERT: B   10 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5857 (tp30)
REVERT: B   17 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: B  300 LEU cc_start: 0.7803 (tt) cc_final: 0.7534 (mm)
REVERT: E   34 MET cc_start: 0.7071 (tpp) cc_final: 0.6831 (tpp)
REVERT: E   38 ARG cc_start: 0.8219 (mtm180) cc_final: 0.7982 (mtp180)
REVERT: E  246 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6532 (mm-30)
REVERT: R  117 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7370 (mtm110)
  outliers start: 21
  outliers final: 10
  residues processed: 103
  average time/residue: 0.2206
  time to fit residues: 29.8616
Evaluate side-chains
  97 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain E residue   80 PHE
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  315 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0370
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7062

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 331 ASN
E 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.137292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.105739 restraints weight = 12339.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.104762 restraints weight = 8417.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.106466 restraints weight = 6887.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7649  Z= 0.102
  Angle     :  0.510   7.765  10447  Z= 0.269
  Chirality :  0.041   0.129   1255
  Planarity :  0.004   0.058   1330
  Dihedral  :  5.066  56.459   1163
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.08 %
    Favored  : 77.54 %
  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 (0.27), residues: 1047
  helix:  1.54 (0.31), residues: 319
  sheet: -1.91 (0.30), residues: 273
  loop : -1.97 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP R 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.016   0.001   TYR R 184 
 ARG   0.003   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02573 (  300)
  hydrogen bonds       : angle       4.18591 (  852)
  SS BOND              : bond        0.00471 (    2)
  SS BOND              : angle       1.12678 (    4)
  covalent geometry    : bond        0.00233 ( 7647)
  covalent geometry    : angle       0.50935 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8108 (pp)
REVERT: B   17 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: B  300 LEU cc_start: 0.7744 (tt) cc_final: 0.7528 (mm)
REVERT: E   34 MET cc_start: 0.7013 (tpp) cc_final: 0.6782 (tpp)
REVERT: E   38 ARG cc_start: 0.8187 (mtm180) cc_final: 0.7930 (mtp180)
REVERT: E  246 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6543 (mm-30)
REVERT: R  117 ARG cc_start: 0.7775 (mtm110) cc_final: 0.7366 (mtm110)
  outliers start: 22
  outliers final: 13
  residues processed: 105
  average time/residue: 0.2117
  time to fit residues: 29.3397
Evaluate side-chains
  98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain E residue   80 PHE
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  315 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0040
   chunk 80 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 100 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0980
   chunk 34 optimal weight:    0.0470
   overall best weight:    0.3490

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 331 ASN
E 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.139792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.108387 restraints weight = 12265.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.107283 restraints weight = 7770.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.109062 restraints weight = 6725.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7649  Z= 0.086
  Angle     :  0.502  10.893  10447  Z= 0.261
  Chirality :  0.040   0.127   1255
  Planarity :  0.004   0.062   1330
  Dihedral  :  4.857  55.716   1163
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.85 %
    Favored  : 77.69 %
  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: -1.09 (0.27), residues: 1047
  helix:  1.79 (0.31), residues: 318
  sheet: -1.71 (0.30), residues: 277
  loop : -1.91 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 169 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.018   0.001   TYR R 184 
 ARG   0.003   0.000   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02297 (  300)
  hydrogen bonds       : angle       4.01493 (  852)
  SS BOND              : bond        0.00420 (    2)
  SS BOND              : angle       1.00983 (    4)
  covalent geometry    : bond        0.00189 ( 7647)
  covalent geometry    : angle       0.50169 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7815 (pp)
REVERT: B   17 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: B   72 SER cc_start: 0.8660 (m) cc_final: 0.8387 (p)
REVERT: E   34 MET cc_start: 0.6733 (tpp) cc_final: 0.6476 (tpp)
REVERT: E   38 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7931 (mtp180)
REVERT: R  117 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7336 (mtm110)
  outliers start: 16
  outliers final: 12
  residues processed: 104
  average time/residue: 0.2207
  time to fit residues: 30.2747
Evaluate side-chains
  99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  315 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0770
   chunk 101 optimal weight:    7.9990
   chunk 78 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.2542

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 331 ASN
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.135237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.103767 restraints weight = 12477.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.102555 restraints weight = 7796.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.104406 restraints weight = 6852.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7649  Z= 0.144
  Angle     :  0.566  10.411  10447  Z= 0.297
  Chirality :  0.042   0.142   1255
  Planarity :  0.004   0.063   1330
  Dihedral  :  5.056  55.643   1163
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.08 %
    Favored  : 76.31 %
  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: -1.21 (0.27), residues: 1047
  helix:  1.65 (0.31), residues: 323
  sheet: -1.85 (0.30), residues: 272
  loop : -1.94 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.015   0.002   PHE B 235 
 TYR   0.016   0.001   TYR R 184 
 ARG   0.006   0.001   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02933 (  300)
  hydrogen bonds       : angle       4.17853 (  852)
  SS BOND              : bond        0.00594 (    2)
  SS BOND              : angle       1.47264 (    4)
  covalent geometry    : bond        0.00343 ( 7647)
  covalent geometry    : angle       0.56584 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8179 (pp)
REVERT: A  251 ASP cc_start: 0.8363 (t0) cc_final: 0.8040 (m-30)
REVERT: B   17 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: E   38 ARG cc_start: 0.8343 (mtm180) cc_final: 0.8106 (mtp180)
REVERT: R  117 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7389 (mtm110)
  outliers start: 17
  outliers final: 11
  residues processed: 101
  average time/residue: 0.2252
  time to fit residues: 29.8119
Evaluate side-chains
  96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  315 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 92 optimal weight:   30.0000
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 231 GLN ** 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 = 0.3834 r_free = 0.3834 target = 0.132235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.101134 restraints weight = 12740.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.099202 restraints weight = 8389.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.101162 restraints weight = 7381.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7649  Z= 0.204
  Angle     :  0.632  10.571  10447  Z= 0.335
  Chirality :  0.045   0.173   1255
  Planarity :  0.004   0.065   1330
  Dihedral  :  5.469  56.159   1163
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.92 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.48 (0.27), residues: 1047
  helix:  1.41 (0.31), residues: 321
  sheet: -1.97 (0.30), residues: 273
  loop : -2.09 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.023   0.002   PHE B 235 
 TYR   0.014   0.002   TYR R 184 
 ARG   0.012   0.001   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03557 (  300)
  hydrogen bonds       : angle       4.57488 (  852)
  SS BOND              : bond        0.00713 (    2)
  SS BOND              : angle       1.65989 (    4)
  covalent geometry    : bond        0.00485 ( 7647)
  covalent geometry    : angle       0.63087 (10443)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7887 (tmm-80)
REVERT: A  251 ASP cc_start: 0.8363 (t0) cc_final: 0.8004 (m-30)
REVERT: A  333 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7675 (tm-30)
REVERT: E   38 ARG cc_start: 0.8492 (mtm180) cc_final: 0.8256 (mtp180)
REVERT: R  117 ARG cc_start: 0.7906 (mtm110) cc_final: 0.7446 (mtm110)
  outliers start: 16
  outliers final: 11
  residues processed: 96
  average time/residue: 0.2244
  time to fit residues: 28.1997
Evaluate side-chains
  92 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain E residue   80 PHE
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  178 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain R residue  197 LEU
Chi-restraints excluded: chain R residue  315 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 97 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0980
   chunk 49 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 331 ASN
E 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.136697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.104855 restraints weight = 12259.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.102998 restraints weight = 7906.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.105132 restraints weight = 7234.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7649  Z= 0.104
  Angle     :  0.545  10.118  10447  Z= 0.286
  Chirality :  0.041   0.129   1255
  Planarity :  0.004   0.065   1330
  Dihedral  :  5.064  55.354   1163
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 22.00 %
    Favored  : 76.15 %
  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: -1.18 (0.27), residues: 1047
  helix:  1.77 (0.31), residues: 314
  sheet: -1.85 (0.31), residues: 273
  loop : -1.92 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.009   0.001   PHE B 234 
 TYR   0.018   0.001   TYR R 184 
 ARG   0.012   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02681 (  300)
  hydrogen bonds       : angle       4.24833 (  852)
  SS BOND              : bond        0.00529 (    2)
  SS BOND              : angle       1.23275 (    4)
  covalent geometry    : bond        0.00240 ( 7647)
  covalent geometry    : angle       0.54458 (10443)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2432.11 seconds
wall clock time: 43 minutes 10.99 seconds (2590.99 seconds total)