Starting phenix.real_space_refine
on Thu Jul 31 17:44:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ye6_33765/07_2025/7ye6_33765.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ye6_33765/07_2025/7ye6_33765.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ye6_33765/07_2025/7ye6_33765.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ye6_33765/07_2025/7ye6_33765.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ye6_33765/07_2025/7ye6_33765.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ye6_33765/07_2025/7ye6_33765.cif"
  }
  resolution = 3.4
  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=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    8707      2.51       5
     N    2351      2.21       5
     O    2706      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13804
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 785, 6205
          Classifications: {'peptide': 785}
          Link IDs: {'PTRANS': 29, 'TRANS': 755}
    Chain: "B"
      Number of atoms: 2695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2695
          Classifications: {'peptide': 365}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 353}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "C"
      Number of atoms: 390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 390
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 5, 'TRANS': 48}
    Chain: "D"
      Number of atoms: 1722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1722
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 10, 'TRANS': 202}
    Chain: "E"
      Number of atoms: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 671
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 5, 'TRANS': 80}
    Chain: "P"
      Number of atoms: 2121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2121
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 275}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 7.55, per 1000 atoms: 0.55
  Number of scatterers: 13804
  At special positions: 0
  Unit cell: (135.876, 120.666, 145.002, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    2706      8.00
     N    2351      7.00
     C    8707      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 427 " - pdb=" SG  CYS P1297 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.86
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3236

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 18 sheets defined
      12.7% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 71
      removed outlier: 4.058A  pdb=" N   GLY A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 84
      removed outlier: 3.602A  pdb=" N   LEU A  84 " --> pdb=" O   GLY A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 135
    Processing helix  chain 'A' and resid 191 through 197
      removed outlier: 4.070A  pdb=" N   SER A 195 " --> pdb=" O   ASP A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
      removed outlier: 3.631A  pdb=" N   ASP A 222 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LEU A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 223'
    Processing helix  chain 'A' and resid 223 through 231
      removed outlier: 3.574A  pdb=" N   ARG A 227 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 234
      No H-bonds generated for 'chain 'A' and resid 232 through 234'
    Processing helix  chain 'A' and resid 284 through 289
    Processing helix  chain 'A' and resid 297 through 303
      removed outlier: 3.892A  pdb=" N   VAL A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   THR A 302 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LYS A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 297 through 303'
    Processing helix  chain 'A' and resid 378 through 381
    Processing helix  chain 'A' and resid 382 through 391
      removed outlier: 3.573A  pdb=" N   ARG A 391 " --> pdb=" O   GLU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 551
      removed outlier: 3.614A  pdb=" N   ARG A 547 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   TYR A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
      removed outlier: 3.805A  pdb=" N   ASN A 651 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 323
      removed outlier: 3.665A  pdb=" N   LEU B 322 " --> pdb=" O   GLN B 319 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU B 323 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 319 through 323'
    Processing helix  chain 'D' and resid 32 through 37
      removed outlier: 3.993A  pdb=" N   TYR D  36 " --> pdb=" O   PRO D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 73
      removed outlier: 4.434A  pdb=" N   LEU D  73 " --> pdb=" O   GLN D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 79
      removed outlier: 3.883A  pdb=" N   ALA D  78 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR D  79 " --> pdb=" O   LEU D  75 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 74 through 79'
    Processing helix  chain 'D' and resid 87 through 92
      removed outlier: 3.703A  pdb=" N   ALA D  90 " --> pdb=" O   LEU D  87 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA D  91 " --> pdb=" O   ALA D  88 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE D  92 " --> pdb=" O   GLN D  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 87 through 92'
    Processing helix  chain 'D' and resid 93 through 98
      removed outlier: 4.434A  pdb=" N   ARG D  97 " --> pdb=" O   ASP D  93 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU D  98 " --> pdb=" O   ARG D  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 93 through 98'
    Processing helix  chain 'D' and resid 104 through 109
      removed outlier: 3.626A  pdb=" N   MET D 109 " --> pdb=" O   ILE D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 154
      removed outlier: 4.338A  pdb=" N   ASP D 146 " --> pdb=" O   ALA D 142 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   PHE D 147 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL D 151 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   TYR D 154 " --> pdb=" O   LEU D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 174
      removed outlier: 4.051A  pdb=" N   LYS D 165 " --> pdb=" O   THR D 161 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL D 168 " --> pdb=" O   THR D 164 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   PHE D 169 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASP D 172 " --> pdb=" O   VAL D 168 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU D 174 " --> pdb=" O   LEU D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 189
      removed outlier: 3.727A  pdb=" N   TYR D 179 " --> pdb=" O   ALA D 175 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   THR D 186 " --> pdb=" O   ALA D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 199
      removed outlier: 3.657A  pdb=" N   VAL D 195 " --> pdb=" O   TRP D 191 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ARG D 197 " --> pdb=" O   ALA D 193 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU D 199 " --> pdb=" O   VAL D 195 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 215
      removed outlier: 4.139A  pdb=" N   ASP D 213 " --> pdb=" O   GLN D 209 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU D 215 " --> pdb=" O   THR D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 215 through 225
      removed outlier: 3.845A  pdb=" N   GLU D 219 " --> pdb=" O   LEU D 215 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA D 221 " --> pdb=" O   LEU D 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 59
      removed outlier: 3.580A  pdb=" N   VAL E  55 " --> pdb=" O   THR E  51 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA E  58 " --> pdb=" O   GLN E  54 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1012 through 1020
      removed outlier: 4.132A  pdb=" N   LYS P1016 " --> pdb=" O   SER P1012 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1024 through 1029
      removed outlier: 3.682A  pdb=" N   ARG P1028 " --> pdb=" O   ASN P1024 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   MET P1029 " --> pdb=" O   LEU P1025 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 1024 through 1029'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 267 through 268
      removed outlier: 6.241A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A 336 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ARG A 338 " --> pdb=" O   MET A 325 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   MET A 325 " --> pdb=" O   ARG A 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354
      removed outlier: 3.622A  pdb=" N   ARG A 353 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   TYR A 416 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457
      removed outlier: 3.512A  pdb=" N   SER A 484 " --> pdb=" O   GLY A 516 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU A 529 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 525 " --> pdb=" O   PHE A 517 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 565 through 569
      removed outlier: 3.836A  pdb=" N   THR A 617 " --> pdb=" O   GLY A 631 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TRP A 745 " --> pdb=" O   ALA A 710 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY A 771 " --> pdb=" O   PHE A 738 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 777 through 778
    Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51
      removed outlier: 4.610A  pdb=" N   THR B  50 " --> pdb=" O   VAL B 387 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   VAL B 387 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ILE B 380 " --> pdb=" O   TYR B 388 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE B 390 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA B 374 " --> pdb=" O   LYS B 377 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 379 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 67
      removed outlier: 4.029A  pdb=" N   VAL B  81 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL B  95 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 117
      removed outlier: 4.117A  pdb=" N   THR B 116 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   VAL B 131 " --> pdb=" O   THR B 145 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   THR B 145 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.655A  pdb=" N   VAL B 156 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL B 185 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203
    Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.775A  pdb=" N   VAL B 252 " --> pdb=" O   PHE B 259 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 296 through 299
    Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 332
      removed outlier: 3.804A  pdb=" N   VAL B 331 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   HIS B 347 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 34
      removed outlier: 3.546A  pdb=" N   GLN E  79 " --> pdb=" O   THR E  87 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   THR E  90 " --> pdb=" O   LYS E 107 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 65 through 66
      removed outlier: 3.991A  pdb=" N   ASP E  66 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR E  72 " --> pdb=" O   ASP E  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'P' and resid 1042 through 1043
      removed outlier: 4.731A  pdb=" N   TRP P1042 " --> pdb=" O   GLY P1066 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLY P1066 " --> pdb=" O   TRP P1042 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASP P1088 " --> pdb=" O   THR P1061 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY P1081 " --> pdb=" O   TYR P1108 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS P1101 " --> pdb=" O   ASP P1129 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ASP P1129 " --> pdb=" O   LYS P1101 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR P1175 " --> pdb=" O   ALA P1151 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLY P1204 " --> pdb=" O   PHE P1231 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   VAL P1208 " --> pdb=" O   LEU P1227 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY P1228 " --> pdb=" O   LEU P1259 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG P1257 " --> pdb=" O   GLN P1230 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'P' and resid 1042 through 1043
      removed outlier: 4.731A  pdb=" N   TRP P1042 " --> pdb=" O   GLY P1066 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLY P1066 " --> pdb=" O   TRP P1042 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   THR P1049 " --> pdb=" O   ASP P1289 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'P' and resid 1213 through 1215
      removed outlier: 3.586A  pdb=" N   LYS P1220 " --> pdb=" O   GLU P1267 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    846 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: 4.31

  Time building geometry restraints manager: 3.49 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4604
        1.34 -     1.46: 3338
        1.46 -     1.58: 6086
        1.58 -     1.70: 1
        1.70 -     1.82: 76
  Bond restraints: 14105
  Sorted by residual:
  bond pdb=" C   PRO A 721 "
       pdb=" N   THR A 722 "
    ideal  model  delta    sigma   weight residual
    1.331  1.369 -0.038 2.07e-02 2.33e+03 3.43e+00
  bond pdb=" CA  THR B 315 "
       pdb=" CB  THR B 315 "
    ideal  model  delta    sigma   weight residual
    1.530  1.554 -0.024 1.69e-02 3.50e+03 2.02e+00
  bond pdb=" N   GLN A  87 "
       pdb=" CA  GLN A  87 "
    ideal  model  delta    sigma   weight residual
    1.460  1.479 -0.019 1.45e-02 4.76e+03 1.79e+00
  bond pdb=" CB  ARG B 273 "
       pdb=" CG  ARG B 273 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.77e+00
  bond pdb=" CA  LEU A 365 "
       pdb=" CB  LEU A 365 "
    ideal  model  delta    sigma   weight residual
    1.539  1.604 -0.064 4.88e-02 4.20e+02 1.73e+00
  ... (remaining 14100 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.63: 19067
        3.63 -     7.26: 83
        7.26 -    10.90: 9
       10.90 -    14.53: 0
       14.53 -    18.16: 1
  Bond angle restraints: 19160
  Sorted by residual:
  angle pdb=" CA  LEU E 101 "
        pdb=" CB  LEU E 101 "
        pdb=" CG  LEU E 101 "
      ideal   model   delta    sigma   weight residual
     116.30  134.46  -18.16 3.50e+00 8.16e-02 2.69e+01
  angle pdb=" C   VAL B 254 "
        pdb=" N   ASN B 255 "
        pdb=" CA  ASN B 255 "
      ideal   model   delta    sigma   weight residual
     121.54  130.16   -8.62 1.91e+00 2.74e-01 2.04e+01
  angle pdb=" C   VAL B 314 "
        pdb=" N   THR B 315 "
        pdb=" CA  THR B 315 "
      ideal   model   delta    sigma   weight residual
     121.54  129.98   -8.44 1.91e+00 2.74e-01 1.95e+01
  angle pdb=" CA  TYR A 504 "
        pdb=" CB  TYR A 504 "
        pdb=" CG  TYR A 504 "
      ideal   model   delta    sigma   weight residual
     113.90  121.23   -7.33 1.80e+00 3.09e-01 1.66e+01
  angle pdb=" C   GLY C  55 "
        pdb=" N   MET C  56 "
        pdb=" CA  MET C  56 "
      ideal   model   delta    sigma   weight residual
     121.54  129.19   -7.65 1.91e+00 2.74e-01 1.60e+01
  ... (remaining 19155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 7486
       17.30 -    34.61: 639
       34.61 -    51.91: 123
       51.91 -    69.22: 17
       69.22 -    86.52: 12
  Dihedral angle restraints: 8277
    sinusoidal: 3175
      harmonic: 5102
  Sorted by residual:
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   13.70   79.30     1      1.00e+01 1.00e-02 7.82e+01
  dihedral pdb=" CA  CYS P1297 "
           pdb=" C   CYS P1297 "
           pdb=" N   TYR P1298 "
           pdb=" CA  TYR P1298 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.11  -30.89     0      5.00e+00 4.00e-02 3.82e+01
  dihedral pdb=" CB  CYS A 427 "
           pdb=" SG  CYS A 427 "
           pdb=" SG  CYS P1297 "
           pdb=" CB  CYS P1297 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.88   51.12     1      1.00e+01 1.00e-02 3.57e+01
  ... (remaining 8274 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1740
       0.062 -    0.124: 308
       0.124 -    0.187: 32
       0.187 -    0.249: 4
       0.249 -    0.311: 1
  Chirality restraints: 2085
  Sorted by residual:
  chirality pdb=" CB  VAL D 234 "
            pdb=" CA  VAL D 234 "
            pdb=" CG1 VAL D 234 "
            pdb=" CG2 VAL D 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  CYS A 427 "
            pdb=" N   CYS A 427 "
            pdb=" C   CYS A 427 "
            pdb=" CB  CYS A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  CYS P1297 "
            pdb=" N   CYS P1297 "
            pdb=" C   CYS P1297 "
            pdb=" CB  CYS P1297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 2082 not shown)

  Planarity restraints: 2518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 215 "    0.037 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO D 216 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO D 216 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D 216 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 722 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.04e+00
        pdb=" N   PRO A 723 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 723 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 723 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  67 "   -0.032 5.00e-02 4.00e+02   4.80e-02 3.69e+00
        pdb=" N   PRO C  68 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO C  68 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C  68 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 2515 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2894
        2.78 -     3.31: 11119
        3.31 -     3.84: 22503
        3.84 -     4.37: 24433
        4.37 -     4.90: 43008
  Nonbonded interactions: 103957
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 285 "
            pdb=" O   VAL B 299 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   SER A 761 "
            pdb=" OG  SER A 761 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG  SER A 715 "
            pdb=" OD1 ASP A 740 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   SER B 112 "
            pdb=" OG  SER B 112 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER A 274 "
            pdb=" O   VAL A 339 "
     model   vdw
     2.345 3.040
  ... (remaining 103952 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.800
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5707
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      :  0.003   0.064  14107  Z= 0.144
  Angle     :  0.678  18.161  19164  Z= 0.365
  Chirality :  0.048   0.311   2085
  Planarity :  0.004   0.055   2518
  Dihedral  : 13.340  86.522   5035
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  7.52 %
    Favored  : 92.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -4.95 (0.15), residues: 1765
  helix: -5.24 (0.09), residues: 184
  sheet: -2.71 (0.21), residues: 484
  loop : -3.36 (0.14), residues: 1097

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 279 
 HIS   0.002   0.000   HIS A 533 
 PHE   0.013   0.001   PHE B 104 
 TYR   0.014   0.001   TYR E  28 
 ARG   0.002   0.000   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31226 (  296)
  hydrogen bonds       : angle      11.37008 (  846)
  SS BOND              : bond        0.00989 (    2)
  SS BOND              : angle       2.95304 (    4)
  covalent geometry    : bond        0.00283 (14105)
  covalent geometry    : angle       0.67669 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 251
  time to evaluate  : 1.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7921 (pp)
REVERT: A  387 GLU cc_start: 0.6840 (pt0) cc_final: 0.6610 (tm-30)
REVERT: A  390 ASN cc_start: 0.8125 (t0) cc_final: 0.7795 (p0)
REVERT: A  399 ASP cc_start: 0.6410 (m-30) cc_final: 0.5816 (m-30)
REVERT: A  519 ILE cc_start: 0.7940 (tp) cc_final: 0.7551 (tp)
REVERT: A  601 ILE cc_start: 0.7569 (pt) cc_final: 0.6876 (mm)
REVERT: A  736 SER cc_start: 0.8183 (m) cc_final: 0.7843 (t)
REVERT: B  306 MET cc_start: 0.3219 (pmm) cc_final: 0.1564 (pmm)
REVERT: E   28 TYR cc_start: 0.5201 (p90) cc_final: 0.4630 (t80)
REVERT: E   31 ASP cc_start: 0.7053 (p0) cc_final: 0.6581 (p0)
REVERT: P 1154 GLU cc_start: 0.6945 (tp30) cc_final: 0.6687 (tp30)
REVERT: P 1170 GLN cc_start: 0.6916 (mt0) cc_final: 0.6493 (tt0)
  outliers start: 4
  outliers final: 2
  residues processed: 255
  average time/residue: 0.3169
  time to fit residues: 111.7481
Evaluate side-chains
  167 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 164
  time to evaluate  : 2.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain B residue  268 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    7.9990
   chunk 132 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 89 optimal weight:   50.0000
   chunk 70 optimal weight:    0.4980
   chunk 137 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 102 optimal weight:   40.0000
   chunk 158 optimal weight:   10.0000
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
A 185 ASN
A 265 GLN
A 371 GLN
** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 ASN
A 561 GLN
B  40 ASN
B 175 ASN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 ASN
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 138 GLN
D 224 GLN
E  34 GLN
E  83 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5169 r_free = 0.5169 target = 0.290870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.247296 restraints weight = 16392.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.4949 rms_B_bonded: 2.84
r_work: 0.4434 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.4268 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14107  Z= 0.146
  Angle     :  0.595  14.894  19164  Z= 0.310
  Chirality :  0.044   0.167   2085
  Planarity :  0.004   0.068   2518
  Dihedral  :  4.046  46.811   1952
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.49 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.37 (0.17), residues: 1765
  helix: -4.31 (0.20), residues: 189
  sheet: -2.41 (0.21), residues: 495
  loop : -2.99 (0.16), residues: 1081

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 228 
 HIS   0.006   0.001   HIS B 121 
 PHE   0.016   0.001   PHE P1214 
 TYR   0.030   0.001   TYR A 477 
 ARG   0.006   0.001   ARG D 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05155 (  296)
  hydrogen bonds       : angle       7.08813 (  846)
  SS BOND              : bond        0.00337 (    2)
  SS BOND              : angle       3.27554 (    4)
  covalent geometry    : bond        0.00320 (14105)
  covalent geometry    : angle       0.59279 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 170
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 GLU cc_start: 0.7856 (pt0) cc_final: 0.7285 (tm-30)
REVERT: A  447 ASP cc_start: 0.5923 (m-30) cc_final: 0.5015 (m-30)
REVERT: A  519 ILE cc_start: 0.8520 (tp) cc_final: 0.8080 (tp)
REVERT: A  630 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7009 (mp)
REVERT: A  727 ASP cc_start: 0.3950 (OUTLIER) cc_final: 0.3689 (p0)
REVERT: B   82 LYS cc_start: 0.5131 (mtmm) cc_final: 0.4590 (mtmt)
REVERT: B  306 MET cc_start: 0.3068 (pmm) cc_final: 0.2410 (pmm)
REVERT: E   28 TYR cc_start: 0.6651 (p90) cc_final: 0.4914 (t80)
REVERT: E   31 ASP cc_start: 0.7347 (p0) cc_final: 0.7022 (p0)
REVERT: E   89 GLN cc_start: 0.6915 (tm-30) cc_final: 0.6701 (tm-30)
REVERT: E  101 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7783 (pt)
  outliers start: 32
  outliers final: 18
  residues processed: 190
  average time/residue: 0.2767
  time to fit residues: 75.9390
Evaluate side-chains
  171 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  727 ASP
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain P residue 1065 VAL
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1128 HIS
Chi-restraints excluded: chain P residue 1172 GLU
Chi-restraints excluded: chain P residue 1262 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 158 optimal weight:    6.9990
   chunk 88 optimal weight:   50.0000
   chunk 152 optimal weight:    2.9990
   chunk 140 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 84 optimal weight:    2.9990
   chunk 106 optimal weight:   30.0000
   chunk 58 optimal weight:    1.9990
   chunk 104 optimal weight:   20.0000
   chunk 103 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 ASN
A 579 ASN
A 678 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 ASN
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 158 GLN
D 226 GLN
E  34 GLN
P1127 HIS
P1170 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5136 r_free = 0.5136 target = 0.285787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.236358 restraints weight = 16481.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.4867 rms_B_bonded: 3.24
r_work: 0.4427 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14107  Z= 0.175
  Angle     :  0.612  13.379  19164  Z= 0.321
  Chirality :  0.044   0.171   2085
  Planarity :  0.004   0.043   2518
  Dihedral  :  4.207  30.800   1949
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.29 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -3.91 (0.17), residues: 1765
  helix: -3.49 (0.25), residues: 206
  sheet: -2.16 (0.22), residues: 490
  loop : -2.72 (0.17), residues: 1069

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 546 
 HIS   0.004   0.001   HIS A 555 
 PHE   0.029   0.002   PHE P1018 
 TYR   0.027   0.002   TYR A 794 
 ARG   0.008   0.001   ARG A 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  296)
  hydrogen bonds       : angle       6.34133 (  846)
  SS BOND              : bond        0.00349 (    2)
  SS BOND              : angle       3.71466 (    4)
  covalent geometry    : bond        0.00390 (14105)
  covalent geometry    : angle       0.60939 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 165
  time to evaluate  : 1.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.5456 (tp-100)
REVERT: A  630 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7132 (mp)
REVERT: B   82 LYS cc_start: 0.4556 (mtmm) cc_final: 0.4019 (mtmt)
REVERT: B  306 MET cc_start: 0.3067 (pmm) cc_final: 0.2728 (pmm)
REVERT: E   31 ASP cc_start: 0.7513 (p0) cc_final: 0.7217 (p0)
REVERT: P 1018 PHE cc_start: 0.8247 (t80) cc_final: 0.8014 (t80)
  outliers start: 48
  outliers final: 32
  residues processed: 197
  average time/residue: 0.2760
  time to fit residues: 77.9029
Evaluate side-chains
  180 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  265 GLN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  646 MET
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain P residue 1065 VAL
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1121 LEU
Chi-restraints excluded: chain P residue 1122 ILE
Chi-restraints excluded: chain P residue 1166 TRP
Chi-restraints excluded: chain P residue 1172 GLU
Chi-restraints excluded: chain P residue 1262 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 134 optimal weight:    0.7980
   chunk 168 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 151 optimal weight:    9.9990
   chunk 97 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
A 579 ASN
A 765 ASN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5128 r_free = 0.5128 target = 0.284909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4924 r_free = 0.4924 target = 0.242287 restraints weight = 16446.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.4912 rms_B_bonded: 2.57
r_work: 0.4428 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.4177 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  14107  Z= 0.183
  Angle     :  0.611  13.208  19164  Z= 0.323
  Chirality :  0.045   0.246   2085
  Planarity :  0.004   0.057   2518
  Dihedral  :  4.327  32.917   1949
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.08 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -3.68 (0.18), residues: 1765
  helix: -3.05 (0.28), residues: 203
  sheet: -1.93 (0.22), residues: 495
  loop : -2.67 (0.17), residues: 1067

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 546 
 HIS   0.007   0.001   HIS A 677 
 PHE   0.019   0.002   PHE A 494 
 TYR   0.029   0.002   TYR A 794 
 ARG   0.008   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  296)
  hydrogen bonds       : angle       6.12602 (  846)
  SS BOND              : bond        0.00682 (    2)
  SS BOND              : angle       4.90421 (    4)
  covalent geometry    : bond        0.00411 (14105)
  covalent geometry    : angle       0.60666 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 160
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.8226 (mtp) cc_final: 0.7860 (ptp)
REVERT: A  365 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8407 (pp)
REVERT: B   82 LYS cc_start: 0.5046 (mtmm) cc_final: 0.4618 (mtmt)
REVERT: B  306 MET cc_start: 0.3043 (pmm) cc_final: 0.2642 (pmm)
REVERT: D  174 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8011 (pp)
REVERT: E   31 ASP cc_start: 0.7426 (p0) cc_final: 0.7078 (p0)
REVERT: E   63 LEU cc_start: 0.7435 (mp) cc_final: 0.7172 (mt)
REVERT: P 1018 PHE cc_start: 0.8441 (t80) cc_final: 0.8172 (t80)
  outliers start: 48
  outliers final: 33
  residues processed: 195
  average time/residue: 0.2732
  time to fit residues: 76.8119
Evaluate side-chains
  183 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1122 ILE
Chi-restraints excluded: chain P residue 1128 HIS
Chi-restraints excluded: chain P residue 1166 TRP
Chi-restraints excluded: chain P residue 1172 GLU
Chi-restraints excluded: chain P residue 1221 VAL
Chi-restraints excluded: chain P residue 1262 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 130 optimal weight:    5.9990
   chunk 162 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 35 optimal weight:    7.9990
   chunk 144 optimal weight:    9.9990
   chunk 97 optimal weight:   30.0000
   chunk 77 optimal weight:    0.7980
   chunk 116 optimal weight:    7.9990
   chunk 62 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 167 optimal weight:    5.9990
   overall best weight:    2.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
A 475 ASN
A 538 ASN
A 625 HIS
B  64 HIS
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 HIS
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5145 r_free = 0.5145 target = 0.288213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.241365 restraints weight = 16905.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.4875 rms_B_bonded: 2.80
r_work: 0.4413 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.4146 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.4141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14107  Z= 0.191
  Angle     :  0.631  13.484  19164  Z= 0.332
  Chirality :  0.045   0.244   2085
  Planarity :  0.004   0.060   2518
  Dihedral  :  4.421  34.218   1949
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.91 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -3.45 (0.18), residues: 1765
  helix: -2.69 (0.31), residues: 201
  sheet: -1.79 (0.23), residues: 485
  loop : -2.55 (0.17), residues: 1079

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 546 
 HIS   0.012   0.001   HIS B 324 
 PHE   0.020   0.002   PHE A 494 
 TYR   0.021   0.002   TYR A 504 
 ARG   0.011   0.001   ARG P1205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03881 (  296)
  hydrogen bonds       : angle       6.04317 (  846)
  SS BOND              : bond        0.00496 (    2)
  SS BOND              : angle       4.62941 (    4)
  covalent geometry    : bond        0.00425 (14105)
  covalent geometry    : angle       0.62723 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 159
  time to evaluate  : 1.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.8099 (mtp) cc_final: 0.7785 (ptp)
REVERT: A  504 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8327 (p90)
REVERT: B   82 LYS cc_start: 0.5031 (mtmm) cc_final: 0.4620 (mtmt)
REVERT: D  174 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8178 (pp)
REVERT: E   28 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.4733 (t80)
REVERT: E   31 ASP cc_start: 0.7470 (p0) cc_final: 0.7142 (p0)
REVERT: E   50 MET cc_start: 0.7691 (mmm) cc_final: 0.7467 (mmm)
REVERT: E   63 LEU cc_start: 0.7342 (mp) cc_final: 0.7103 (mt)
REVERT: P 1018 PHE cc_start: 0.8561 (t80) cc_final: 0.8040 (t80)
  outliers start: 59
  outliers final: 44
  residues processed: 203
  average time/residue: 0.2815
  time to fit residues: 82.9648
Evaluate side-chains
  191 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 144
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  504 TYR
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  646 MET
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  766 ILE
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 ARG
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain E residue   28 TYR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1100 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1122 ILE
Chi-restraints excluded: chain P residue 1128 HIS
Chi-restraints excluded: chain P residue 1146 THR
Chi-restraints excluded: chain P residue 1166 TRP
Chi-restraints excluded: chain P residue 1221 VAL
Chi-restraints excluded: chain P residue 1262 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 161 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9980
   chunk 163 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 167 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 114 optimal weight:    8.9990
   chunk 111 optimal weight:    7.9990
   chunk 158 optimal weight:    9.9990
   chunk 144 optimal weight:    9.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 533 HIS
B 230 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS
C  34 GLN
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1127 HIS
** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P1170 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5083 r_free = 0.5083 target = 0.283184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.227905 restraints weight = 17449.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.4813 rms_B_bonded: 3.06
r_work: 0.4349 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3983 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.123  14107  Z= 0.341
  Angle     :  0.801  14.023  19164  Z= 0.428
  Chirality :  0.050   0.289   2085
  Planarity :  0.006   0.104   2518
  Dihedral  :  5.269  38.224   1949
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 19.81 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -3.37 (0.18), residues: 1765
  helix: -2.45 (0.32), residues: 197
  sheet: -1.91 (0.23), residues: 486
  loop : -2.44 (0.17), residues: 1082

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 206 
 HIS   0.010   0.002   HIS A 677 
 PHE   0.032   0.002   PHE A 494 
 TYR   0.030   0.003   TYR A 794 
 ARG   0.014   0.001   ARG P1205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04951 (  296)
  hydrogen bonds       : angle       6.52121 (  846)
  SS BOND              : bond        0.00585 (    2)
  SS BOND              : angle       5.38591 (    4)
  covalent geometry    : bond        0.00763 (14105)
  covalent geometry    : angle       0.79685 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 155
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.8316 (mtp) cc_final: 0.7920 (ptp)
REVERT: A  365 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8516 (pp)
REVERT: A  428 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7622 (m-10)
REVERT: A  504 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8409 (p90)
REVERT: A  791 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6033 (t80)
REVERT: B   82 LYS cc_start: 0.5224 (mtmm) cc_final: 0.4813 (mtmt)
REVERT: B  278 MET cc_start: 0.6257 (mmm) cc_final: 0.5975 (mmp)
REVERT: C   80 LEU cc_start: 0.5018 (OUTLIER) cc_final: 0.4307 (pt)
REVERT: D  174 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8139 (pp)
REVERT: E   28 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.4367 (t80)
REVERT: E   31 ASP cc_start: 0.7643 (p0) cc_final: 0.7370 (p0)
REVERT: E   50 MET cc_start: 0.7893 (mmm) cc_final: 0.7300 (mmm)
REVERT: P 1142 ARG cc_start: 0.7749 (mtm180) cc_final: 0.7474 (mtm180)
REVERT: P 1212 LYS cc_start: 0.8272 (tppp) cc_final: 0.7815 (mtmt)
  outliers start: 69
  outliers final: 52
  residues processed: 208
  average time/residue: 0.2820
  time to fit residues: 85.7566
Evaluate side-chains
  196 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 137
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  504 TYR
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain A residue  791 PHE
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain D residue   84 ASP
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 ARG
Chi-restraints excluded: chain E residue   28 TYR
Chi-restraints excluded: chain E residue   37 TYR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain P residue 1063 VAL
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1100 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1121 LEU
Chi-restraints excluded: chain P residue 1128 HIS
Chi-restraints excluded: chain P residue 1146 THR
Chi-restraints excluded: chain P residue 1166 TRP
Chi-restraints excluded: chain P residue 1221 VAL
Chi-restraints excluded: chain P residue 1227 LEU
Chi-restraints excluded: chain P residue 1261 SER
Chi-restraints excluded: chain P residue 1262 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 137 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 156 optimal weight:    2.9990
   chunk 130 optimal weight:    8.9990
   chunk 93 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1023 ASN
** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P1295 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5104 r_free = 0.5104 target = 0.284310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.229445 restraints weight = 17023.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.4851 rms_B_bonded: 3.06
r_work: 0.4290 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.4054 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.5041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14107  Z= 0.151
  Angle     :  0.638  13.485  19164  Z= 0.336
  Chirality :  0.045   0.290   2085
  Planarity :  0.004   0.068   2518
  Dihedral  :  4.640  34.327   1949
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 21.95 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -3.21 (0.19), residues: 1765
  helix: -2.22 (0.33), residues: 199
  sheet: -1.80 (0.23), residues: 489
  loop : -2.35 (0.18), residues: 1077

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 546 
 HIS   0.005   0.001   HIS A 677 
 PHE   0.016   0.001   PHE A 494 
 TYR   0.027   0.001   TYR A 468 
 ARG   0.013   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03571 (  296)
  hydrogen bonds       : angle       6.00370 (  846)
  SS BOND              : bond        0.00964 (    2)
  SS BOND              : angle       5.70999 (    4)
  covalent geometry    : bond        0.00337 (14105)
  covalent geometry    : angle       0.63283 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 152
  time to evaluate  : 1.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.8260 (mtp) cc_final: 0.7909 (ptp)
REVERT: A  365 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8359 (pp)
REVERT: A  521 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7290 (mm-30)
REVERT: B   82 LYS cc_start: 0.5307 (mtmm) cc_final: 0.4915 (mtmt)
REVERT: B  278 MET cc_start: 0.6043 (mmm) cc_final: 0.5812 (mmp)
REVERT: C   80 LEU cc_start: 0.4770 (mm) cc_final: 0.4158 (pt)
REVERT: D  174 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8105 (pp)
REVERT: E   28 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.4550 (t80)
REVERT: E   50 MET cc_start: 0.7783 (mmm) cc_final: 0.7261 (mmm)
REVERT: P 1018 PHE cc_start: 0.8568 (t80) cc_final: 0.8242 (t80)
REVERT: P 1070 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8205 (ttpp)
REVERT: P 1212 LYS cc_start: 0.8205 (tppp) cc_final: 0.7778 (mtmt)
  outliers start: 55
  outliers final: 45
  residues processed: 193
  average time/residue: 0.2733
  time to fit residues: 76.7816
Evaluate side-chains
  191 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 143
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  545 MET
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue   84 ASP
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 ARG
Chi-restraints excluded: chain E residue   28 TYR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain P residue 1063 VAL
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1100 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1121 LEU
Chi-restraints excluded: chain P residue 1122 ILE
Chi-restraints excluded: chain P residue 1128 HIS
Chi-restraints excluded: chain P residue 1146 THR
Chi-restraints excluded: chain P residue 1166 TRP
Chi-restraints excluded: chain P residue 1209 ASP
Chi-restraints excluded: chain P residue 1221 VAL
Chi-restraints excluded: chain P residue 1262 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1296 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 6 optimal weight:    0.0370
   chunk 47 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 130 optimal weight:    5.9990
   chunk 122 optimal weight:   30.0000
   chunk 165 optimal weight:    0.2980
   chunk 127 optimal weight:   10.0000
   chunk 25 optimal weight:    0.4980
   chunk 148 optimal weight:    6.9990
   chunk 145 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.3460

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 226 GLN
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P1170 GLN
P1295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5165 r_free = 0.5165 target = 0.283416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4933 r_free = 0.4933 target = 0.240431 restraints weight = 16416.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.4896 rms_B_bonded: 3.34
r_work: 0.4324 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.4055 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14107  Z= 0.132
  Angle     :  0.620  14.600  19164  Z= 0.324
  Chirality :  0.044   0.270   2085
  Planarity :  0.004   0.054   2518
  Dihedral  :  4.396  33.233   1949
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 22.08 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -2.99 (0.19), residues: 1765
  helix: -1.79 (0.35), residues: 191
  sheet: -1.66 (0.24), residues: 472
  loop : -2.25 (0.18), residues: 1102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 546 
 HIS   0.005   0.001   HIS P1062 
 PHE   0.015   0.001   PHE A 802 
 TYR   0.026   0.001   TYR A 468 
 ARG   0.006   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  296)
  hydrogen bonds       : angle       5.73360 (  846)
  SS BOND              : bond        0.00453 (    2)
  SS BOND              : angle       5.04337 (    4)
  covalent geometry    : bond        0.00297 (14105)
  covalent geometry    : angle       0.61600 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 152
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.8411 (mtp) cc_final: 0.7963 (ptp)
REVERT: A  365 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8334 (pp)
REVERT: A  504 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8246 (p90)
REVERT: B   82 LYS cc_start: 0.5514 (mtmm) cc_final: 0.5182 (mtmt)
REVERT: C   80 LEU cc_start: 0.4761 (mm) cc_final: 0.4129 (pt)
REVERT: D  174 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8079 (pp)
REVERT: E   28 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.4691 (t80)
REVERT: E   50 MET cc_start: 0.7827 (mmm) cc_final: 0.7283 (mmm)
REVERT: P 1070 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8254 (ttpp)
REVERT: P 1212 LYS cc_start: 0.8021 (tppp) cc_final: 0.7603 (mtmt)
  outliers start: 55
  outliers final: 42
  residues processed: 193
  average time/residue: 0.2791
  time to fit residues: 78.4853
Evaluate side-chains
  188 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 142
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  504 TYR
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  545 MET
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue   84 ASP
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 ARG
Chi-restraints excluded: chain E residue   28 TYR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain P residue 1063 VAL
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1089 SER
Chi-restraints excluded: chain P residue 1100 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1121 LEU
Chi-restraints excluded: chain P residue 1122 ILE
Chi-restraints excluded: chain P residue 1128 HIS
Chi-restraints excluded: chain P residue 1146 THR
Chi-restraints excluded: chain P residue 1166 TRP
Chi-restraints excluded: chain P residue 1209 ASP
Chi-restraints excluded: chain P residue 1221 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1296 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 116 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 96 optimal weight:   50.0000
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 161 optimal weight:   20.0000
   chunk 111 optimal weight:   20.0000
   chunk 63 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0570
   overall best weight:    2.0106

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1062 HIS
** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P1295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5142 r_free = 0.5142 target = 0.285975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.231764 restraints weight = 16462.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.4837 rms_B_bonded: 3.42
r_work: 0.4407 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.5258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14107  Z= 0.166
  Angle     :  0.654  14.453  19164  Z= 0.341
  Chirality :  0.045   0.277   2085
  Planarity :  0.004   0.076   2518
  Dihedral  :  4.520  34.672   1949
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 22.91 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -2.92 (0.19), residues: 1765
  helix: -1.77 (0.35), residues: 198
  sheet: -1.64 (0.24), residues: 472
  loop : -2.18 (0.18), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 546 
 HIS   0.007   0.001   HIS A 677 
 PHE   0.027   0.001   PHE P1018 
 TYR   0.027   0.002   TYR A 468 
 ARG   0.008   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03541 (  296)
  hydrogen bonds       : angle       5.77116 (  846)
  SS BOND              : bond        0.00520 (    2)
  SS BOND              : angle       5.17321 (    4)
  covalent geometry    : bond        0.00373 (14105)
  covalent geometry    : angle       0.64932 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 149
  time to evaluate  : 1.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.2160 (OUTLIER) cc_final: 0.1733 (m)
REVERT: A  365 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8247 (pp)
REVERT: A  504 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8220 (p90)
REVERT: A  521 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6802 (mm-30)
REVERT: B   82 LYS cc_start: 0.4649 (mtmm) cc_final: 0.4271 (mtmt)
REVERT: C   80 LEU cc_start: 0.4213 (OUTLIER) cc_final: 0.3957 (pt)
REVERT: D  174 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8097 (pp)
REVERT: E   28 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.4684 (t80)
  outliers start: 55
  outliers final: 45
  residues processed: 190
  average time/residue: 0.2698
  time to fit residues: 75.6182
Evaluate side-chains
  194 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 143
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  504 TYR
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  545 MET
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain D residue   84 ASP
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 ARG
Chi-restraints excluded: chain E residue   28 TYR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain P residue 1063 VAL
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1089 SER
Chi-restraints excluded: chain P residue 1100 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1121 LEU
Chi-restraints excluded: chain P residue 1122 ILE
Chi-restraints excluded: chain P residue 1128 HIS
Chi-restraints excluded: chain P residue 1146 THR
Chi-restraints excluded: chain P residue 1166 TRP
Chi-restraints excluded: chain P residue 1209 ASP
Chi-restraints excluded: chain P residue 1221 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1296 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 160 optimal weight:    2.9990
   chunk 142 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 78 optimal weight:    0.0470
   chunk 122 optimal weight:    0.0770
   chunk 5 optimal weight:    9.9990
   chunk 149 optimal weight:    0.9980
   chunk 169 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    1.2240

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 GLN
** P1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P1170 GLN
P1295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5143 r_free = 0.5143 target = 0.290917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.232468 restraints weight = 17398.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.4821 rms_B_bonded: 3.64
r_work: 0.4302 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.5277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14107  Z= 0.126
  Angle     :  0.634  14.631  19164  Z= 0.325
  Chirality :  0.044   0.257   2085
  Planarity :  0.004   0.054   2518
  Dihedral  :  4.342  32.342   1949
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.60 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -2.83 (0.19), residues: 1765
  helix: -1.70 (0.35), residues: 194
  sheet: -1.51 (0.24), residues: 466
  loop : -2.16 (0.18), residues: 1105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 546 
 HIS   0.003   0.001   HIS P1062 
 PHE   0.018   0.001   PHE P1018 
 TYR   0.026   0.001   TYR A 468 
 ARG   0.008   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03141 (  296)
  hydrogen bonds       : angle       5.53678 (  846)
  SS BOND              : bond        0.00340 (    2)
  SS BOND              : angle       4.80965 (    4)
  covalent geometry    : bond        0.00287 (14105)
  covalent geometry    : angle       0.63021 (19160)

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

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

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3530 Ramachandran restraints generated.
    1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 151
  time to evaluate  : 1.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.2474 (OUTLIER) cc_final: 0.2050 (m)
REVERT: A  365 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8137 (pp)
REVERT: A  791 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.5703 (t80)
REVERT: B   82 LYS cc_start: 0.4959 (mtmm) cc_final: 0.4331 (mtmt)
REVERT: C   80 LEU cc_start: 0.4315 (mm) cc_final: 0.3927 (pt)
REVERT: D  174 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8113 (pp)
REVERT: E   28 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.4712 (t80)
REVERT: P 1006 ASN cc_start: 0.5771 (m-40) cc_final: 0.5461 (t0)
  outliers start: 50
  outliers final: 39
  residues processed: 185
  average time/residue: 0.2717
  time to fit residues: 74.0970
Evaluate side-chains
  192 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 148
  time to evaluate  : 1.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  494 PHE
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  545 MET
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  791 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  345 TYR
Chi-restraints excluded: chain D residue   84 ASP
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain E residue   28 TYR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain P residue 1063 VAL
Chi-restraints excluded: chain P residue 1085 THR
Chi-restraints excluded: chain P residue 1100 THR
Chi-restraints excluded: chain P residue 1107 LEU
Chi-restraints excluded: chain P residue 1121 LEU
Chi-restraints excluded: chain P residue 1122 ILE
Chi-restraints excluded: chain P residue 1128 HIS
Chi-restraints excluded: chain P residue 1146 THR
Chi-restraints excluded: chain P residue 1166 TRP
Chi-restraints excluded: chain P residue 1209 ASP
Chi-restraints excluded: chain P residue 1221 VAL
Chi-restraints excluded: chain P residue 1283 PHE
Chi-restraints excluded: chain P residue 1296 PHE
Chi-restraints excluded: chain P residue 1297 CYS
Chi-restraints excluded: chain P residue 1300 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 151 optimal weight:    0.0370
   chunk 35 optimal weight:   10.0000
   chunk 171 optimal weight:    4.9990
   chunk 86 optimal weight:    9.9990
   chunk 5 optimal weight:   30.0000
   chunk 135 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 97 optimal weight:   20.0000
   chunk 121 optimal weight:   10.0000
   chunk 168 optimal weight:    4.9990
   overall best weight:    2.6066

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 677 HIS
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P1295 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5125 r_free = 0.5125 target = 0.287080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.232169 restraints weight = 17340.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.4832 rms_B_bonded: 2.99
r_work: 0.4300 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4020 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.5567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  14107  Z= 0.198
  Angle     :  0.691  14.396  19164  Z= 0.359
  Chirality :  0.046   0.281   2085
  Planarity :  0.005   0.061   2518
  Dihedral  :  4.670  35.582   1949
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 23.46 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -2.77 (0.19), residues: 1765
  helix: -1.67 (0.35), residues: 199
  sheet: -1.48 (0.25), residues: 437
  loop : -2.11 (0.18), residues: 1129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 745 
 HIS   0.005   0.001   HIS A 677 
 PHE   0.021   0.002   PHE A 494 
 TYR   0.030   0.002   TYR A 468 
 ARG   0.011   0.001   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (  296)
  hydrogen bonds       : angle       5.75282 (  846)
  SS BOND              : bond        0.00483 (    2)
  SS BOND              : angle       5.16535 (    4)
  covalent geometry    : bond        0.00444 (14105)
  covalent geometry    : angle       0.68749 (19160)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8561.46 seconds
wall clock time: 146 minutes 54.52 seconds (8814.52 seconds total)