Starting phenix.real_space_refine
on Sun Aug 24 01:44:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v2g_42911/08_2025/8v2g_42911.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v2g_42911/08_2025/8v2g_42911.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v2g_42911/08_2025/8v2g_42911.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v2g_42911/08_2025/8v2g_42911.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v2g_42911/08_2025/8v2g_42911.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v2g_42911/08_2025/8v2g_42911.map"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     Ca      8      9.91       5
     K       4      8.98       5
     S     124      5.16       5
     C   10324      2.51       5
     N    2724      2.21       5
     O    2979      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16163
  Number of models: 1
  Model: ""
    Number of chains: 17
    Chain: "A"
      Number of atoms: 2883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2883
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 6, 'TRANS': 354}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 1152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1152
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 143}
    Chain: "B"
      Number of atoms: 2884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2884
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 6, 'TRANS': 354}
    Chain: "F"
      Number of atoms: 1152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1152
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 143}
    Chain: "C"
      Number of atoms: 2884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2884
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 6, 'TRANS': 354}
    Chain: "G"
      Number of atoms: 1152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1152
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 143}
    Chain: "D"
      Number of atoms: 2884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2884
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 6, 'TRANS': 354}
    Chain: "H"
      Number of atoms: 1152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1152
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 143}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {'  K': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "H"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.28, per 1000 atoms: 0.26
  Number of scatterers: 16163
  At special positions: 0
  Unit cell: (143.62, 141.9, 98.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      8     19.99
     K       4     19.00
     S     124     16.00
     O    2979      8.00
     N    2724      7.00
     C   10324      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 371 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 371 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 333 " - pdb=" SG  CYS C 371 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 333 " - pdb=" SG  CYS D 371 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 876.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3824

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 8 sheets defined
      74.5% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 160
      removed outlier: 3.580A  pdb=" N   SER A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ASP A 137 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   TYR A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ALA A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU A 140 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TRP A 158 " --> pdb=" O   THR A 154 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   GLY A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 202
      removed outlier: 3.846A  pdb=" N   LEU A 169 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY A 202 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 209
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 255 through 261
      removed outlier: 3.594A  pdb=" N   LEU A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE A 261 " --> pdb=" O   ILE A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 267
    Processing helix  chain 'A' and resid 268 through 278
      removed outlier: 3.503A  pdb=" N   ARG A 272 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 293
    Processing helix  chain 'A' and resid 298 through 310
      removed outlier: 3.626A  pdb=" N   VAL A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 335
      removed outlier: 3.617A  pdb=" N   ILE A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 358
    Processing helix  chain 'A' and resid 369 through 396
      removed outlier: 4.645A  pdb=" N   ALA A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   LEU A 389 " --> pdb=" O   GLY A 385 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA A 395 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ARG A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 439
      removed outlier: 3.661A  pdb=" N   LYS A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU A 430 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   THR A 431 " --> pdb=" O   VAL A 427 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TRP A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 478
      removed outlier: 4.056A  pdb=" N   VAL A 449 " --> pdb=" O   ASP A 445 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ARG A 450 " --> pdb=" O   HIS A 446 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LYS A 451 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 5 through 17
    Processing helix  chain 'E' and resid 28 through 38
      removed outlier: 3.551A  pdb=" N   SER E  38 " --> pdb=" O   THR E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.811A  pdb=" N   VAL E  55 " --> pdb=" O   MET E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 76
    Processing helix  chain 'E' and resid 80 through 93
      removed outlier: 3.667A  pdb=" N   ILE E  85 " --> pdb=" O   SER E  81 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ARG E  86 " --> pdb=" O   GLU E  82 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   PHE E  89 " --> pdb=" O   ILE E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 112
    Processing helix  chain 'E' and resid 117 through 129
    Processing helix  chain 'E' and resid 138 through 147
      removed outlier: 4.184A  pdb=" N   VAL E 142 " --> pdb=" O   TYR E 138 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLN E 143 " --> pdb=" O   GLU E 139 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   MET E 144 " --> pdb=" O   GLU E 140 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET E 145 " --> pdb=" O   PHE E 141 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ALA E 147 " --> pdb=" O   GLN E 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 158
      removed outlier: 3.556A  pdb=" N   SER B 136 " --> pdb=" O   ARG B 132 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ASP B 137 " --> pdb=" O   LYS B 133 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   TYR B 138 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ALA B 139 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLY B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   TRP B 158 " --> pdb=" O   THR B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 201
      removed outlier: 3.849A  pdb=" N   LEU B 169 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE B 175 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 209
    Processing helix  chain 'B' and resid 212 through 226
    Processing helix  chain 'B' and resid 256 through 258
      No H-bonds generated for 'chain 'B' and resid 256 through 258'
    Processing helix  chain 'B' and resid 260 through 267
    Processing helix  chain 'B' and resid 268 through 278
      removed outlier: 3.521A  pdb=" N   ARG B 272 " --> pdb=" O   TYR B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 294
    Processing helix  chain 'B' and resid 298 through 310
      removed outlier: 3.823A  pdb=" N   VAL B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET B 303 " --> pdb=" O   THR B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 335
    Processing helix  chain 'B' and resid 345 through 358
    Processing helix  chain 'B' and resid 369 through 396
      removed outlier: 4.755A  pdb=" N   ALA B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LEU B 389 " --> pdb=" O   GLY B 385 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG B 396 " --> pdb=" O   ALA B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 440
      removed outlier: 3.734A  pdb=" N   LYS B 418 " --> pdb=" O   THR B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 478
      removed outlier: 4.006A  pdb=" N   VAL B 449 " --> pdb=" O   ASP B 445 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ARG B 450 " --> pdb=" O   HIS B 446 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LYS B 451 " --> pdb=" O   ALA B 447 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 5 through 17
    Processing helix  chain 'F' and resid 28 through 39
    Processing helix  chain 'F' and resid 44 through 56
      removed outlier: 3.750A  pdb=" N   ILE F  52 " --> pdb=" O   LEU F  48 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   GLU F  54 " --> pdb=" O   ASP F  50 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL F  55 " --> pdb=" O   MET F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 64 through 76
    Processing helix  chain 'F' and resid 80 through 93
      removed outlier: 3.682A  pdb=" N   ILE F  85 " --> pdb=" O   SER F  81 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ARG F  86 " --> pdb=" O   GLU F  82 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE F  92 " --> pdb=" O   ALA F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 112
    Processing helix  chain 'F' and resid 117 through 126
    Processing helix  chain 'F' and resid 138 through 144
      removed outlier: 4.056A  pdb=" N   VAL F 142 " --> pdb=" O   TYR F 138 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLN F 143 " --> pdb=" O   GLU F 139 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   MET F 144 " --> pdb=" O   GLU F 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 138 through 144'
    Processing helix  chain 'C' and resid 123 through 157
      removed outlier: 3.586A  pdb=" N   SER C 136 " --> pdb=" O   ARG C 132 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ASP C 137 " --> pdb=" O   LYS C 133 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   TYR C 138 " --> pdb=" O   ARG C 134 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ALA C 139 " --> pdb=" O   LEU C 135 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU C 140 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY C 146 " --> pdb=" O   PHE C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 202
      removed outlier: 3.762A  pdb=" N   ILE C 175 " --> pdb=" O   LEU C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 209
    Processing helix  chain 'C' and resid 212 through 226
    Processing helix  chain 'C' and resid 256 through 258
      No H-bonds generated for 'chain 'C' and resid 256 through 258'
    Processing helix  chain 'C' and resid 260 through 266
    Processing helix  chain 'C' and resid 267 through 278
      removed outlier: 4.210A  pdb=" N   ALA C 271 " --> pdb=" O   LEU C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 293
    Processing helix  chain 'C' and resid 298 through 310
      removed outlier: 3.560A  pdb=" N   VAL C 302 " --> pdb=" O   ASN C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 335
    Processing helix  chain 'C' and resid 345 through 358
    Processing helix  chain 'C' and resid 369 through 396
      removed outlier: 4.646A  pdb=" N   ALA C 388 " --> pdb=" O   ALA C 384 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   LEU C 389 " --> pdb=" O   GLY C 385 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA C 395 " --> pdb=" O   VAL C 391 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ARG C 396 " --> pdb=" O   ALA C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 401 through 440
      removed outlier: 3.653A  pdb=" N   LYS C 418 " --> pdb=" O   THR C 414 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN C 426 " --> pdb=" O   ASN C 422 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   VAL C 427 " --> pdb=" O   ALA C 423 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LEU C 428 " --> pdb=" O   ALA C 424 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 478
      removed outlier: 3.990A  pdb=" N   VAL C 449 " --> pdb=" O   ASP C 445 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG C 450 " --> pdb=" O   HIS C 446 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LYS C 451 " --> pdb=" O   ALA C 447 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 5 through 18
      removed outlier: 3.566A  pdb=" N   LEU G  18 " --> pdb=" O   GLU G  14 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 39
    Processing helix  chain 'G' and resid 44 through 56
      removed outlier: 3.853A  pdb=" N   VAL G  55 " --> pdb=" O   MET G  51 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 64 through 77
      removed outlier: 4.125A  pdb=" N   LYS G  77 " --> pdb=" O   ALA G  73 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 92
      removed outlier: 4.193A  pdb=" N   ILE G  85 " --> pdb=" O   SER G  81 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG G  86 " --> pdb=" O   GLU G  82 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   PHE G  92 " --> pdb=" O   ALA G  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 102 through 112
    Processing helix  chain 'G' and resid 117 through 129
    Processing helix  chain 'G' and resid 138 through 147
      removed outlier: 3.593A  pdb=" N   VAL G 142 " --> pdb=" O   TYR G 138 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ALA G 147 " --> pdb=" O   GLN G 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 160
      removed outlier: 3.573A  pdb=" N   SER D 136 " --> pdb=" O   ARG D 132 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ASP D 137 " --> pdb=" O   LYS D 133 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   TYR D 138 " --> pdb=" O   ARG D 134 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   ALA D 139 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU D 140 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLY D 146 " --> pdb=" O   PHE D 142 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TRP D 158 " --> pdb=" O   THR D 154 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   GLY D 159 " --> pdb=" O   GLU D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 202
      removed outlier: 3.849A  pdb=" N   LEU D 169 " --> pdb=" O   SER D 165 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE D 175 " --> pdb=" O   LEU D 171 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 209
    Processing helix  chain 'D' and resid 212 through 226
    Processing helix  chain 'D' and resid 256 through 258
      No H-bonds generated for 'chain 'D' and resid 256 through 258'
    Processing helix  chain 'D' and resid 260 through 267
    Processing helix  chain 'D' and resid 268 through 278
      removed outlier: 3.541A  pdb=" N   ARG D 272 " --> pdb=" O   TYR D 268 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 283 through 293
    Processing helix  chain 'D' and resid 298 through 310
      removed outlier: 3.704A  pdb=" N   VAL D 302 " --> pdb=" O   ASN D 298 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 312 through 335
      removed outlier: 3.603A  pdb=" N   ILE D 324 " --> pdb=" O   ILE D 320 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 358
    Processing helix  chain 'D' and resid 369 through 396
      removed outlier: 4.784A  pdb=" N   ALA D 388 " --> pdb=" O   ALA D 384 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LEU D 389 " --> pdb=" O   GLY D 385 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 401 through 440
      removed outlier: 3.634A  pdb=" N   LYS D 418 " --> pdb=" O   THR D 414 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ASN D 426 " --> pdb=" O   ASN D 422 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   VAL D 427 " --> pdb=" O   ALA D 423 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU D 428 " --> pdb=" O   ALA D 424 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 445 through 478
      removed outlier: 3.661A  pdb=" N   VAL D 449 " --> pdb=" O   ASP D 445 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 5 through 20
      removed outlier: 3.526A  pdb=" N   ILE H   9 " --> pdb=" O   THR H   5 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU H  11 " --> pdb=" O   GLU H   7 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU H  18 " --> pdb=" O   GLU H  14 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE H  19 " --> pdb=" O   ALA H  15 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 39
    Processing helix  chain 'H' and resid 44 through 56
      removed outlier: 3.813A  pdb=" N   VAL H  55 " --> pdb=" O   MET H  51 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 64 through 76
    Processing helix  chain 'H' and resid 80 through 93
      removed outlier: 3.814A  pdb=" N   ILE H  85 " --> pdb=" O   SER H  81 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA H  88 " --> pdb=" O   GLU H  84 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE H  89 " --> pdb=" O   ILE H  85 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 102 through 112
    Processing helix  chain 'H' and resid 117 through 129
    Processing helix  chain 'H' and resid 140 through 146
      removed outlier: 4.117A  pdb=" N   MET H 144 " --> pdb=" O   GLU H 140 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   MET H 145 " --> pdb=" O   PHE H 141 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 241
    Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 101
    Processing sheet with id=AA3, first strand: chain 'B' and resid 235 through 241
    Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 101
    Processing sheet with id=AA5, first strand: chain 'C' and resid 235 through 241
    Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'D' and resid 235 through 241
    Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 101

    1078 hydrogen bonds defined for protein.
    3147 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.25

  Time building geometry restraints manager: 1.75 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: 5232
        1.34 -     1.46: 3703
        1.46 -     1.58: 7276
        1.58 -     1.70: 0
        1.70 -     1.82: 216
  Bond restraints: 16427
  Sorted by residual:
  bond pdb=" C   ILE C 261 "
       pdb=" N   PRO C 262 "
    ideal  model  delta    sigma   weight residual
    1.337  1.347 -0.011 9.80e-03 1.04e+04 1.23e+00
  bond pdb=" CB  ASN H  53 "
       pdb=" CG  ASN H  53 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.12e+00
  bond pdb=" C   ILE A 261 "
       pdb=" N   PRO A 262 "
    ideal  model  delta    sigma   weight residual
    1.337  1.347 -0.010 9.80e-03 1.04e+04 1.06e+00
  bond pdb=" CB  GLU E   7 "
       pdb=" CG  GLU E   7 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.89e-01
  bond pdb=" CB  GLU F 114 "
       pdb=" CG  GLU F 114 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.84e-01
  ... (remaining 16422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 21784
        1.53 -     3.07: 324
        3.07 -     4.60: 41
        4.60 -     6.14: 18
        6.14 -     7.67: 7
  Bond angle restraints: 22174
  Sorted by residual:
  angle pdb=" N   SER B 245 "
        pdb=" CA  SER B 245 "
        pdb=" C   SER B 245 "
      ideal   model   delta    sigma   weight residual
     114.56  110.43    4.13 1.27e+00 6.20e-01 1.06e+01
  angle pdb=" N   SER D 245 "
        pdb=" CA  SER D 245 "
        pdb=" C   SER D 245 "
      ideal   model   delta    sigma   weight residual
     114.56  110.52    4.04 1.27e+00 6.20e-01 1.01e+01
  angle pdb=" N   SER C 245 "
        pdb=" CA  SER C 245 "
        pdb=" C   SER C 245 "
      ideal   model   delta    sigma   weight residual
     114.56  110.54    4.02 1.27e+00 6.20e-01 1.00e+01
  angle pdb=" N   SER A 245 "
        pdb=" CA  SER A 245 "
        pdb=" C   SER A 245 "
      ideal   model   delta    sigma   weight residual
     114.56  110.59    3.97 1.27e+00 6.20e-01 9.79e+00
  angle pdb=" N   VAL G  55 "
        pdb=" CA  VAL G  55 "
        pdb=" C   VAL G  55 "
      ideal   model   delta    sigma   weight residual
     113.39  108.85    4.54 1.47e+00 4.63e-01 9.55e+00
  ... (remaining 22169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 8690
       17.81 -    35.61: 946
       35.61 -    53.42: 183
       53.42 -    71.22: 68
       71.22 -    89.03: 5
  Dihedral angle restraints: 9892
    sinusoidal: 3988
      harmonic: 5904
  Sorted by residual:
  dihedral pdb=" CA  ASP A 200 "
           pdb=" CB  ASP A 200 "
           pdb=" CG  ASP A 200 "
           pdb=" OD1 ASP A 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.60   56.60     1      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CA  ASP A 445 "
           pdb=" CB  ASP A 445 "
           pdb=" CG  ASP A 445 "
           pdb=" OD1 ASP A 445 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.34   56.34     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" CB  GLU G   6 "
           pdb=" CG  GLU G   6 "
           pdb=" CD  GLU G   6 "
           pdb=" OE1 GLU G   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.03   89.03     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 9889 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1800
       0.036 -    0.071: 620
       0.071 -    0.107: 113
       0.107 -    0.142: 26
       0.142 -    0.178: 5
  Chirality restraints: 2564
  Sorted by residual:
  chirality pdb=" CA  ASP H  24 "
            pdb=" N   ASP H  24 "
            pdb=" C   ASP H  24 "
            pdb=" CB  ASP H  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.90e-01
  chirality pdb=" CB  THR C 379 "
            pdb=" CA  THR C 379 "
            pdb=" OG1 THR C 379 "
            pdb=" CG2 THR C 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.07e-01
  chirality pdb=" CB  THR D 379 "
            pdb=" CA  THR D 379 "
            pdb=" OG1 THR D 379 "
            pdb=" CG2 THR D 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.73e-01
  ... (remaining 2561 not shown)

  Planarity restraints: 2783
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 261 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO C 262 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO C 262 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 262 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 261 "    0.024 5.00e-02 4.00e+02   3.66e-02 2.15e+00
        pdb=" N   PRO D 262 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D 262 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D 262 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 261 "    0.024 5.00e-02 4.00e+02   3.66e-02 2.14e+00
        pdb=" N   PRO A 262 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 262 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 262 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2780 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.76: 2739
        2.76 -     3.35: 18766
        3.35 -     3.95: 28784
        3.95 -     4.54: 40003
        4.54 -     5.14: 59595
  Nonbonded interactions: 149887
  Sorted by model distance:
  nonbonded pdb=" O   ARG G 106 "
            pdb=" OG1 THR G 110 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" N   GLU E   7 "
            pdb=" OE1 GLU E   7 "
     model   vdw
     2.194 3.120
  nonbonded pdb=" OG1 THR G  28 "
            pdb=" OE1 GLU G  31 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   HOH B 502 "
            pdb=" O   HOH C 501 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   HOH C 502 "
            pdb=" O   HOH D 501 "
     model   vdw
     2.270 3.040
  ... (remaining 149882 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 118 through 478)
  selection = (chain 'B' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ 
me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ 
ugh 478))
  selection = (chain 'C' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ 
me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ 
ugh 478))
  selection = (chain 'D' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ 
me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ 
ugh 478))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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:             12.520
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.350
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
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   0.039  16431  Z= 0.137
  Angle     :  0.506   7.675  22182  Z= 0.280
  Chirality :  0.037   0.178   2564
  Planarity :  0.003   0.037   2783
  Dihedral  : 15.723  89.031   6056
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.03 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.47 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.20), residues: 2012
  helix:  2.23 (0.14), residues: 1440
  sheet: -0.05 (0.81), residues: 48
  loop : -1.44 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  86 
 TYR   0.009   0.001   TYR D 120 
 PHE   0.017   0.001   PHE F 141 
 TRP   0.008   0.001   TRP B 432 
 HIS   0.004   0.001   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (16427)
  covalent geometry    : angle       0.50554 (22174)
  SS BOND              : bond        0.00471 (    4)
  SS BOND              : angle       1.13910 (    8)
  hydrogen bonds       : bond        0.13758 ( 1078)
  hydrogen bonds       : angle       4.33598 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 253
  time to evaluate  : 0.505 
Fit side-chains
REVERT: E   85 ILE cc_start: 0.8870 (pt) cc_final: 0.8595 (pt)
REVERT: F  111 ASN cc_start: 0.8812 (m110) cc_final: 0.8491 (m110)
REVERT: F  143 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8440 (tm-30)
  outliers start: 22
  outliers final: 20
  residues processed: 260
  average time/residue: 0.1384
  time to fit residues: 51.2962
Evaluate side-chains
  268 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 247
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain E residue  121 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain F residue  143 GLN
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain G residue   38 SER
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   85 ILE
Chi-restraints excluded: chain G residue   89 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain G residue  142 VAL
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain H residue   48 LEU
Chi-restraints excluded: chain H residue   85 ILE
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    0.9980
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 426 ASN
E 111 ASN
F 143 GLN
H   8 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.120611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.093862 restraints weight = 29574.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.46
r_work: 0.2973 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start:          0.0642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16431  Z= 0.126
  Angle     :  0.456   6.173  22182  Z= 0.249
  Chirality :  0.037   0.186   2564
  Planarity :  0.003   0.034   2783
  Dihedral  :  5.165  62.850   2227
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.18 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.30 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.20), residues: 2012
  helix:  2.46 (0.14), residues: 1408
  sheet:  1.16 (0.70), residues: 40
  loop : -1.32 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  90 
 TYR   0.014   0.001   TYR G  99 
 PHE   0.013   0.001   PHE C 357 
 TRP   0.007   0.001   TRP B 432 
 HIS   0.004   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (16427)
  covalent geometry    : angle       0.45622 (22174)
  SS BOND              : bond        0.00390 (    4)
  SS BOND              : angle       0.92063 (    8)
  hydrogen bonds       : bond        0.05754 ( 1078)
  hydrogen bonds       : angle       3.52062 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 270
  time to evaluate  : 0.528 
Fit side-chains
REVERT: E   85 ILE cc_start: 0.8598 (pt) cc_final: 0.8359 (pt)
REVERT: F  111 ASN cc_start: 0.8827 (m110) cc_final: 0.8563 (m110)
REVERT: G   48 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7820 (pp)
REVERT: G   86 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7964 (mtm110)
  outliers start: 27
  outliers final: 18
  residues processed: 281
  average time/residue: 0.1334
  time to fit residues: 53.8052
Evaluate side-chains
  267 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 248
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  468 MET
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   89 PHE
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 173 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 163 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0370
   chunk 83 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 190 optimal weight:    3.9990
   overall best weight:    1.2864

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

Flipped N/Q/H residues before XYZ refinement:
E 111 ASN
B 422 ASN
C 409 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.119015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.084940 restraints weight = 29684.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.76
r_work: 0.2987 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.0787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16431  Z= 0.153
  Angle     :  0.482   6.596  22182  Z= 0.260
  Chirality :  0.038   0.185   2564
  Planarity :  0.003   0.035   2783
  Dihedral  :  4.775  51.479   2209
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.28 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 10.64 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.20), residues: 2012
  helix:  2.36 (0.14), residues: 1408
  sheet: -0.51 (0.68), residues: 48
  loop : -1.29 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  90 
 TYR   0.009   0.001   TYR A 268 
 PHE   0.015   0.001   PHE A 357 
 TRP   0.008   0.001   TRP C 158 
 HIS   0.005   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (16427)
  covalent geometry    : angle       0.48167 (22174)
  SS BOND              : bond        0.00386 (    4)
  SS BOND              : angle       0.92108 (    8)
  hydrogen bonds       : bond        0.06373 ( 1078)
  hydrogen bonds       : angle       3.48824 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 263
  time to evaluate  : 0.573 
Fit side-chains
REVERT: E   85 ILE cc_start: 0.8640 (pt) cc_final: 0.8432 (pt)
REVERT: F  111 ASN cc_start: 0.8827 (m110) cc_final: 0.8579 (m110)
REVERT: G   86 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.8032 (mtm110)
REVERT: G   99 TYR cc_start: 0.7716 (m-80) cc_final: 0.7478 (m-80)
REVERT: G  126 ARG cc_start: 0.8770 (ptp-110) cc_final: 0.8512 (ttp80)
  outliers start: 47
  outliers final: 34
  residues processed: 278
  average time/residue: 0.1392
  time to fit residues: 55.3771
Evaluate side-chains
  285 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 251
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  468 MET
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  141 PHE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  468 MET
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   89 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain G residue  142 VAL
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain D residue  394 VAL
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 131 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0980
   chunk 13 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 199 optimal weight:    0.9990
   chunk 190 optimal weight:    4.9990
   chunk 179 optimal weight:    2.9990
   chunk 191 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
H   8 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.119949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.093422 restraints weight = 29575.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.61
r_work: 0.2955 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16431  Z= 0.126
  Angle     :  0.448   6.525  22182  Z= 0.244
  Chirality :  0.037   0.183   2564
  Planarity :  0.003   0.033   2783
  Dihedral  :  4.740  53.244   2209
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.98 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 11.44 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.20), residues: 2012
  helix:  2.43 (0.14), residues: 1408
  sheet: -0.45 (0.66), residues: 48
  loop : -1.29 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  86 
 TYR   0.008   0.001   TYR D 120 
 PHE   0.014   0.001   PHE C 357 
 TRP   0.007   0.001   TRP C 158 
 HIS   0.004   0.001   HIS D 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (16427)
  covalent geometry    : angle       0.44802 (22174)
  SS BOND              : bond        0.00331 (    4)
  SS BOND              : angle       0.74075 (    8)
  hydrogen bonds       : bond        0.05690 ( 1078)
  hydrogen bonds       : angle       3.38583 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 264
  time to evaluate  : 0.434 
Fit side-chains
REVERT: F  111 ASN cc_start: 0.8873 (m110) cc_final: 0.8648 (m110)
REVERT: G   86 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8067 (mtm110)
REVERT: G   99 TYR cc_start: 0.7846 (m-80) cc_final: 0.7589 (m-80)
REVERT: G  126 ARG cc_start: 0.8860 (ptp-110) cc_final: 0.8560 (ttp80)
REVERT: H    8 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7900 (pm20)
  outliers start: 44
  outliers final: 36
  residues processed: 283
  average time/residue: 0.1323
  time to fit residues: 53.5868
Evaluate side-chains
  290 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 253
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  468 MET
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  141 PHE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  109 MET
Chi-restraints excluded: chain F residue  122 ASP
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   89 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain G residue  142 VAL
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 142 optimal weight:    0.9980
   chunk 171 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 165 optimal weight:    2.9990
   chunk 158 optimal weight:    4.9990
   chunk 141 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 190 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.120549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.093945 restraints weight = 29633.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.57
r_work: 0.2969 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16431  Z= 0.119
  Angle     :  0.445   6.841  22182  Z= 0.241
  Chirality :  0.037   0.183   2564
  Planarity :  0.003   0.032   2783
  Dihedral  :  4.716  54.118   2209
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.28 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.78 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.20), residues: 2012
  helix:  2.46 (0.14), residues: 1408
  sheet: -0.43 (0.65), residues: 48
  loop : -1.30 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 126 
 TYR   0.008   0.001   TYR D 120 
 PHE   0.013   0.001   PHE C 357 
 TRP   0.006   0.001   TRP B 328 
 HIS   0.003   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (16427)
  covalent geometry    : angle       0.44513 (22174)
  SS BOND              : bond        0.00307 (    4)
  SS BOND              : angle       0.62282 (    8)
  hydrogen bonds       : bond        0.05416 ( 1078)
  hydrogen bonds       : angle       3.34299 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 264
  time to evaluate  : 0.527 
Fit side-chains
REVERT: E  109 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8199 (mtp)
REVERT: E  145 MET cc_start: 0.7190 (mmp) cc_final: 0.6544 (ttt)
REVERT: F  111 ASN cc_start: 0.8887 (m110) cc_final: 0.8608 (m110)
REVERT: G   99 TYR cc_start: 0.7857 (m-80) cc_final: 0.7593 (m-80)
REVERT: G  126 ARG cc_start: 0.8881 (ptp-110) cc_final: 0.8596 (ttp80)
  outliers start: 41
  outliers final: 33
  residues processed: 280
  average time/residue: 0.1302
  time to fit residues: 52.0529
Evaluate side-chains
  286 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 252
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  468 MET
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  141 PHE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  109 MET
Chi-restraints excluded: chain F residue  122 ASP
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   89 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  142 VAL
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 185 optimal weight:    4.9990
   chunk 194 optimal weight:    0.9990
   chunk 180 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 153 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 141 optimal weight:    3.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.119997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.086034 restraints weight = 29603.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.77
r_work: 0.3012 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16431  Z= 0.126
  Angle     :  0.456   7.123  22182  Z= 0.245
  Chirality :  0.037   0.181   2564
  Planarity :  0.003   0.032   2783
  Dihedral  :  4.381  54.871   2203
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.18 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 11.67 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.20), residues: 2012
  helix:  2.46 (0.14), residues: 1408
  sheet: -0.48 (0.64), residues: 48
  loop : -1.30 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 126 
 TYR   0.008   0.001   TYR D 120 
 PHE   0.013   0.001   PHE C 357 
 TRP   0.006   0.001   TRP C 158 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (16427)
  covalent geometry    : angle       0.45641 (22174)
  SS BOND              : bond        0.00316 (    4)
  SS BOND              : angle       0.63508 (    8)
  hydrogen bonds       : bond        0.05549 ( 1078)
  hydrogen bonds       : angle       3.33099 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 265
  time to evaluate  : 0.411 
Fit side-chains
REVERT: E  109 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8088 (mtp)
REVERT: E  145 MET cc_start: 0.7111 (mmp) cc_final: 0.6578 (ttt)
REVERT: F  111 ASN cc_start: 0.8801 (m110) cc_final: 0.8572 (m110)
REVERT: G   48 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7802 (pp)
REVERT: G   99 TYR cc_start: 0.7650 (m-80) cc_final: 0.7379 (m-80)
REVERT: G  126 ARG cc_start: 0.8796 (ptp-110) cc_final: 0.8517 (ttp80)
REVERT: G  145 MET cc_start: 0.6839 (mmp) cc_final: 0.6536 (ttt)
  outliers start: 45
  outliers final: 38
  residues processed: 283
  average time/residue: 0.1267
  time to fit residues: 51.6768
Evaluate side-chains
  295 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 255
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  468 MET
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  141 PHE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  109 MET
Chi-restraints excluded: chain F residue  122 ASP
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  394 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain G residue  142 VAL
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 169 optimal weight:    2.9990
   chunk 154 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 151 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 196 optimal weight:    4.9990
   chunk 192 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 157 optimal weight:    0.8980
   chunk 172 optimal weight:    0.1980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
H   8 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.119079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.084978 restraints weight = 29397.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.77
r_work: 0.2994 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16431  Z= 0.140
  Angle     :  0.478   7.537  22182  Z= 0.255
  Chirality :  0.038   0.180   2564
  Planarity :  0.003   0.033   2783
  Dihedral  :  4.372  59.618   2201
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.38 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 11.78 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.20), residues: 2012
  helix:  2.38 (0.14), residues: 1415
  sheet: -0.60 (0.64), residues: 48
  loop : -1.28 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 126 
 TYR   0.008   0.001   TYR A 268 
 PHE   0.014   0.001   PHE C 357 
 TRP   0.007   0.001   TRP C 158 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (16427)
  covalent geometry    : angle       0.47764 (22174)
  SS BOND              : bond        0.00324 (    4)
  SS BOND              : angle       0.64720 (    8)
  hydrogen bonds       : bond        0.05972 ( 1078)
  hydrogen bonds       : angle       3.36414 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 267
  time to evaluate  : 0.650 
Fit side-chains
REVERT: E  109 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8145 (mtp)
REVERT: E  145 MET cc_start: 0.7231 (mmp) cc_final: 0.6754 (ttt)
REVERT: F  105 LEU cc_start: 0.9022 (mt) cc_final: 0.8821 (tt)
REVERT: F  111 ASN cc_start: 0.8819 (m110) cc_final: 0.8582 (m110)
REVERT: G   48 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7813 (pp)
REVERT: G   99 TYR cc_start: 0.7695 (m-80) cc_final: 0.7446 (m-80)
REVERT: G  145 MET cc_start: 0.6766 (mmp) cc_final: 0.6496 (ttt)
REVERT: H    8 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7984 (pm20)
  outliers start: 51
  outliers final: 42
  residues processed: 286
  average time/residue: 0.1394
  time to fit residues: 57.2528
Evaluate side-chains
  305 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 260
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain A residue  468 MET
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   53 ASN
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  141 PHE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  109 MET
Chi-restraints excluded: chain F residue  122 ASP
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  394 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 114 optimal weight:    0.5980
   chunk 198 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 172 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 102 optimal weight:    0.8980
   chunk 138 optimal weight:    0.0370
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
B 409 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.120780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.086964 restraints weight = 29597.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.76
r_work: 0.3026 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  16431  Z= 0.115
  Angle     :  0.457   7.411  22182  Z= 0.244
  Chirality :  0.037   0.180   2564
  Planarity :  0.003   0.030   2783
  Dihedral  :  4.293  59.569   2201
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.68 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.93 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.20), residues: 2012
  helix:  2.46 (0.14), residues: 1415
  sheet: -0.45 (0.65), residues: 48
  loop : -1.23 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 126 
 TYR   0.008   0.001   TYR D 120 
 PHE   0.012   0.001   PHE C 357 
 TRP   0.007   0.001   TRP B 432 
 HIS   0.003   0.001   HIS D 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (16427)
  covalent geometry    : angle       0.45668 (22174)
  SS BOND              : bond        0.00299 (    4)
  SS BOND              : angle       0.57946 (    8)
  hydrogen bonds       : bond        0.05236 ( 1078)
  hydrogen bonds       : angle       3.30685 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 264
  time to evaluate  : 0.566 
Fit side-chains
REVERT: G   48 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7820 (pp)
REVERT: G   82 GLU cc_start: 0.8055 (tp30) cc_final: 0.7756 (mp0)
REVERT: G   90 ARG cc_start: 0.8307 (mtm180) cc_final: 0.8070 (mtm-85)
REVERT: G   99 TYR cc_start: 0.7685 (m-80) cc_final: 0.7441 (m-80)
  outliers start: 39
  outliers final: 32
  residues processed: 283
  average time/residue: 0.1326
  time to fit residues: 54.1382
Evaluate side-chains
  293 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 260
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  141 PHE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  109 MET
Chi-restraints excluded: chain F residue  122 ASP
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   48 LEU
Chi-restraints excluded: chain G residue   89 PHE
Chi-restraints excluded: chain G residue  142 VAL
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 136 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 199 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0770
   chunk 89 optimal weight:    0.9990
   chunk 132 optimal weight:    0.5980
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
H   8 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.121734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.088059 restraints weight = 29386.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.78
r_work: 0.3049 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  16431  Z= 0.107
  Angle     :  0.452   7.683  22182  Z= 0.241
  Chirality :  0.037   0.178   2564
  Planarity :  0.003   0.030   2783
  Dihedral  :  3.876  56.429   2197
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.83 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.76 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.20), residues: 2012
  helix:  2.54 (0.14), residues: 1415
  sheet: -0.39 (0.65), residues: 48
  loop : -1.17 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 126 
 TYR   0.007   0.001   TYR D 120 
 PHE   0.011   0.001   PHE A 357 
 TRP   0.008   0.001   TRP B 432 
 HIS   0.003   0.001   HIS D 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (16427)
  covalent geometry    : angle       0.45212 (22174)
  SS BOND              : bond        0.00296 (    4)
  SS BOND              : angle       0.54842 (    8)
  hydrogen bonds       : bond        0.04701 ( 1078)
  hydrogen bonds       : angle       3.24599 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 271
  time to evaluate  : 0.495 
Fit side-chains
REVERT: E  145 MET cc_start: 0.7127 (mmp) cc_final: 0.6669 (mtp)
REVERT: G   99 TYR cc_start: 0.7690 (m-80) cc_final: 0.7454 (m-80)
REVERT: G  126 ARG cc_start: 0.8631 (ptp-110) cc_final: 0.8417 (ttp80)
REVERT: G  145 MET cc_start: 0.6527 (mmp) cc_final: 0.6027 (mtm)
  outliers start: 37
  outliers final: 32
  residues processed: 291
  average time/residue: 0.1317
  time to fit residues: 55.4062
Evaluate side-chains
  292 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 260
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  141 PHE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue    8 GLN
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  109 MET
Chi-restraints excluded: chain F residue  122 ASP
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  394 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   26 THR
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain H residue    8 GLN
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 154 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 140 optimal weight:    0.8980
   chunk 163 optimal weight:    0.2980
   chunk 177 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 133 optimal weight:    2.9990
   chunk 125 optimal weight:    0.7980
   chunk 171 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.121331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.087510 restraints weight = 29469.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 1.76
r_work: 0.3038 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16431  Z= 0.118
  Angle     :  0.481   8.147  22182  Z= 0.254
  Chirality :  0.037   0.190   2564
  Planarity :  0.003   0.030   2783
  Dihedral  :  3.844  56.761   2197
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.88 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.39 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.20), residues: 2012
  helix:  2.53 (0.14), residues: 1411
  sheet: -0.36 (0.65), residues: 48
  loop : -1.16 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 126 
 TYR   0.007   0.001   TYR D 120 
 PHE   0.013   0.001   PHE C 357 
 TRP   0.006   0.001   TRP B 328 
 HIS   0.004   0.001   HIS D 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (16427)
  covalent geometry    : angle       0.48131 (22174)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       0.54461 (    8)
  hydrogen bonds       : bond        0.04993 ( 1078)
  hydrogen bonds       : angle       3.26819 ( 3147)

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

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

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4024 Ramachandran restraints generated.
    2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 265
  time to evaluate  : 0.633 
Fit side-chains
REVERT: E  145 MET cc_start: 0.7194 (mmp) cc_final: 0.6766 (mtp)
REVERT: F   53 ASN cc_start: 0.8737 (p0) cc_final: 0.8523 (p0)
REVERT: G   90 ARG cc_start: 0.8351 (mtm180) cc_final: 0.8136 (mtm-85)
REVERT: G   99 TYR cc_start: 0.7670 (m-80) cc_final: 0.7443 (m-80)
REVERT: G  126 ARG cc_start: 0.8622 (ptp-110) cc_final: 0.8417 (ttp80)
  outliers start: 36
  outliers final: 33
  residues processed: 284
  average time/residue: 0.1349
  time to fit residues: 55.1585
Evaluate side-chains
  295 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 262
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  404 GLU
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  141 PHE
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain F residue    8 GLN
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  109 MET
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain F residue  142 VAL
Chi-restraints excluded: chain C residue  322 LEU
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  394 VAL
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   26 THR
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   89 PHE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain D residue  322 LEU
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain H residue   91 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 122 optimal weight:    0.0370
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 154 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 188 optimal weight:    0.7980
   chunk 158 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
H   8 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.121669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.087932 restraints weight = 29414.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.77
r_work: 0.3047 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  16431  Z= 0.111
  Angle     :  0.474   8.253  22182  Z= 0.250
  Chirality :  0.037   0.178   2564
  Planarity :  0.003   0.031   2783
  Dihedral  :  3.736  56.665   2197
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.63 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.62 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.20), residues: 2012
  helix:  2.56 (0.14), residues: 1411
  sheet: -0.30 (0.65), residues: 48
  loop : -1.14 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 126 
 TYR   0.007   0.001   TYR B 435 
 PHE   0.011   0.001   PHE C 357 
 TRP   0.007   0.001   TRP B 432 
 HIS   0.004   0.001   HIS D 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (16427)
  covalent geometry    : angle       0.47430 (22174)
  SS BOND              : bond        0.00287 (    4)
  SS BOND              : angle       0.53467 (    8)
  hydrogen bonds       : bond        0.04760 ( 1078)
  hydrogen bonds       : angle       3.25917 ( 3147)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4465.28 seconds
wall clock time: 76 minutes 56.51 seconds (4616.51 seconds total)