Starting phenix.real_space_refine
on Mon Mar 11 03:22:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fbl_28964/03_2024/8fbl_28964_updated.pdb"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      30      5.16       5
     C    4440      2.51       5
     N    1104      2.21       5
     O    1245      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 6822
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2190
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "B"
      Number of atoms: 2190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2190
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "C"
      Number of atoms: 2190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2190
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 84
          Unusual residues: {'NAG': 4, 'PIO': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 10
    Chain: "B"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 84
          Unusual residues: {'NAG': 4, 'PIO': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 10
    Chain: "C"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 84
          Unusual residues: {'NAG': 4, 'PIO': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 10
  Time building chain proxies: 4.05, per 1000 atoms: 0.59
  Number of scatterers: 6822
  At special positions: 0
  Unit cell: (80.122, 81.774, 124.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       3     15.00
     O    1245      8.00
     N    1104      7.00
     C    4440      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 149 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A 148 "
      " NAG A 402 " - " ASN A 162 "
      " NAG A 403 " - " ASN A 190 "
      " NAG A 404 " - " ASN A 155 "
      " NAG B 401 " - " ASN B 148 "
      " NAG B 402 " - " ASN B 162 "
      " NAG B 403 " - " ASN B 190 "
      " NAG B 404 " - " ASN B 155 "
      " NAG C 401 " - " ASN C 148 "
      " NAG C 402 " - " ASN C 162 "
      " NAG C 403 " - " ASN C 190 "
      " NAG C 404 " - " ASN C 155 "
  Time building additional restraints: 2.80
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1608

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      18 helices and 9 sheets defined
      33.5% alpha, 33.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 95
      removed outlier: 3.775A  pdb=" N   LYS A  95 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 211
    Processing helix  chain 'A' and resid 216 through 225
    Processing helix  chain 'A' and resid 273 through 277
      removed outlier: 4.191A  pdb=" N   SER A 277 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 301
      No H-bonds generated for 'chain 'A' and resid 298 through 301'
    Processing helix  chain 'A' and resid 303 through 338
      removed outlier: 3.536A  pdb=" N   LYS A 329 " --> pdb=" O   LYS A 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 95
      removed outlier: 3.775A  pdb=" N   LYS B  95 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 211
    Processing helix  chain 'B' and resid 216 through 225
    Processing helix  chain 'B' and resid 273 through 277
      removed outlier: 4.191A  pdb=" N   SER B 277 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 301
      No H-bonds generated for 'chain 'B' and resid 298 through 301'
    Processing helix  chain 'B' and resid 303 through 338
      removed outlier: 3.536A  pdb=" N   LYS B 329 " --> pdb=" O   LYS B 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 95
      removed outlier: 3.774A  pdb=" N   LYS C  95 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 211
    Processing helix  chain 'C' and resid 216 through 225
    Processing helix  chain 'C' and resid 273 through 277
      removed outlier: 4.190A  pdb=" N   SER C 277 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 301
      No H-bonds generated for 'chain 'C' and resid 298 through 301'
    Processing helix  chain 'C' and resid 303 through 338
      removed outlier: 3.536A  pdb=" N   LYS C 329 " --> pdb=" O   LYS C 325 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 101 through 107
      removed outlier: 8.379A  pdb=" N   PHE A 291 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   LEU A 244 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ASP A 297 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS A 241 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 229 through 233
      removed outlier: 3.619A  pdb=" N   PHE A 232 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A 199 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASP A 200 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLY A 115 " --> pdb=" O   PHE A 204 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 237 through 242
      removed outlier: 8.819A  pdb=" N   THR A 238 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   PHE A 282 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   VAL A 240 " --> pdb=" O   PHE A 282 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL A 284 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   MET A 242 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLU A 286 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   TRP A 287 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLU A 181 " --> pdb=" O   TRP A 287 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER A 127 " --> pdb=" O   GLN A 186 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ARG A 188 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   LEU A 125 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 101 through 107
      removed outlier: 8.379A  pdb=" N   PHE B 291 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   LEU B 244 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS B 241 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 229 through 233
      removed outlier: 3.619A  pdb=" N   PHE B 232 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE B 199 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASP B 200 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 115 " --> pdb=" O   PHE B 204 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 237 through 242
      removed outlier: 8.819A  pdb=" N   THR B 238 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   PHE B 282 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   VAL B 240 " --> pdb=" O   PHE B 282 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL B 284 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   MET B 242 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   GLU B 286 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   TRP B 287 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   GLU B 181 " --> pdb=" O   TRP B 287 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER B 127 " --> pdb=" O   GLN B 186 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ARG B 188 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   LEU B 125 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 101 through 107
      removed outlier: 8.379A  pdb=" N   PHE C 291 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   LEU C 244 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS C 241 " --> pdb=" O   GLU C 261 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'C' and resid 229 through 233
      removed outlier: 3.618A  pdb=" N   PHE C 232 " --> pdb=" O   ILE C 199 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE C 199 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY C 115 " --> pdb=" O   PHE C 204 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'C' and resid 237 through 242
      removed outlier: 8.819A  pdb=" N   THR C 238 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   PHE C 282 " --> pdb=" O   THR C 238 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   VAL C 240 " --> pdb=" O   PHE C 282 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL C 284 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   MET C 242 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLU C 286 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   TRP C 287 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLU C 181 " --> pdb=" O   TRP C 287 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER C 127 " --> pdb=" O   GLN C 186 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ARG C 188 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   LEU C 125 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)

    351 hydrogen bonds defined for protein.
    1035 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: 1.97

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1066
        1.32 -     1.44: 1969
        1.44 -     1.56: 3901
        1.56 -     1.69: 6
        1.69 -     1.81: 48
  Bond restraints: 6990
  Sorted by residual:
  bond pdb=" O1  PIO C 405 "
       pdb=" P1  PIO C 405 "
    ideal  model  delta    sigma   weight residual
    1.648  1.478  0.170 2.00e-02 2.50e+03 7.21e+01
  bond pdb=" O1  PIO B 405 "
       pdb=" P1  PIO B 405 "
    ideal  model  delta    sigma   weight residual
    1.648  1.478  0.170 2.00e-02 2.50e+03 7.21e+01
  bond pdb=" O1  PIO A 405 "
       pdb=" P1  PIO A 405 "
    ideal  model  delta    sigma   weight residual
    1.648  1.479  0.169 2.00e-02 2.50e+03 7.18e+01
  bond pdb=" C1B PIO B 405 "
       pdb=" O3C PIO B 405 "
    ideal  model  delta    sigma   weight residual
    1.399  1.329  0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" C1B PIO A 405 "
       pdb=" O3C PIO A 405 "
    ideal  model  delta    sigma   weight residual
    1.399  1.329  0.070 2.00e-02 2.50e+03 1.24e+01
  ... (remaining 6985 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   107.23: 242
      107.23 -   113.92: 3930
      113.92 -   120.60: 2694
      120.60 -   127.29: 2530
      127.29 -   133.97: 78
  Bond angle restraints: 9474
  Sorted by residual:
  angle pdb=" C   ARG B  93 "
        pdb=" CA  ARG B  93 "
        pdb=" CB  ARG B  93 "
      ideal   model   delta    sigma   weight residual
     110.90  104.03    6.87 1.58e+00 4.01e-01 1.89e+01
  angle pdb=" C   ARG C  93 "
        pdb=" CA  ARG C  93 "
        pdb=" CB  ARG C  93 "
      ideal   model   delta    sigma   weight residual
     110.90  104.04    6.86 1.58e+00 4.01e-01 1.89e+01
  angle pdb=" C   ARG A  93 "
        pdb=" CA  ARG A  93 "
        pdb=" CB  ARG A  93 "
      ideal   model   delta    sigma   weight residual
     110.90  104.08    6.82 1.58e+00 4.01e-01 1.87e+01
  angle pdb=" N   TYR B 227 "
        pdb=" CA  TYR B 227 "
        pdb=" C   TYR B 227 "
      ideal   model   delta    sigma   weight residual
     109.62  115.44   -5.82 1.50e+00 4.44e-01 1.50e+01
  angle pdb=" N   TYR A 227 "
        pdb=" CA  TYR A 227 "
        pdb=" C   TYR A 227 "
      ideal   model   delta    sigma   weight residual
     109.62  115.43   -5.81 1.50e+00 4.44e-01 1.50e+01
  ... (remaining 9469 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.00: 4062
       23.00 -    45.99: 195
       45.99 -    68.99: 30
       68.99 -    91.99: 9
       91.99 -   114.99: 24
  Dihedral angle restraints: 4320
    sinusoidal: 1851
      harmonic: 2469
  Sorted by residual:
  dihedral pdb=" N2  NAG A 404 "
           pdb=" C2  NAG A 404 "
           pdb=" C3  NAG A 404 "
           pdb=" O3  NAG A 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.25  177.24 -114.99     1      3.00e+01 1.11e-03 1.52e+01
  dihedral pdb=" N2  NAG B 404 "
           pdb=" C2  NAG B 404 "
           pdb=" C3  NAG B 404 "
           pdb=" O3  NAG B 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.25  177.24 -114.99     1      3.00e+01 1.11e-03 1.52e+01
  dihedral pdb=" N2  NAG C 404 "
           pdb=" C2  NAG C 404 "
           pdb=" C3  NAG C 404 "
           pdb=" O3  NAG C 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.25  177.18 -114.93     1      3.00e+01 1.11e-03 1.52e+01
  ... (remaining 4317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 922
       0.058 -    0.116: 146
       0.116 -    0.175: 9
       0.175 -    0.233: 0
       0.233 -    0.291: 6
  Chirality restraints: 1083
  Sorted by residual:
  chirality pdb=" C1  NAG C 401 "
            pdb=" ND2 ASN C 148 "
            pdb=" C2  NAG C 401 "
            pdb=" O5  NAG C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" C1  NAG B 401 "
            pdb=" ND2 ASN B 148 "
            pdb=" C2  NAG B 401 "
            pdb=" O5  NAG B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" C1  NAG A 401 "
            pdb=" ND2 ASN A 148 "
            pdb=" C2  NAG A 401 "
            pdb=" O5  NAG A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 1080 not shown)

  Planarity restraints: 1188
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 403 "    0.304 2.00e-02 2.50e+03   2.57e-01 8.29e+02
        pdb=" C7  NAG A 403 "   -0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG A 403 "    0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG A 403 "   -0.445 2.00e-02 2.50e+03
        pdb=" O7  NAG A 403 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 403 "   -0.304 2.00e-02 2.50e+03   2.57e-01 8.28e+02
        pdb=" C7  NAG C 403 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG C 403 "   -0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG C 403 "    0.445 2.00e-02 2.50e+03
        pdb=" O7  NAG C 403 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 403 "   -0.303 2.00e-02 2.50e+03   2.57e-01 8.27e+02
        pdb=" C7  NAG B 403 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG B 403 "   -0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG B 403 "    0.445 2.00e-02 2.50e+03
        pdb=" O7  NAG B 403 "   -0.035 2.00e-02 2.50e+03
  ... (remaining 1185 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1080
        2.77 -     3.30: 6525
        3.30 -     3.83: 11010
        3.83 -     4.37: 12715
        4.37 -     4.90: 22644
  Nonbonded interactions: 53974
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 119 "
            pdb=" OE2 GLU B 224 "
     model   vdw
     2.233 2.440
  nonbonded pdb=" OH  TYR A 119 "
            pdb=" OE2 GLU A 224 "
     model   vdw
     2.233 2.440
  nonbonded pdb=" OH  TYR C 119 "
            pdb=" OE2 GLU C 224 "
     model   vdw
     2.233 2.440
  nonbonded pdb=" ND2 ASN C 302 "
            pdb=" OD1 ASN C 305 "
     model   vdw
     2.363 2.520
  nonbonded pdb=" ND2 ASN A 302 "
            pdb=" OD1 ASN A 305 "
     model   vdw
     2.364 2.520
  ... (remaining 53969 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          6.020
  Check model and map are aligned:         0.100
  Set scattering table:                    0.080
  Process input model:                     22.810
  Find NCS groups from input model:        0.510
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.170   6990  Z= 0.396
  Angle     :  0.740  10.089   9474  Z= 0.326
  Chirality :  0.047   0.291   1083
  Planarity :  0.020   0.257   1176
  Dihedral  : 16.506 114.987   2703
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.30), residues: 828
  helix:  2.89 (0.27), residues: 300
  sheet: -0.31 (0.29), residues: 330
  loop : -0.66 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 330 
 HIS   0.003   0.001   HIS A 131 
 PHE   0.011   0.001   PHE A 204 
 TYR   0.008   0.001   TYR C  86 
 ARG   0.002   0.000   ARG B 253 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ILE cc_start: 0.6960 (mm) cc_final: 0.6757 (mp)
REVERT: A  106 LYS cc_start: 0.7924 (tttt) cc_final: 0.7547 (tttm)
REVERT: A  107 GLU cc_start: 0.8165 (tt0) cc_final: 0.7754 (tt0)
REVERT: A  110 ARG cc_start: 0.6724 (ttm110) cc_final: 0.6511 (ttm110)
REVERT: A  124 GLN cc_start: 0.6408 (mm-40) cc_final: 0.5713 (pm20)
REVERT: A  176 GLU cc_start: 0.6895 (mp0) cc_final: 0.6563 (mp0)
REVERT: A  179 LYS cc_start: 0.7208 (mttt) cc_final: 0.6944 (mttm)
REVERT: A  188 ARG cc_start: 0.7334 (ttt90) cc_final: 0.6793 (ttt90)
REVERT: A  236 PHE cc_start: 0.7087 (m-80) cc_final: 0.6842 (m-80)
REVERT: A  257 GLU cc_start: 0.8013 (pt0) cc_final: 0.7589 (pt0)
REVERT: A  259 ARG cc_start: 0.6633 (mtt-85) cc_final: 0.6195 (mtm-85)
REVERT: A  262 THR cc_start: 0.7652 (p) cc_final: 0.7431 (m)
REVERT: A  294 LYS cc_start: 0.6829 (tttt) cc_final: 0.5930 (ttmm)
REVERT: B  106 LYS cc_start: 0.7958 (tttt) cc_final: 0.7468 (tttt)
REVERT: B  107 GLU cc_start: 0.8196 (tt0) cc_final: 0.7865 (tt0)
REVERT: B  124 GLN cc_start: 0.6431 (mm-40) cc_final: 0.5733 (pm20)
REVERT: B  157 THR cc_start: 0.7841 (p) cc_final: 0.7605 (t)
REVERT: B  179 LYS cc_start: 0.7427 (mttt) cc_final: 0.7109 (mtpt)
REVERT: B  188 ARG cc_start: 0.7483 (ttt90) cc_final: 0.7024 (ttt90)
REVERT: B  236 PHE cc_start: 0.7234 (m-80) cc_final: 0.6945 (m-80)
REVERT: B  248 LYS cc_start: 0.6888 (ttmt) cc_final: 0.6521 (ttpp)
REVERT: B  257 GLU cc_start: 0.8090 (pt0) cc_final: 0.7682 (pt0)
REVERT: B  259 ARG cc_start: 0.6543 (mtt-85) cc_final: 0.6224 (mtt-85)
REVERT: B  262 THR cc_start: 0.7693 (p) cc_final: 0.7450 (m)
REVERT: B  263 SER cc_start: 0.7717 (m) cc_final: 0.7460 (t)
REVERT: C  106 LYS cc_start: 0.7767 (tttt) cc_final: 0.7352 (ttmm)
REVERT: C  107 GLU cc_start: 0.8123 (tt0) cc_final: 0.7719 (tt0)
REVERT: C  124 GLN cc_start: 0.6335 (mm-40) cc_final: 0.5678 (pt0)
REVERT: C  132 TYR cc_start: 0.8116 (m-80) cc_final: 0.7766 (m-80)
REVERT: C  179 LYS cc_start: 0.7430 (mttt) cc_final: 0.7030 (mtpt)
REVERT: C  188 ARG cc_start: 0.7413 (ttt90) cc_final: 0.7005 (ttt90)
REVERT: C  209 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7197 (mt-10)
REVERT: C  225 SER cc_start: 0.6793 (t) cc_final: 0.6587 (m)
REVERT: C  249 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6500 (mm-30)
REVERT: C  257 GLU cc_start: 0.8004 (pt0) cc_final: 0.7638 (pt0)
REVERT: C  259 ARG cc_start: 0.6621 (mtt-85) cc_final: 0.6268 (mtt-85)
REVERT: C  263 SER cc_start: 0.7820 (m) cc_final: 0.7598 (t)
  outliers start: 0
  outliers final: 1
  residues processed: 167
  average time/residue: 1.4178
  time to fit residues: 247.0048
Evaluate side-chains
  124 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 61 optimal weight:    0.1980
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 47 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN
** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6990  Z= 0.189
  Angle     :  0.561   5.274   9474  Z= 0.274
  Chirality :  0.048   0.317   1083
  Planarity :  0.003   0.034   1176
  Dihedral  : 14.336  89.478   1203
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.77 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.29), residues: 828
  helix:  2.60 (0.27), residues: 300
  sheet: -0.13 (0.28), residues: 312
  loop : -0.27 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 330 
 HIS   0.003   0.001   HIS A 131 
 PHE   0.019   0.001   PHE C 204 
 TYR   0.010   0.001   TYR A  74 
 ARG   0.006   0.000   ARG B 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.7577 (tttt) cc_final: 0.7368 (tttp)
REVERT: A  107 GLU cc_start: 0.8107 (tt0) cc_final: 0.7727 (tt0)
REVERT: A  124 GLN cc_start: 0.6394 (mm-40) cc_final: 0.5815 (pm20)
REVERT: A  179 LYS cc_start: 0.7207 (mttt) cc_final: 0.6955 (mttm)
REVERT: A  188 ARG cc_start: 0.7513 (ttt90) cc_final: 0.6920 (ttt90)
REVERT: A  236 PHE cc_start: 0.7111 (m-80) cc_final: 0.6883 (m-80)
REVERT: A  257 GLU cc_start: 0.8109 (pt0) cc_final: 0.7559 (pt0)
REVERT: A  294 LYS cc_start: 0.7122 (tttt) cc_final: 0.6061 (ttmm)
REVERT: B  107 GLU cc_start: 0.8276 (tt0) cc_final: 0.7928 (tt0)
REVERT: B  124 GLN cc_start: 0.6542 (mm-40) cc_final: 0.5986 (pm20)
REVERT: B  157 THR cc_start: 0.7926 (p) cc_final: 0.7667 (t)
REVERT: B  176 GLU cc_start: 0.7160 (mp0) cc_final: 0.6662 (mm-30)
REVERT: B  179 LYS cc_start: 0.7418 (mttt) cc_final: 0.7094 (mtpp)
REVERT: B  188 ARG cc_start: 0.7653 (ttt90) cc_final: 0.7014 (ttt90)
REVERT: B  248 LYS cc_start: 0.6876 (ttmt) cc_final: 0.6424 (tttt)
REVERT: B  257 GLU cc_start: 0.8173 (pt0) cc_final: 0.7563 (pt0)
REVERT: B  259 ARG cc_start: 0.6939 (mtt-85) cc_final: 0.6560 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7235 (tttt) cc_final: 0.6976 (tttm)
REVERT: C  106 LYS cc_start: 0.7511 (tttt) cc_final: 0.7087 (tttt)
REVERT: C  107 GLU cc_start: 0.8108 (tt0) cc_final: 0.7742 (tt0)
REVERT: C  124 GLN cc_start: 0.6341 (mm-40) cc_final: 0.5746 (pm20)
REVERT: C  132 TYR cc_start: 0.8157 (m-80) cc_final: 0.7809 (m-80)
REVERT: C  167 SER cc_start: 0.7435 (p) cc_final: 0.7208 (m)
REVERT: C  179 LYS cc_start: 0.7377 (mttt) cc_final: 0.6989 (mtpt)
REVERT: C  188 ARG cc_start: 0.7618 (ttt90) cc_final: 0.6985 (ttt90)
REVERT: C  225 SER cc_start: 0.6864 (t) cc_final: 0.6597 (m)
REVERT: C  249 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6369 (mm-30)
REVERT: C  257 GLU cc_start: 0.8195 (pt0) cc_final: 0.7636 (pt0)
REVERT: C  259 ARG cc_start: 0.6986 (mtt-85) cc_final: 0.6557 (mtt-85)
REVERT: C  262 THR cc_start: 0.7796 (p) cc_final: 0.7588 (m)
  outliers start: 6
  outliers final: 3
  residues processed: 130
  average time/residue: 1.5065
  time to fit residues: 204.0476
Evaluate side-chains
  119 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 116
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0970
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6990  Z= 0.243
  Angle     :  0.578   7.429   9474  Z= 0.281
  Chirality :  0.049   0.331   1083
  Planarity :  0.004   0.030   1176
  Dihedral  : 11.641  69.975   1200
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.54 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.28), residues: 828
  helix:  2.42 (0.27), residues: 300
  sheet: -0.22 (0.28), residues: 312
  loop : -0.09 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 330 
 HIS   0.002   0.001   HIS C  98 
 PHE   0.019   0.002   PHE B 204 
 TYR   0.011   0.002   TYR A  74 
 ARG   0.005   0.001   ARG C 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.7579 (tttt) cc_final: 0.7328 (tttp)
REVERT: A  107 GLU cc_start: 0.8172 (tt0) cc_final: 0.7713 (tt0)
REVERT: A  124 GLN cc_start: 0.6394 (mm-40) cc_final: 0.5403 (mp10)
REVERT: A  179 LYS cc_start: 0.7252 (mttt) cc_final: 0.6960 (mttm)
REVERT: A  188 ARG cc_start: 0.7459 (ttt90) cc_final: 0.6058 (ttp-110)
REVERT: A  206 SER cc_start: 0.8033 (t) cc_final: 0.7766 (p)
REVERT: A  225 SER cc_start: 0.6996 (t) cc_final: 0.6646 (m)
REVERT: A  227 TYR cc_start: 0.6755 (m-80) cc_final: 0.6513 (m-80)
REVERT: A  257 GLU cc_start: 0.8133 (pt0) cc_final: 0.7466 (pt0)
REVERT: A  259 ARG cc_start: 0.7202 (mtt-85) cc_final: 0.6705 (mtt-85)
REVERT: A  294 LYS cc_start: 0.7195 (tttt) cc_final: 0.6174 (ttmm)
REVERT: B  107 GLU cc_start: 0.8378 (tt0) cc_final: 0.7943 (tt0)
REVERT: B  124 GLN cc_start: 0.6573 (mm-40) cc_final: 0.5884 (pt0)
REVERT: B  157 THR cc_start: 0.8059 (p) cc_final: 0.7775 (t)
REVERT: B  176 GLU cc_start: 0.7217 (mp0) cc_final: 0.6624 (mm-30)
REVERT: B  179 LYS cc_start: 0.7489 (mttt) cc_final: 0.7192 (mtpp)
REVERT: B  188 ARG cc_start: 0.7674 (ttt90) cc_final: 0.7048 (ttt90)
REVERT: B  225 SER cc_start: 0.6896 (t) cc_final: 0.6296 (m)
REVERT: B  248 LYS cc_start: 0.6832 (ttmt) cc_final: 0.6377 (tttp)
REVERT: B  253 ARG cc_start: 0.5484 (ptt90) cc_final: 0.5236 (ttp-110)
REVERT: B  257 GLU cc_start: 0.8161 (pt0) cc_final: 0.7501 (pt0)
REVERT: B  259 ARG cc_start: 0.7069 (mtt-85) cc_final: 0.6775 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7308 (tttt) cc_final: 0.6658 (mtpp)
REVERT: C  106 LYS cc_start: 0.7625 (tttt) cc_final: 0.7420 (tttp)
REVERT: C  107 GLU cc_start: 0.8157 (tt0) cc_final: 0.7766 (tt0)
REVERT: C  124 GLN cc_start: 0.6322 (mm-40) cc_final: 0.5613 (pt0)
REVERT: C  132 TYR cc_start: 0.8108 (m-80) cc_final: 0.7771 (m-80)
REVERT: C  179 LYS cc_start: 0.7335 (mttt) cc_final: 0.6963 (mtpt)
REVERT: C  188 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7085 (ttt90)
REVERT: C  225 SER cc_start: 0.7064 (t) cc_final: 0.6821 (m)
REVERT: C  227 TYR cc_start: 0.6744 (m-80) cc_final: 0.6504 (m-80)
REVERT: C  249 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6280 (mm-30)
REVERT: C  257 GLU cc_start: 0.8179 (pt0) cc_final: 0.7511 (pt0)
REVERT: C  259 ARG cc_start: 0.7122 (mtt-85) cc_final: 0.6653 (mtt-85)
REVERT: C  262 THR cc_start: 0.8014 (p) cc_final: 0.7702 (m)
REVERT: C  294 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6349 (ttmm)
  outliers start: 16
  outliers final: 9
  residues processed: 127
  average time/residue: 1.4420
  time to fit residues: 191.1075
Evaluate side-chains
  121 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  294 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 49 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   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 279 GLN
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN
C 279 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6990  Z= 0.199
  Angle     :  0.550   7.634   9474  Z= 0.265
  Chirality :  0.048   0.325   1083
  Planarity :  0.003   0.038   1176
  Dihedral  : 10.293  61.503   1200
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.56 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.28), residues: 828
  helix:  2.42 (0.27), residues: 300
  sheet: -0.33 (0.27), residues: 312
  loop : -0.07 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 304 
 HIS   0.002   0.001   HIS C  98 
 PHE   0.016   0.001   PHE B 204 
 TYR   0.009   0.001   TYR A  74 
 ARG   0.008   0.001   ARG A 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.7558 (tttt) cc_final: 0.7312 (tttp)
REVERT: A  107 GLU cc_start: 0.8265 (tt0) cc_final: 0.7810 (tt0)
REVERT: A  124 GLN cc_start: 0.6386 (mm-40) cc_final: 0.5353 (mp10)
REVERT: A  143 GLN cc_start: 0.7320 (mm110) cc_final: 0.7081 (mm-40)
REVERT: A  179 LYS cc_start: 0.7245 (mttt) cc_final: 0.6826 (mtpt)
REVERT: A  188 ARG cc_start: 0.7489 (ttt90) cc_final: 0.6064 (ttp-110)
REVERT: A  206 SER cc_start: 0.7966 (t) cc_final: 0.7658 (p)
REVERT: A  225 SER cc_start: 0.7044 (t) cc_final: 0.6659 (m)
REVERT: A  227 TYR cc_start: 0.6712 (m-80) cc_final: 0.6429 (m-80)
REVERT: A  257 GLU cc_start: 0.8117 (pt0) cc_final: 0.7458 (pt0)
REVERT: A  259 ARG cc_start: 0.7224 (mtt-85) cc_final: 0.6684 (mtt-85)
REVERT: A  294 LYS cc_start: 0.7211 (tttt) cc_final: 0.6195 (ttmm)
REVERT: B  107 GLU cc_start: 0.8357 (tt0) cc_final: 0.7921 (tt0)
REVERT: B  124 GLN cc_start: 0.6531 (mm-40) cc_final: 0.5765 (pt0)
REVERT: B  157 THR cc_start: 0.7993 (p) cc_final: 0.7732 (t)
REVERT: B  176 GLU cc_start: 0.7179 (mp0) cc_final: 0.6612 (mm-30)
REVERT: B  179 LYS cc_start: 0.7458 (mttt) cc_final: 0.7257 (mmmt)
REVERT: B  188 ARG cc_start: 0.7690 (ttt90) cc_final: 0.7234 (ttt90)
REVERT: B  225 SER cc_start: 0.6910 (t) cc_final: 0.6286 (m)
REVERT: B  248 LYS cc_start: 0.6834 (ttmt) cc_final: 0.6339 (tttp)
REVERT: B  253 ARG cc_start: 0.5539 (ptt90) cc_final: 0.5257 (ttp-110)
REVERT: B  259 ARG cc_start: 0.7160 (mtt-85) cc_final: 0.6824 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7350 (tttt) cc_final: 0.6683 (mtpp)
REVERT: C  107 GLU cc_start: 0.8137 (tt0) cc_final: 0.7701 (tt0)
REVERT: C  124 GLN cc_start: 0.6341 (mm-40) cc_final: 0.5588 (pt0)
REVERT: C  132 TYR cc_start: 0.8097 (m-80) cc_final: 0.7786 (m-80)
REVERT: C  143 GLN cc_start: 0.6992 (mm110) cc_final: 0.6738 (mm-40)
REVERT: C  179 LYS cc_start: 0.7353 (mttt) cc_final: 0.6981 (mtpt)
REVERT: C  188 ARG cc_start: 0.7504 (ttt90) cc_final: 0.7134 (ttt90)
REVERT: C  225 SER cc_start: 0.7067 (t) cc_final: 0.6814 (m)
REVERT: C  227 TYR cc_start: 0.6766 (m-80) cc_final: 0.6541 (m-80)
REVERT: C  249 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6359 (mm-30)
REVERT: C  257 GLU cc_start: 0.8158 (pt0) cc_final: 0.7542 (pt0)
REVERT: C  259 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6707 (mtt-85)
  outliers start: 19
  outliers final: 14
  residues processed: 132
  average time/residue: 1.4359
  time to fit residues: 198.1329
Evaluate side-chains
  124 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6990  Z= 0.186
  Angle     :  0.539   7.393   9474  Z= 0.258
  Chirality :  0.047   0.322   1083
  Planarity :  0.003   0.041   1176
  Dihedral  :  9.472  57.509   1200
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 13.68 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.28), residues: 828
  helix:  2.34 (0.27), residues: 303
  sheet: -0.33 (0.27), residues: 309
  loop : -0.00 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 304 
 HIS   0.002   0.001   HIS B 131 
 PHE   0.017   0.001   PHE B 204 
 TYR   0.010   0.001   TYR A  74 
 ARG   0.010   0.001   ARG A 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.7607 (tttt) cc_final: 0.7374 (tttp)
REVERT: A  107 GLU cc_start: 0.8263 (tt0) cc_final: 0.7801 (tt0)
REVERT: A  124 GLN cc_start: 0.6409 (mm-40) cc_final: 0.5395 (mp10)
REVERT: A  143 GLN cc_start: 0.7340 (mm110) cc_final: 0.7123 (mm-40)
REVERT: A  176 GLU cc_start: 0.7099 (mp0) cc_final: 0.6614 (mm-30)
REVERT: A  179 LYS cc_start: 0.7259 (mttt) cc_final: 0.6841 (mtpt)
REVERT: A  188 ARG cc_start: 0.7462 (ttt90) cc_final: 0.6045 (ttp-110)
REVERT: A  225 SER cc_start: 0.7060 (t) cc_final: 0.6687 (m)
REVERT: A  227 TYR cc_start: 0.6794 (m-80) cc_final: 0.6492 (m-80)
REVERT: A  249 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6418 (mm-30)
REVERT: A  257 GLU cc_start: 0.8097 (pt0) cc_final: 0.7519 (pt0)
REVERT: A  294 LYS cc_start: 0.7213 (tttt) cc_final: 0.6207 (ttmm)
REVERT: B   77 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5437 (mp)
REVERT: B  107 GLU cc_start: 0.8352 (tt0) cc_final: 0.7901 (tt0)
REVERT: B  124 GLN cc_start: 0.6585 (mm-40) cc_final: 0.5673 (mp10)
REVERT: B  157 THR cc_start: 0.7880 (p) cc_final: 0.7634 (t)
REVERT: B  176 GLU cc_start: 0.7147 (mp0) cc_final: 0.6561 (mm-30)
REVERT: B  179 LYS cc_start: 0.7471 (mttt) cc_final: 0.7266 (mmmt)
REVERT: B  188 ARG cc_start: 0.7649 (ttt90) cc_final: 0.6217 (ttp-170)
REVERT: B  225 SER cc_start: 0.6891 (t) cc_final: 0.6216 (m)
REVERT: B  248 LYS cc_start: 0.6824 (ttmt) cc_final: 0.6338 (tttt)
REVERT: B  253 ARG cc_start: 0.5455 (ptt90) cc_final: 0.5226 (ttp-110)
REVERT: B  259 ARG cc_start: 0.7215 (mtt-85) cc_final: 0.6851 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7358 (tttt) cc_final: 0.6691 (mtpp)
REVERT: C  107 GLU cc_start: 0.8144 (tt0) cc_final: 0.7584 (tt0)
REVERT: C  124 GLN cc_start: 0.6332 (mm-40) cc_final: 0.5570 (pt0)
REVERT: C  132 TYR cc_start: 0.8116 (m-80) cc_final: 0.7681 (m-80)
REVERT: C  143 GLN cc_start: 0.7064 (mm110) cc_final: 0.6832 (mm-40)
REVERT: C  161 SER cc_start: 0.5855 (OUTLIER) cc_final: 0.5491 (t)
REVERT: C  179 LYS cc_start: 0.7331 (mttt) cc_final: 0.6941 (mtpt)
REVERT: C  188 ARG cc_start: 0.7507 (ttt90) cc_final: 0.7210 (ttt90)
REVERT: C  206 SER cc_start: 0.8078 (t) cc_final: 0.7770 (p)
REVERT: C  209 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7266 (mt-10)
REVERT: C  225 SER cc_start: 0.7095 (t) cc_final: 0.6826 (m)
REVERT: C  227 TYR cc_start: 0.6745 (m-80) cc_final: 0.6496 (m-80)
REVERT: C  249 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6287 (mm-30)
REVERT: C  257 GLU cc_start: 0.8141 (pt0) cc_final: 0.7528 (pt0)
REVERT: C  259 ARG cc_start: 0.7238 (mtt-85) cc_final: 0.6707 (mtt-85)
  outliers start: 26
  outliers final: 15
  residues processed: 135
  average time/residue: 1.2936
  time to fit residues: 183.1337
Evaluate side-chains
  126 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0010
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6990  Z= 0.154
  Angle     :  0.527   8.117   9474  Z= 0.251
  Chirality :  0.046   0.318   1083
  Planarity :  0.003   0.044   1176
  Dihedral  :  9.014  53.697   1200
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.57 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.28), residues: 828
  helix:  2.40 (0.27), residues: 303
  sheet: -0.29 (0.26), residues: 309
  loop : -0.00 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 304 
 HIS   0.002   0.001   HIS B 131 
 PHE   0.017   0.001   PHE B 204 
 TYR   0.007   0.001   TYR B  74 
 ARG   0.012   0.001   ARG A 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.7604 (tttt) cc_final: 0.7378 (tttp)
REVERT: A  107 GLU cc_start: 0.8195 (tt0) cc_final: 0.7733 (tt0)
REVERT: A  124 GLN cc_start: 0.6354 (mm-40) cc_final: 0.5365 (mp10)
REVERT: A  143 GLN cc_start: 0.7343 (mm110) cc_final: 0.7090 (mm-40)
REVERT: A  176 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6618 (mm-30)
REVERT: A  179 LYS cc_start: 0.7260 (mttt) cc_final: 0.6886 (mtpt)
REVERT: A  188 ARG cc_start: 0.7491 (ttt90) cc_final: 0.6033 (ttp-110)
REVERT: A  225 SER cc_start: 0.7035 (t) cc_final: 0.6662 (m)
REVERT: A  227 TYR cc_start: 0.6796 (m-80) cc_final: 0.6506 (m-80)
REVERT: A  257 GLU cc_start: 0.8064 (pt0) cc_final: 0.7508 (pt0)
REVERT: A  294 LYS cc_start: 0.7206 (tttt) cc_final: 0.6209 (ttmm)
REVERT: B  107 GLU cc_start: 0.8366 (tt0) cc_final: 0.7932 (tt0)
REVERT: B  124 GLN cc_start: 0.6540 (mm-40) cc_final: 0.5635 (mp10)
REVERT: B  157 THR cc_start: 0.7850 (p) cc_final: 0.7630 (t)
REVERT: B  176 GLU cc_start: 0.7126 (mp0) cc_final: 0.6604 (mm-30)
REVERT: B  179 LYS cc_start: 0.7468 (mttt) cc_final: 0.7251 (mmmt)
REVERT: B  188 ARG cc_start: 0.7637 (ttt90) cc_final: 0.6207 (ttp-170)
REVERT: B  225 SER cc_start: 0.6885 (t) cc_final: 0.6209 (m)
REVERT: B  248 LYS cc_start: 0.6822 (ttmt) cc_final: 0.6334 (tttt)
REVERT: B  253 ARG cc_start: 0.5475 (ptt90) cc_final: 0.5264 (ttp-110)
REVERT: B  259 ARG cc_start: 0.7245 (mtt-85) cc_final: 0.6850 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7350 (tttt) cc_final: 0.6675 (mtpp)
REVERT: C  107 GLU cc_start: 0.8108 (tt0) cc_final: 0.7645 (tt0)
REVERT: C  124 GLN cc_start: 0.6309 (mm-40) cc_final: 0.5519 (pt0)
REVERT: C  132 TYR cc_start: 0.8163 (m-80) cc_final: 0.7752 (m-80)
REVERT: C  143 GLN cc_start: 0.7070 (mm110) cc_final: 0.6819 (mm-40)
REVERT: C  179 LYS cc_start: 0.7324 (mttt) cc_final: 0.6941 (mtpt)
REVERT: C  188 ARG cc_start: 0.7462 (ttt90) cc_final: 0.7142 (ttt90)
REVERT: C  206 SER cc_start: 0.8074 (t) cc_final: 0.7767 (p)
REVERT: C  225 SER cc_start: 0.7068 (t) cc_final: 0.6792 (m)
REVERT: C  227 TYR cc_start: 0.6717 (m-80) cc_final: 0.6483 (m-80)
REVERT: C  249 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6307 (mm-30)
REVERT: C  257 GLU cc_start: 0.8150 (pt0) cc_final: 0.7553 (pt0)
REVERT: C  259 ARG cc_start: 0.7254 (mtt-85) cc_final: 0.6756 (mtt-85)
  outliers start: 20
  outliers final: 17
  residues processed: 124
  average time/residue: 1.3429
  time to fit residues: 174.5066
Evaluate side-chains
  125 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6990  Z= 0.194
  Angle     :  0.541   8.647   9474  Z= 0.259
  Chirality :  0.046   0.327   1083
  Planarity :  0.003   0.043   1176
  Dihedral  :  8.783  54.011   1200
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.72 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.28), residues: 828
  helix:  2.37 (0.27), residues: 303
  sheet: -0.26 (0.26), residues: 309
  loop :  0.02 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 304 
 HIS   0.001   0.001   HIS C  98 
 PHE   0.016   0.001   PHE B 204 
 TYR   0.008   0.001   TYR A  74 
 ARG   0.006   0.000   ARG A 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5683 (mp)
REVERT: A  106 LYS cc_start: 0.7650 (tttt) cc_final: 0.7414 (tttp)
REVERT: A  107 GLU cc_start: 0.8244 (tt0) cc_final: 0.7783 (tt0)
REVERT: A  124 GLN cc_start: 0.6322 (mm-40) cc_final: 0.5344 (mp10)
REVERT: A  143 GLN cc_start: 0.7281 (mm110) cc_final: 0.7025 (mm-40)
REVERT: A  176 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6547 (mm-30)
REVERT: A  179 LYS cc_start: 0.7255 (mttt) cc_final: 0.6877 (mtpt)
REVERT: A  188 ARG cc_start: 0.7464 (ttt90) cc_final: 0.5983 (ttp-110)
REVERT: A  225 SER cc_start: 0.7136 (t) cc_final: 0.6751 (m)
REVERT: A  227 TYR cc_start: 0.6882 (m-80) cc_final: 0.6556 (m-80)
REVERT: A  257 GLU cc_start: 0.8080 (pt0) cc_final: 0.7535 (pt0)
REVERT: A  294 LYS cc_start: 0.7196 (tttt) cc_final: 0.6204 (ttmm)
REVERT: B   77 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5494 (mp)
REVERT: B  107 GLU cc_start: 0.8354 (tt0) cc_final: 0.7916 (tt0)
REVERT: B  124 GLN cc_start: 0.6537 (mm-40) cc_final: 0.5564 (mp10)
REVERT: B  157 THR cc_start: 0.7806 (p) cc_final: 0.7600 (t)
REVERT: B  176 GLU cc_start: 0.7146 (mp0) cc_final: 0.6600 (mm-30)
REVERT: B  179 LYS cc_start: 0.7482 (mttt) cc_final: 0.7273 (mmmt)
REVERT: B  188 ARG cc_start: 0.7574 (ttt90) cc_final: 0.6195 (ttp-170)
REVERT: B  225 SER cc_start: 0.6929 (t) cc_final: 0.6246 (m)
REVERT: B  248 LYS cc_start: 0.6801 (ttmt) cc_final: 0.6312 (tttt)
REVERT: B  253 ARG cc_start: 0.5469 (ptt90) cc_final: 0.5259 (ttp-110)
REVERT: B  259 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6858 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7306 (tttt) cc_final: 0.6634 (mtpp)
REVERT: C  107 GLU cc_start: 0.8091 (tt0) cc_final: 0.7623 (tt0)
REVERT: C  124 GLN cc_start: 0.6347 (mm-40) cc_final: 0.5346 (mp10)
REVERT: C  132 TYR cc_start: 0.8128 (m-80) cc_final: 0.7775 (m-80)
REVERT: C  143 GLN cc_start: 0.7116 (mm110) cc_final: 0.6860 (mm-40)
REVERT: C  161 SER cc_start: 0.5799 (OUTLIER) cc_final: 0.5444 (t)
REVERT: C  176 GLU cc_start: 0.7242 (mp0) cc_final: 0.6766 (mm-30)
REVERT: C  179 LYS cc_start: 0.7326 (mttt) cc_final: 0.6957 (mtpt)
REVERT: C  188 ARG cc_start: 0.7429 (ttt90) cc_final: 0.6174 (ttp-170)
REVERT: C  206 SER cc_start: 0.8133 (t) cc_final: 0.7845 (p)
REVERT: C  225 SER cc_start: 0.7137 (t) cc_final: 0.6852 (m)
REVERT: C  227 TYR cc_start: 0.6816 (m-80) cc_final: 0.6558 (m-80)
REVERT: C  249 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6412 (mm-30)
REVERT: C  257 GLU cc_start: 0.8157 (pt0) cc_final: 0.7558 (pt0)
REVERT: C  259 ARG cc_start: 0.7238 (mtt-85) cc_final: 0.6718 (mtt-85)
  outliers start: 22
  outliers final: 16
  residues processed: 124
  average time/residue: 1.4766
  time to fit residues: 192.8514
Evaluate side-chains
  125 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0060
   chunk 61 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
A 266 ASN
B 143 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6990  Z= 0.182
  Angle     :  0.531   8.493   9474  Z= 0.256
  Chirality :  0.046   0.320   1083
  Planarity :  0.003   0.036   1176
  Dihedral  :  8.399  53.028   1200
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.43 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.28), residues: 828
  helix:  2.36 (0.27), residues: 303
  sheet: -0.21 (0.27), residues: 309
  loop : -0.02 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 304 
 HIS   0.002   0.001   HIS B 131 
 PHE   0.017   0.001   PHE B 204 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.007   0.000   ARG A 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5677 (mp)
REVERT: A  106 LYS cc_start: 0.7626 (tttt) cc_final: 0.7413 (tttp)
REVERT: A  107 GLU cc_start: 0.8192 (tt0) cc_final: 0.7707 (tt0)
REVERT: A  124 GLN cc_start: 0.6310 (mm-40) cc_final: 0.5318 (mp10)
REVERT: A  143 GLN cc_start: 0.7212 (mm110) cc_final: 0.6928 (mm-40)
REVERT: A  176 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6590 (mm-30)
REVERT: A  179 LYS cc_start: 0.7246 (mttt) cc_final: 0.6884 (mtpt)
REVERT: A  188 ARG cc_start: 0.7463 (ttt90) cc_final: 0.5995 (ttp-110)
REVERT: A  225 SER cc_start: 0.7162 (t) cc_final: 0.6771 (m)
REVERT: A  227 TYR cc_start: 0.6829 (m-80) cc_final: 0.6541 (m-80)
REVERT: A  257 GLU cc_start: 0.8078 (pt0) cc_final: 0.7535 (pt0)
REVERT: A  294 LYS cc_start: 0.7207 (tttt) cc_final: 0.6204 (ttmm)
REVERT: B   77 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5472 (mp)
REVERT: B  107 GLU cc_start: 0.8325 (tt0) cc_final: 0.7881 (tt0)
REVERT: B  124 GLN cc_start: 0.6547 (mm-40) cc_final: 0.5529 (mp10)
REVERT: B  176 GLU cc_start: 0.7119 (mp0) cc_final: 0.6583 (mm-30)
REVERT: B  179 LYS cc_start: 0.7489 (mttt) cc_final: 0.7279 (mmmt)
REVERT: B  188 ARG cc_start: 0.7573 (ttt90) cc_final: 0.6178 (ttp-170)
REVERT: B  225 SER cc_start: 0.6931 (t) cc_final: 0.6240 (m)
REVERT: B  248 LYS cc_start: 0.6770 (ttmt) cc_final: 0.6260 (tttt)
REVERT: B  253 ARG cc_start: 0.5491 (ptt90) cc_final: 0.5278 (ttp-110)
REVERT: B  259 ARG cc_start: 0.7252 (mtt-85) cc_final: 0.6852 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7317 (tttt) cc_final: 0.6652 (mtpp)
REVERT: C  107 GLU cc_start: 0.8110 (tt0) cc_final: 0.7646 (tt0)
REVERT: C  124 GLN cc_start: 0.6337 (mm-40) cc_final: 0.5330 (mp10)
REVERT: C  132 TYR cc_start: 0.8131 (m-80) cc_final: 0.7774 (m-80)
REVERT: C  143 GLN cc_start: 0.7179 (mm110) cc_final: 0.6933 (mm-40)
REVERT: C  161 SER cc_start: 0.5676 (OUTLIER) cc_final: 0.5358 (t)
REVERT: C  176 GLU cc_start: 0.7224 (mp0) cc_final: 0.6779 (mm-30)
REVERT: C  179 LYS cc_start: 0.7330 (mttt) cc_final: 0.6960 (mtpt)
REVERT: C  188 ARG cc_start: 0.7433 (ttt90) cc_final: 0.6201 (ttp-170)
REVERT: C  206 SER cc_start: 0.8123 (t) cc_final: 0.7819 (p)
REVERT: C  224 GLU cc_start: 0.6912 (tp30) cc_final: 0.6630 (tp30)
REVERT: C  225 SER cc_start: 0.7163 (t) cc_final: 0.6889 (m)
REVERT: C  227 TYR cc_start: 0.6825 (m-80) cc_final: 0.6566 (m-80)
REVERT: C  249 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6519 (mm-30)
REVERT: C  257 GLU cc_start: 0.8156 (pt0) cc_final: 0.7557 (pt0)
REVERT: C  259 ARG cc_start: 0.7278 (mtt-85) cc_final: 0.6763 (mtt-85)
  outliers start: 25
  outliers final: 16
  residues processed: 123
  average time/residue: 1.3622
  time to fit residues: 175.6663
Evaluate side-chains
  124 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0370
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6990  Z= 0.157
  Angle     :  0.520   9.748   9474  Z= 0.251
  Chirality :  0.045   0.320   1083
  Planarity :  0.003   0.031   1176
  Dihedral  :  8.139  53.461   1200
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.74 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.28), residues: 828
  helix:  2.42 (0.27), residues: 303
  sheet: -0.17 (0.27), residues: 309
  loop : -0.02 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 304 
 HIS   0.001   0.001   HIS A 131 
 PHE   0.016   0.001   PHE B 204 
 TYR   0.008   0.001   TYR B 201 
 ARG   0.005   0.000   ARG A 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5654 (mp)
REVERT: A  106 LYS cc_start: 0.7630 (tttt) cc_final: 0.7426 (tttp)
REVERT: A  107 GLU cc_start: 0.8184 (tt0) cc_final: 0.7721 (tt0)
REVERT: A  124 GLN cc_start: 0.6342 (mm-40) cc_final: 0.5321 (mp10)
REVERT: A  143 GLN cc_start: 0.7206 (mm110) cc_final: 0.6921 (mm-40)
REVERT: A  176 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6581 (mm-30)
REVERT: A  179 LYS cc_start: 0.7275 (mttt) cc_final: 0.6903 (mtpt)
REVERT: A  188 ARG cc_start: 0.7450 (ttt90) cc_final: 0.6003 (ttp-110)
REVERT: A  225 SER cc_start: 0.7190 (t) cc_final: 0.6803 (m)
REVERT: A  227 TYR cc_start: 0.6869 (m-80) cc_final: 0.6622 (m-80)
REVERT: A  257 GLU cc_start: 0.8037 (pt0) cc_final: 0.7831 (pt0)
REVERT: A  294 LYS cc_start: 0.7201 (tttt) cc_final: 0.6201 (ttmm)
REVERT: A  300 THR cc_start: 0.6920 (OUTLIER) cc_final: 0.6458 (p)
REVERT: B   77 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5482 (mp)
REVERT: B  107 GLU cc_start: 0.8306 (tt0) cc_final: 0.7867 (tt0)
REVERT: B  124 GLN cc_start: 0.6540 (mm-40) cc_final: 0.5528 (mp10)
REVERT: B  176 GLU cc_start: 0.7120 (mp0) cc_final: 0.6601 (mm-30)
REVERT: B  188 ARG cc_start: 0.7514 (ttt90) cc_final: 0.6183 (ttp-170)
REVERT: B  225 SER cc_start: 0.6913 (t) cc_final: 0.6228 (m)
REVERT: B  248 LYS cc_start: 0.6757 (ttmt) cc_final: 0.6237 (tttt)
REVERT: B  253 ARG cc_start: 0.5488 (ptt90) cc_final: 0.5270 (ttp-110)
REVERT: B  259 ARG cc_start: 0.7253 (mtt-85) cc_final: 0.6868 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7343 (tttt) cc_final: 0.6673 (mtpp)
REVERT: C  107 GLU cc_start: 0.8092 (tt0) cc_final: 0.7664 (tt0)
REVERT: C  124 GLN cc_start: 0.6305 (mm-40) cc_final: 0.5311 (mp10)
REVERT: C  132 TYR cc_start: 0.8109 (m-80) cc_final: 0.7751 (m-80)
REVERT: C  143 GLN cc_start: 0.7176 (mm110) cc_final: 0.6931 (mm-40)
REVERT: C  176 GLU cc_start: 0.7225 (mp0) cc_final: 0.6786 (mm-30)
REVERT: C  179 LYS cc_start: 0.7309 (mttt) cc_final: 0.6944 (mtpt)
REVERT: C  188 ARG cc_start: 0.7433 (ttt90) cc_final: 0.6150 (ttp-170)
REVERT: C  206 SER cc_start: 0.8112 (t) cc_final: 0.7814 (p)
REVERT: C  225 SER cc_start: 0.7125 (t) cc_final: 0.6840 (m)
REVERT: C  227 TYR cc_start: 0.6811 (m-80) cc_final: 0.6567 (m-80)
REVERT: C  249 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6538 (mm-30)
REVERT: C  257 GLU cc_start: 0.8147 (pt0) cc_final: 0.7566 (pt0)
REVERT: C  259 ARG cc_start: 0.7260 (mtt-85) cc_final: 0.6743 (mtt-85)
  outliers start: 18
  outliers final: 14
  residues processed: 116
  average time/residue: 1.3265
  time to fit residues: 161.3583
Evaluate side-chains
  121 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0770
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6990  Z= 0.181
  Angle     :  0.524  10.246   9474  Z= 0.256
  Chirality :  0.045   0.323   1083
  Planarity :  0.003   0.032   1176
  Dihedral  :  7.946  53.222   1200
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.03 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.28), residues: 828
  helix:  2.41 (0.27), residues: 303
  sheet: -0.22 (0.26), residues: 318
  loop : -0.09 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 304 
 HIS   0.002   0.001   HIS C  98 
 PHE   0.016   0.001   PHE B 204 
 TYR   0.007   0.001   TYR A  74 
 ARG   0.005   0.000   ARG A 110 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5661 (mp)
REVERT: A  106 LYS cc_start: 0.7698 (tttt) cc_final: 0.7489 (tttp)
REVERT: A  107 GLU cc_start: 0.8184 (tt0) cc_final: 0.7724 (tt0)
REVERT: A  124 GLN cc_start: 0.6337 (mm-40) cc_final: 0.5351 (mp10)
REVERT: A  143 GLN cc_start: 0.7129 (mm110) cc_final: 0.6864 (mm-40)
REVERT: A  176 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6586 (mm-30)
REVERT: A  179 LYS cc_start: 0.7283 (mttt) cc_final: 0.6909 (mtpt)
REVERT: A  188 ARG cc_start: 0.7427 (ttt90) cc_final: 0.6073 (ttp-110)
REVERT: A  225 SER cc_start: 0.7243 (t) cc_final: 0.6846 (m)
REVERT: A  227 TYR cc_start: 0.6812 (m-80) cc_final: 0.6534 (m-80)
REVERT: A  257 GLU cc_start: 0.8063 (pt0) cc_final: 0.7549 (pt0)
REVERT: A  294 LYS cc_start: 0.7229 (tttt) cc_final: 0.6225 (ttmm)
REVERT: A  300 THR cc_start: 0.6937 (OUTLIER) cc_final: 0.6483 (p)
REVERT: B  107 GLU cc_start: 0.8286 (tt0) cc_final: 0.7854 (tt0)
REVERT: B  124 GLN cc_start: 0.6480 (mm-40) cc_final: 0.5463 (mp10)
REVERT: B  176 GLU cc_start: 0.7101 (mp0) cc_final: 0.6573 (mm-30)
REVERT: B  225 SER cc_start: 0.6937 (t) cc_final: 0.6249 (m)
REVERT: B  248 LYS cc_start: 0.6740 (ttmt) cc_final: 0.6231 (tttt)
REVERT: B  253 ARG cc_start: 0.5497 (ptt90) cc_final: 0.5280 (ttp-110)
REVERT: B  259 ARG cc_start: 0.7256 (mtt-85) cc_final: 0.6857 (mtt-85)
REVERT: B  294 LYS cc_start: 0.7282 (tttt) cc_final: 0.6631 (mtpp)
REVERT: C  107 GLU cc_start: 0.8121 (tt0) cc_final: 0.7705 (tt0)
REVERT: C  124 GLN cc_start: 0.6317 (mm-40) cc_final: 0.5306 (mp10)
REVERT: C  132 TYR cc_start: 0.8104 (m-80) cc_final: 0.7803 (m-80)
REVERT: C  143 GLN cc_start: 0.7169 (mm110) cc_final: 0.6902 (mm-40)
REVERT: C  176 GLU cc_start: 0.7243 (mp0) cc_final: 0.6741 (mm-30)
REVERT: C  179 LYS cc_start: 0.7310 (mttt) cc_final: 0.6956 (mtpt)
REVERT: C  188 ARG cc_start: 0.7399 (ttt90) cc_final: 0.6182 (ttp-170)
REVERT: C  206 SER cc_start: 0.8107 (t) cc_final: 0.7837 (p)
REVERT: C  225 SER cc_start: 0.7171 (t) cc_final: 0.6899 (m)
REVERT: C  227 TYR cc_start: 0.6839 (m-80) cc_final: 0.6580 (m-80)
REVERT: C  249 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6438 (mm-30)
REVERT: C  257 GLU cc_start: 0.8145 (pt0) cc_final: 0.7561 (pt0)
REVERT: C  259 ARG cc_start: 0.7306 (mtt-85) cc_final: 0.6770 (mtt-85)
  outliers start: 18
  outliers final: 14
  residues processed: 113
  average time/residue: 1.4099
  time to fit residues: 167.2303
Evaluate side-chains
  117 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  300 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0970
   chunk 66 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.157026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.124992 restraints weight = 7902.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.87
r_work: 0.3295 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6990  Z= 0.178
  Angle     :  0.516  10.272   9474  Z= 0.253
  Chirality :  0.045   0.326   1083
  Planarity :  0.003   0.030   1176
  Dihedral  :  7.848  52.600   1200
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.18 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.28), residues: 828
  helix:  2.41 (0.27), residues: 303
  sheet: -0.23 (0.26), residues: 318
  loop : -0.15 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 304 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.016   0.001   PHE B 204 
 TYR   0.007   0.001   TYR A 201 
 ARG   0.005   0.000   ARG A 110 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3644.10 seconds
wall clock time: 65 minutes 27.75 seconds (3927.75 seconds total)