Starting phenix.real_space_refine
on Fri Dec  8 00:18:23 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/12_2023/7qa8_13880.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/12_2023/7qa8_13880.map

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 {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/12_2023/7qa8_13880.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/12_2023/7qa8_13880.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/12_2023/7qa8_13880.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qa8_13880/12_2023/7qa8_13880.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=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    4235      2.51       5
     N     769      2.21       5
     O    1087      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  203": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  203": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 6111
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2299
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 9
    Chain: "K"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 97
          Classifications: {'peptide': 12}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "I"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 97
          Classifications: {'peptide': 12}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2302
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 588
          Unusual residues: {'NAG': 2, 'Y01': 16}
          Classifications: {'undetermined': 18}
          Link IDs: {None: 17}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 623
          Unusual residues: {'NAG': 2, 'Y01': 17}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 32
          Classifications: {'water': 32}
          Link IDs: {None: 31}
    Chain: "K"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "I"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 30
          Classifications: {'water': 30}
          Link IDs: {None: 29}
  Time building chain proxies: 5.17, per 1000 atoms: 0.85
  Number of scatterers: 6111
  At special positions: 0
  Unit cell: (80.84, 93.74, 98.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1087      8.00
     N     769      7.00
     C    4235      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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 501 " - " ASN A  25 "
      " NAG A 502 " - " ASN A  32 "
      " NAG B 501 " - " ASN B  32 "
      " NAG B 502 " - " ASN B  25 "
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1180

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 2 sheets defined
      75.2% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 14
      removed outlier: 3.504A  pdb=" N   ASP A  14 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 72
      removed outlier: 3.712A  pdb=" N   SER A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE A  53 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   MET A  54 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   PHE A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 103
      removed outlier: 3.708A  pdb=" N   LEU A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A  92 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 114
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.584A  pdb=" N   ILE A 120 " --> pdb=" O   PRO A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 154
      removed outlier: 3.697A  pdb=" N   VAL A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR A 128 " --> pdb=" O   ASP A 124 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL A 136 " --> pdb=" O   ASN A 132 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 195
      removed outlier: 3.867A  pdb=" N   GLY A 163 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 164 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   THR A 167 " --> pdb=" O   GLY A 163 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 236
      removed outlier: 3.775A  pdb=" N   SER A 207 " --> pdb=" O   TYR A 203 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ILE A 209 " --> pdb=" O   ASN A 205 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG A 234 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 236 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 251
      removed outlier: 4.182A  pdb=" N   LEU A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.618A  pdb=" N   TYR A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 272
    Processing helix  chain 'A' and resid 273 through 297
      removed outlier: 3.514A  pdb=" N   LEU A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR A 278 " --> pdb=" O   THR A 274 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   THR A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
      Proline residue:  A 290  - end of helix
      removed outlier: 3.683A  pdb=" N   MET A 294 " --> pdb=" O   PRO A 290 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   TRP A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 14
      removed outlier: 3.504A  pdb=" N   ASP B  14 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 72
      removed outlier: 3.712A  pdb=" N   SER B  47 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE B  53 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   MET B  54 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 103
      removed outlier: 3.708A  pdb=" N   LEU B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE B  89 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE B  92 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 114
    Processing helix  chain 'B' and resid 116 through 120
      removed outlier: 3.584A  pdb=" N   ILE B 120 " --> pdb=" O   PRO B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 154
      removed outlier: 3.698A  pdb=" N   VAL B 127 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR B 128 " --> pdb=" O   ASP B 124 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL B 136 " --> pdb=" O   ASN B 132 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   PHE B 154 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 195
      removed outlier: 3.866A  pdb=" N   GLY B 163 " --> pdb=" O   PHE B 159 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 164 " --> pdb=" O   LYS B 160 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET B 165 " --> pdb=" O   ARG B 161 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR B 167 " --> pdb=" O   GLY B 163 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER B 168 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 236
      removed outlier: 3.696A  pdb=" N   SER B 207 " --> pdb=" O   TYR B 203 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ILE B 209 " --> pdb=" O   ASN B 205 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG B 233 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE B 235 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B 236 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 251
      removed outlier: 4.182A  pdb=" N   LEU B 247 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 268
      removed outlier: 3.617A  pdb=" N   TYR B 266 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU B 268 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 272
    Processing helix  chain 'B' and resid 273 through 297
      removed outlier: 3.514A  pdb=" N   LEU B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR B 278 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR B 279 " --> pdb=" O   ASP B 275 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL B 280 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU B 283 " --> pdb=" O   THR B 279 " (cutoff:3.500A)
      Proline residue:  B 290  - end of helix
      removed outlier: 3.683A  pdb=" N   MET B 294 " --> pdb=" O   PRO B 290 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   TRP B 295 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   THR B 297 " --> pdb=" O   SER B 293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28
      removed outlier: 6.477A  pdb=" N   ILE A  24 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR A  35 " --> pdb=" O   ILE A  24 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   TYR A  26 " --> pdb=" O   GLY A  33 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY A  33 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 28
      removed outlier: 6.478A  pdb=" N   ILE B  24 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR B  35 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   TYR B  26 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    864 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: 1.53

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 819
        1.31 -     1.43: 1417
        1.43 -     1.56: 3916
        1.56 -     1.68: 55
        1.68 -     1.80: 36
  Bond restraints: 6243
  Sorted by residual:
  bond pdb=" C7  NAG B 501 "
       pdb=" N2  NAG B 501 "
    ideal  model  delta    sigma   weight residual
    1.346  1.461 -0.115 2.00e-02 2.50e+03 3.31e+01
  bond pdb=" C7  NAG A 502 "
       pdb=" N2  NAG A 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.461 -0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" C7  NAG B 502 "
       pdb=" N2  NAG B 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.460 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C7  NAG A 501 "
       pdb=" N2  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.346  1.458 -0.112 2.00e-02 2.50e+03 3.12e+01
  bond pdb=" C1  NAG A 501 "
       pdb=" O5  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.516 -0.110 2.00e-02 2.50e+03 3.05e+01
  ... (remaining 6238 not shown)

  Histogram of bond angle deviations from ideal:
       98.74 -   105.83: 229
      105.83 -   112.91: 3678
      112.91 -   119.99: 2483
      119.99 -   127.07: 2256
      127.07 -   134.16: 36
  Bond angle restraints: 8682
  Sorted by residual:
  angle pdb=" N   PHE A  99 "
        pdb=" CA  PHE A  99 "
        pdb=" C   PHE A  99 "
      ideal   model   delta    sigma   weight residual
     111.36  105.46    5.90 1.09e+00 8.42e-01 2.93e+01
  angle pdb=" N   PHE B  99 "
        pdb=" CA  PHE B  99 "
        pdb=" C   PHE B  99 "
      ideal   model   delta    sigma   weight residual
     111.36  105.63    5.73 1.09e+00 8.42e-01 2.76e+01
  angle pdb=" N   PHE A 204 "
        pdb=" CA  PHE A 204 "
        pdb=" C   PHE A 204 "
      ideal   model   delta    sigma   weight residual
     113.41  107.33    6.08 1.22e+00 6.72e-01 2.48e+01
  angle pdb=" N   LYS B 202 "
        pdb=" CA  LYS B 202 "
        pdb=" C   LYS B 202 "
      ideal   model   delta    sigma   weight residual
     113.97  107.77    6.20 1.28e+00 6.10e-01 2.35e+01
  angle pdb=" N   TYR B 106 "
        pdb=" CA  TYR B 106 "
        pdb=" C   TYR B 106 "
      ideal   model   delta    sigma   weight residual
     113.28  107.50    5.78 1.22e+00 6.72e-01 2.24e+01
  ... (remaining 8677 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.95: 5010
       20.95 -    41.90: 261
       41.90 -    62.85: 98
       62.85 -    83.80: 6
       83.80 -   104.75: 5
  Dihedral angle restraints: 5380
    sinusoidal: 3554
      harmonic: 1826
  Sorted by residual:
  dihedral pdb=" C   ASP B 275 "
           pdb=" N   ASP B 275 "
           pdb=" CA  ASP B 275 "
           pdb=" CB  ASP B 275 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.06   -9.54     0      2.50e+00 1.60e-01 1.46e+01
  dihedral pdb=" C1  NAG A 501 "
           pdb=" C5  NAG A 501 "
           pdb=" O5  NAG A 501 "
           pdb=" C6  NAG A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -84.09 -104.75     1      3.00e+01 1.11e-03 1.34e+01
  dihedral pdb=" C1  NAG A 501 "
           pdb=" C5  NAG A 501 "
           pdb=" O5  NAG A 501 "
           pdb=" C4  NAG A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   40.38 -104.49     1      3.00e+01 1.11e-03 1.33e+01
  ... (remaining 5377 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 890
       0.062 -    0.124: 172
       0.124 -    0.186: 46
       0.186 -    0.248: 10
       0.248 -    0.310: 4
  Chirality restraints: 1122
  Sorted by residual:
  chirality pdb=" CBC Y01 A 518 "
            pdb=" CAR Y01 A 518 "
            pdb=" CAV Y01 A 518 "
            pdb=" OAW Y01 A 518 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.23   -0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" C1  NAG A 501 "
            pdb=" ND2 ASN A  25 "
            pdb=" C2  NAG A 501 "
            pdb=" O5  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CBC Y01 A 514 "
            pdb=" CAR Y01 A 514 "
            pdb=" CAV Y01 A 514 "
            pdb=" OAW Y01 A 514 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.27   -0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 1119 not shown)

  Planarity restraints: 883
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 104 "   -0.021 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   SER A 104 "    0.075 2.00e-02 2.50e+03
        pdb=" O   SER A 104 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ASN A 105 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 104 "    0.020 2.00e-02 2.50e+03   4.10e-02 1.68e+01
        pdb=" C   SER B 104 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   SER B 104 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ASN B 105 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 186 "   -0.018 2.00e-02 2.50e+03   3.63e-02 1.32e+01
        pdb=" C   VAL B 186 "    0.063 2.00e-02 2.50e+03
        pdb=" O   VAL B 186 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS B 187 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 880 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1617
        2.84 -     3.35: 5592
        3.35 -     3.87: 9104
        3.87 -     4.38: 10853
        4.38 -     4.90: 18087
  Nonbonded interactions: 45253
  Sorted by model distance:
  nonbonded pdb=" O   ASN A  46 "
            pdb=" OG1 THR A  50 "
     model   vdw
     2.323 2.440
  nonbonded pdb=" O   ASN B  46 "
            pdb=" OG1 THR B  50 "
     model   vdw
     2.324 2.440
  nonbonded pdb=" OXT TYR K  13 "
            pdb=" O   HOH K 101 "
     model   vdw
     2.338 2.440
  nonbonded pdb=" O   LYS B 151 "
            pdb=" OG1 THR B 155 "
     model   vdw
     2.338 2.440
  nonbonded pdb=" O   LYS A 151 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.339 2.440
  ... (remaining 45248 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' and (resid 5 through 157 or (resid 158 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 159 through 303 or resid 501 through 518))
}
ncs_group {
  reference = (chain 'I' and resid 2 through 13)
  selection = chain 'K'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.400
  Check model and map are aligned:         0.090
  Set scattering table:                    0.070
  Process input model:                     21.680
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
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      :  0.009   0.115   6243  Z= 0.511
  Angle     :  1.114   8.003   8682  Z= 0.597
  Chirality :  0.059   0.310   1122
  Planarity :  0.009   0.055    879
  Dihedral  : 13.163 104.748   4200
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  1.50 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.28), residues: 610
  helix: -1.93 (0.22), residues: 396
  sheet:  None (None), residues: 0
  loop : -1.71 (0.33), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP A 295 
   HIS   0.006   0.003   HIS A  94 
   PHE   0.031   0.003   PHE A  55 
   TYR   0.022   0.003   TYR B  26 
   ARG   0.003   0.001   ARG B 231 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.556 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 71
  average time/residue: 0.9576
  time to fit residues: 72.2988
Evaluate side-chains
  52 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.548 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 0.6974
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0670
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A  94 HIS
B  51 GLN
B  94 HIS
B 118 GLN
B 135 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6243  Z= 0.146
  Angle     :  0.551  10.094   8682  Z= 0.264
  Chirality :  0.035   0.210   1122
  Planarity :  0.004   0.036    879
  Dihedral  : 10.159  59.585   3166
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  7.48 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.33), residues: 610
  helix:  0.56 (0.26), residues: 404
  sheet:  None (None), residues: 0
  loop : -1.40 (0.35), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.003   0.001   TRP B 295 
   HIS   0.005   0.001   HIS B  94 
   PHE   0.011   0.001   PHE A 204 
   TYR   0.008   0.001   TYR B 266 
   ARG   0.002   0.000   ARG B 161 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 9
  residues processed: 72
  average time/residue: 0.8892
  time to fit residues: 68.5049
Evaluate side-chains
  63 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.637 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 7
  residues processed: 2
  average time/residue: 0.1082
  time to fit residues: 1.1375
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 16 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6243  Z= 0.273
  Angle     :  0.733   5.666   8682  Z= 0.337
  Chirality :  0.042   0.164   1122
  Planarity :  0.005   0.035    879
  Dihedral  : 11.050  59.693   3166
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  :  8.60 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.33), residues: 610
  helix:  1.22 (0.26), residues: 418
  sheet:  None (None), residues: 0
  loop : -1.57 (0.36), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.002   TRP B 295 
   HIS   0.007   0.002   HIS A  94 
   PHE   0.017   0.002   PHE B 244 
   TYR   0.009   0.002   TYR A  17 
   ARG   0.004   0.001   ARG A 161 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 51
  time to evaluate  : 0.606 
Fit side-chains
  outliers start: 28
  outliers final: 15
  residues processed: 72
  average time/residue: 0.8044
  time to fit residues: 62.3618
Evaluate side-chains
  65 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.625 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 13
  residues processed: 2
  average time/residue: 0.0825
  time to fit residues: 1.0625
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 54 optimal weight:    8.9990
   chunk 57 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6243  Z= 0.141
  Angle     :  0.535   6.483   8682  Z= 0.251
  Chirality :  0.035   0.157   1122
  Planarity :  0.003   0.031    879
  Dihedral  : 10.336  58.562   3166
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 10.28 %
    Favored  : 85.42 %
  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:  1.51 (0.34), residues: 610
  helix:  2.04 (0.26), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.46 (0.37), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 295 
   HIS   0.003   0.001   HIS A  94 
   PHE   0.012   0.001   PHE B  81 
   TYR   0.006   0.001   TYR B 128 
   ARG   0.002   0.000   ARG B 233 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.622 
Fit side-chains
  outliers start: 23
  outliers final: 15
  residues processed: 74
  average time/residue: 0.8347
  time to fit residues: 66.7423
Evaluate side-chains
  67 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.639 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 12
  residues processed: 3
  average time/residue: 0.0989
  time to fit residues: 1.2621
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.7388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6243  Z= 0.250
  Angle     :  0.696   8.019   8682  Z= 0.315
  Chirality :  0.041   0.159   1122
  Planarity :  0.004   0.034    879
  Dihedral  : 10.960  59.934   3166
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 11.40 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.46 (0.34), residues: 610
  helix:  2.09 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop : -1.63 (0.37), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.002   TRP B 295 
   HIS   0.005   0.001   HIS B  94 
   PHE   0.016   0.002   PHE B 244 
   TYR   0.007   0.002   TYR B  17 
   ARG   0.004   0.001   ARG B 161 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.658 
Fit side-chains
  outliers start: 21
  outliers final: 15
  residues processed: 66
  average time/residue: 0.9240
  time to fit residues: 65.3066
Evaluate side-chains
  59 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.624 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 12
  residues processed: 3
  average time/residue: 0.0956
  time to fit residues: 1.2495
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6243  Z= 0.165
  Angle     :  0.579   8.733   8682  Z= 0.267
  Chirality :  0.036   0.149   1122
  Planarity :  0.004   0.033    879
  Dihedral  : 10.521  59.747   3166
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 13.27 %
    Favored  : 82.80 %
  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:  1.93 (0.34), residues: 610
  helix:  2.42 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.46 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP B 295 
   HIS   0.003   0.001   HIS B  94 
   PHE   0.012   0.001   PHE A  81 
   TYR   0.006   0.001   TYR B 128 
   ARG   0.002   0.000   ARG A  74 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 0.634 
Fit side-chains
  outliers start: 21
  outliers final: 16
  residues processed: 62
  average time/residue: 0.8016
  time to fit residues: 53.6756
Evaluate side-chains
  59 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.602 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 15
  residues processed: 1
  average time/residue: 0.0554
  time to fit residues: 0.8606
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0870
   chunk 36 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.9160

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6243  Z= 0.165
  Angle     :  0.578   9.158   8682  Z= 0.264
  Chirality :  0.036   0.142   1122
  Planarity :  0.004   0.033    879
  Dihedral  : 10.369  59.775   3166
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 14.58 %
    Favored  : 81.68 %
  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:  2.16 (0.34), residues: 610
  helix:  2.58 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.34 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 295 
   HIS   0.003   0.001   HIS B  94 
   PHE   0.011   0.001   PHE B  81 
   TYR   0.006   0.001   TYR B 128 
   ARG   0.002   0.000   ARG A  74 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.638 
Fit side-chains
  outliers start: 20
  outliers final: 19
  residues processed: 65
  average time/residue: 0.8347
  time to fit residues: 58.4022
Evaluate side-chains
  62 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.607 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 16
  residues processed: 3
  average time/residue: 0.0873
  time to fit residues: 1.1933
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6243  Z= 0.198
  Angle     :  0.630   9.394   8682  Z= 0.286
  Chirality :  0.038   0.146   1122
  Planarity :  0.004   0.033    879
  Dihedral  : 10.636  59.907   3166
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 14.95 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.34), residues: 610
  helix:  2.51 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.51 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 295 
   HIS   0.004   0.001   HIS A  94 
   PHE   0.011   0.002   PHE B 244 
   TYR   0.007   0.001   TYR B  98 
   ARG   0.003   0.001   ARG A  74 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.641 
Fit side-chains
  outliers start: 21
  outliers final: 20
  residues processed: 62
  average time/residue: 0.8752
  time to fit residues: 58.3558
Evaluate side-chains
  62 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 42
  time to evaluate  : 0.596 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 18
  residues processed: 2
  average time/residue: 0.0803
  time to fit residues: 1.0244
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6243  Z= 0.172
  Angle     :  0.590  10.356   8682  Z= 0.269
  Chirality :  0.037   0.145   1122
  Planarity :  0.004   0.033    879
  Dihedral  : 10.495  59.914   3166
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 15.14 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.34), residues: 610
  helix:  2.65 (0.25), residues: 422
  sheet:  None (None), residues: 0
  loop : -1.37 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 295 
   HIS   0.003   0.001   HIS A  94 
   PHE   0.011   0.001   PHE B  81 
   TYR   0.007   0.001   TYR A 128 
   ARG   0.002   0.000   ARG A  74 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 0.578 
Fit side-chains
  outliers start: 24
  outliers final: 19
  residues processed: 66
  average time/residue: 0.8104
  time to fit residues: 57.6687
Evaluate side-chains
  65 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.617 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 17
  residues processed: 2
  average time/residue: 0.0984
  time to fit residues: 1.0425
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 19 optimal weight:    9.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6243  Z= 0.147
  Angle     :  0.555   9.719   8682  Z= 0.254
  Chirality :  0.035   0.154   1122
  Planarity :  0.003   0.033    879
  Dihedral  : 10.259  59.626   3166
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.70 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.34), residues: 610
  helix:  2.86 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.30 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A  70 
   HIS   0.003   0.001   HIS B  94 
   PHE   0.011   0.001   PHE B  81 
   TYR   0.007   0.001   TYR B 128 
   ARG   0.001   0.000   ARG B 161 

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.604 
Fit side-chains
  outliers start: 21
  outliers final: 18
  residues processed: 68
  average time/residue: 0.7710
  time to fit residues: 56.7100
Evaluate side-chains
  64 residues out of total 542 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.621 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 17
  residues processed: 1
  average time/residue: 0.0983
  time to fit residues: 0.8929
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 32 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.168267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.119338 restraints weight = 6951.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.89
r_work: 0.3160 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6243  Z= 0.204
  Angle     :  0.629  10.334   8682  Z= 0.285
  Chirality :  0.038   0.147   1122
  Planarity :  0.004   0.033    879
  Dihedral  : 10.541  59.268   3166
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 15.89 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.34), residues: 610
  helix:  2.67 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.40 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A  70 
   HIS   0.003   0.001   HIS B  94 
   PHE   0.011   0.001   PHE A  55 
   TYR   0.006   0.001   TYR B 128 
   ARG   0.003   0.000   ARG B 161 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1907.03 seconds
wall clock time: 35 minutes 1.41 seconds (2101.41 seconds total)