Starting phenix.real_space_refine
on Mon Dec 30 12:09:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bcq_44434/12_2024/9bcq_44434_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bcq_44434/12_2024/9bcq_44434.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bcq_44434/12_2024/9bcq_44434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bcq_44434/12_2024/9bcq_44434.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bcq_44434/12_2024/9bcq_44434_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bcq_44434/12_2024/9bcq_44434_trim.cif"
  }
  resolution = 3.1
  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=   0.005 sd=   0.224
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     Cl      2      4.86       5
     C    4426      2.51       5
     N    1189      2.21       5
     O    1289      1.98       5
     H    6466      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 13401
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 6460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 6460
          Classifications: {'peptide': 425}
          Link IDs: {'PTRANS': 27, 'TRANS': 397}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 6476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 6476
          Classifications: {'peptide': 425}
          Link IDs: {'PTRANS': 27, 'TRANS': 397}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 326
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' CL': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.76, per 1000 atoms: 0.50
  Number of scatterers: 13401
  At special positions: 0
  Unit cell: (101.764, 68.2038, 89.8558, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      29     16.00
     O    1289      8.00
     N    1189      7.00
     C    4426      6.00
     H    6466      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 164 " - pdb=" SG  CYS B 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C   7 " - pdb=" SG  CYS C  23 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " NAG G   2 " - " MAN G   3 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG B1102 " - " ASN B 354 "
      " NAG D   1 " - " ASN A  13 "
      " NAG E   1 " - " ASN A 395 "
      " NAG F   1 " - " ASN B  13 "
      " NAG G   1 " - " ASN B 395 "
  Time building additional restraints: 4.03
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1586

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      39.7% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 34
      Proline residue:  A  25  - end of helix
    Processing helix  chain 'A' and resid 64 through 77
    Processing helix  chain 'A' and resid 86 through 101
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 3.708A  pdb=" N   PHE A 114 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A 116 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 132
      No H-bonds generated for 'chain 'A' and resid 130 through 132'
    Processing helix  chain 'A' and resid 133 through 144
    Processing helix  chain 'A' and resid 162 through 175
    Processing helix  chain 'A' and resid 192 through 203
      removed outlier: 3.697A  pdb=" N   TYR A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR A 197 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ARG A 198 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 206
      No H-bonds generated for 'chain 'A' and resid 204 through 206'
    Processing helix  chain 'A' and resid 215 through 230
    Processing helix  chain 'A' and resid 287 through 306
      removed outlier: 3.670A  pdb=" N   LEU A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU A 292 " --> pdb=" O   PRO A 288 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 314
      No H-bonds generated for 'chain 'A' and resid 312 through 314'
    Processing helix  chain 'A' and resid 315 through 338
      removed outlier: 3.525A  pdb=" N   ALA A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 351
      removed outlier: 3.665A  pdb=" N   GLN A 350 " --> pdb=" O   GLU A 346 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      Proline residue:  B  25  - end of helix
      removed outlier: 3.737A  pdb=" N   LYS B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 76
      removed outlier: 3.789A  pdb=" N   LEU B  67 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 101
      Proline residue:  B  92  - end of helix
    Processing helix  chain 'B' and resid 111 through 116
      removed outlier: 3.718A  pdb=" N   PHE B 114 " --> pdb=" O   ALA B 111 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL B 116 " --> pdb=" O   GLY B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 145
      removed outlier: 4.038A  pdb=" N   GLY B 134 " --> pdb=" O   TYR B 130 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ASP B 135 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   PHE B 136 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 179
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 4.091A  pdb=" N   TYR B 196 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 229
    Processing helix  chain 'B' and resid 245 through 249
    Processing helix  chain 'B' and resid 268 through 274
      removed outlier: 3.839A  pdb=" N   GLN B 272 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 306
      removed outlier: 3.710A  pdb=" N   LEU B 291 " --> pdb=" O   ASN B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 338
    Processing helix  chain 'B' and resid 344 through 353
      removed outlier: 3.573A  pdb=" N   ARG B 351 " --> pdb=" O   ASN B 347 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   MET B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 18
      removed outlier: 3.662A  pdb=" N   GLY C  16 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA C  17 " --> pdb=" O   ARG C  14 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLN C  18 " --> pdb=" O   ILE C  15 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 13 through 18'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51
      removed outlier: 6.060A  pdb=" N   LEU A   3 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   VAL A  49 " --> pdb=" O   LEU A   3 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   VAL A   5 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   GLY A  51 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   VAL A   7 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A  80 " --> pdb=" O   THR A   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106
      removed outlier: 5.797A  pdb=" N   LEU A 104 " --> pdb=" O   THR A 124 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 189
      removed outlier: 3.695A  pdb=" N   ASP A 184 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   VAL A 209 " --> pdb=" O   GLN A 149 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ILE A 210 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU A 241 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ILE A 212 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   PHE A 238 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   ILE A 280 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   HIS A 240 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   TYR A 282 " --> pdb=" O   HIS A 240 " (cutoff:3.500A)
      removed outlier: 8.703A  pdb=" N   ALA A 277 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   MET A 381 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   PHE A 376 " --> pdb=" O   ASN A 393 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   ASN A 393 " --> pdb=" O   PHE A 376 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LEU A 378 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLU A 400 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 359
    Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 52
      removed outlier: 6.488A  pdb=" N   LEU B   3 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   VAL B  49 " --> pdb=" O   LEU B   3 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL B   5 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   GLY B  51 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   VAL B   7 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B  80 " --> pdb=" O   THR B   4 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 106
      removed outlier: 6.075A  pdb=" N   LEU B 104 " --> pdb=" O   THR B 124 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 189
      removed outlier: 3.535A  pdb=" N   ALA B 150 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
      removed outlier: 5.441A  pdb=" N   VAL B 209 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   PHE B 238 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   ILE B 280 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   HIS B 240 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   TYR B 282 " --> pdb=" O   HIS B 240 " (cutoff:3.500A)
      removed outlier: 9.044A  pdb=" N   ALA B 277 " --> pdb=" O   MET B 381 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   MET B 381 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE B 279 " --> pdb=" O   TRP B 379 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU B 392 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   ASP B 380 " --> pdb=" O   VAL B 390 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   VAL B 390 " --> pdb=" O   ASP B 380 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 358
      removed outlier: 3.612A  pdb=" N   ARG B 355 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    756 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.99

  Time building geometry restraints manager: 4.76 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 6459
        1.04 -     1.23: 249
        1.23 -     1.43: 2844
        1.43 -     1.63: 3990
        1.63 -     1.82: 44
  Bond restraints: 13586
  Sorted by residual:
  bond pdb=" C   GLU A 373 "
       pdb=" O   GLU A 373 "
    ideal  model  delta    sigma   weight residual
    1.236  1.182  0.053 1.17e-02 7.31e+03 2.09e+01
  bond pdb=" C   GLU B 373 "
       pdb=" O   GLU B 373 "
    ideal  model  delta    sigma   weight residual
    1.236  1.187  0.048 1.21e-02 6.83e+03 1.61e+01
  bond pdb=" C1  NAG G   1 "
       pdb=" O5  NAG G   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.470 -0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" CD  GLU A 373 "
       pdb=" OE2 GLU A 373 "
    ideal  model  delta    sigma   weight residual
    1.249  1.198  0.051 1.90e-02 2.77e+03 7.19e+00
  bond pdb=" N   GLU A 373 "
       pdb=" H   GLU A 373 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.67e+00
  ... (remaining 13581 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.11: 24343
        7.11 -    14.21: 4
       14.21 -    21.32: 1
       21.32 -    28.42: 7
       28.42 -    35.53: 12
  Bond angle restraints: 24367
  Sorted by residual:
  angle pdb=" N   TRP B 146 "
        pdb=" CA  TRP B 146 "
        pdb=" HA  TRP B 146 "
      ideal   model   delta    sigma   weight residual
     110.00   74.47   35.53 3.00e+00 1.11e-01 1.40e+02
  angle pdb=" C   ARG B 148 "
        pdb=" CA  ARG B 148 "
        pdb=" HA  ARG B 148 "
      ideal   model   delta    sigma   weight residual
     109.00   73.97   35.03 3.00e+00 1.11e-01 1.36e+02
  angle pdb=" N   ARG B 148 "
        pdb=" CA  ARG B 148 "
        pdb=" HA  ARG B 148 "
      ideal   model   delta    sigma   weight residual
     110.00   75.29   34.71 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" C   TRP B 146 "
        pdb=" CA  TRP B 146 "
        pdb=" HA  TRP B 146 "
      ideal   model   delta    sigma   weight residual
     109.00   74.38   34.62 3.00e+00 1.11e-01 1.33e+02
  angle pdb=" CB  TRP B 146 "
        pdb=" CA  TRP B 146 "
        pdb=" HA  TRP B 146 "
      ideal   model   delta    sigma   weight residual
     109.00   76.50   32.50 3.00e+00 1.11e-01 1.17e+02
  ... (remaining 24362 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.11: 6175
       23.11 -    46.22: 371
       46.22 -    69.33: 85
       69.33 -    92.43: 11
       92.43 -   115.54: 1
  Dihedral angle restraints: 6643
    sinusoidal: 3626
      harmonic: 3017
  Sorted by residual:
  dihedral pdb=" CA  LEU A  82 "
           pdb=" C   LEU A  82 "
           pdb=" N   GLY A  83 "
           pdb=" CA  GLY A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.48   23.52     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  LEU B  82 "
           pdb=" C   LEU B  82 "
           pdb=" N   GLY B  83 "
           pdb=" CA  GLY B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.61   22.39     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  LYS B 117 "
           pdb=" C   LYS B 117 "
           pdb=" N   ASP B 118 "
           pdb=" CA  ASP B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.70   22.30     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 6640 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.287: 1071
       0.287 -    0.575: 3
       0.575 -    0.862: 0
       0.862 -    1.150: 0
       1.150 -    1.437: 1
  Chirality restraints: 1075
  Sorted by residual:
  chirality pdb=" CB  VAL B 183 "
            pdb=" CA  VAL B 183 "
            pdb=" CG1 VAL B 183 "
            pdb=" CG2 VAL B 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.19   -1.44 2.00e-01 2.50e+01 5.16e+01
  chirality pdb=" CA  ARG B 148 "
            pdb=" N   ARG B 148 "
            pdb=" C   ARG B 148 "
            pdb=" CB  ARG B 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.51e+00
  chirality pdb=" C4  NAG G   1 "
            pdb=" C3  NAG G   1 "
            pdb=" C5  NAG G   1 "
            pdb=" O4  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.13   -0.40 2.00e-01 2.50e+01 4.02e+00
  ... (remaining 1072 not shown)

  Planarity restraints: 2079
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 317 "    0.069 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO B 318 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO B 318 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 318 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 372 "   -0.020 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" N   GLU A 373 "    0.062 2.00e-02 2.50e+03
        pdb=" CA  GLU A 373 "   -0.016 2.00e-02 2.50e+03
        pdb=" H   GLU A 373 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 317 "   -0.053 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO A 318 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A 318 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 318 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 2076 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 672
        2.19 -     2.79: 26346
        2.79 -     3.40: 36204
        3.40 -     4.00: 49641
        4.00 -     4.60: 76973
  Nonbonded interactions: 189836
  Sorted by model distance:
  nonbonded pdb=" H   ARG B 148 "
            pdb=" HA  ARG B 148 "
     model   vdw
     1.588 1.816
  nonbonded pdb=" H   TRP B 146 "
            pdb=" HA  TRP B 146 "
     model   vdw
     1.599 1.816
  nonbonded pdb=" O   PRO A 204 "
            pdb="HH12 ARG A 208 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" HB3 MET A 203 "
            pdb=" HG2 MET A 203 "
     model   vdw
     1.645 1.952
  nonbonded pdb=" HB2 MET A 203 "
            pdb=" HG3 MET A 203 "
     model   vdw
     1.655 1.952
  ... (remaining 189831 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 34 or (resid 35 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ 
ame HA )) or resid 36 through 147 or (resid 148 and (name N or name CA or name C \ 
 or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ 
 name NH2 or name H or name HA )) or resid 149 through 179 or (resid 180 and (na \ 
me N or name CA or name C or name O or name CB or name H or name HA )) or resid  \ 
181 through 204 or (resid 205 and (name N or name CA or name C or name O or name \ 
 CB or name H or name HA )) or resid 206 through 291 or (resid 292 and (name N o \ 
r name CA or name C or name O or name CB or name CG or name CD or name OE1 or na \ 
me OE2 or name H or name HA )) or resid 293 through 404 or (resid 405 and (name  \ 
N or name CA or name C or name O or name CB or name OG or name H or name HA )) o \ 
r resid 406 through 422 or (resid 423 and (name N or name CA or name C or name O \ 
 or name CB or name SG or name H or name HA )) or resid 424 through 425 or resid \ 
 1101))
  selection = (chain 'B' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ 
 or name O or name CB or name H or name HA )) or resid 76 through 160 or (resid  \ 
161 and (name N or name CA or name C or name O or name CB or name CG or name CD  \ 
or name OE1 or name OE2 or name H or name HA )) or resid 162 through 200 or (res \ 
id 201 and (name N or name CA or name C or name O or name CB or name CG or name  \ 
CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) or resi \ 
d 202 through 227 or (resid 228 and (name N or name CA or name C or name O or na \ 
me CB or name CG or name CD or name OE1 or name OE2 or name H or name HA )) or r \ 
esid 229 through 285 or (resid 286 and (name N or name CA or name C or name O or \ 
 name CB or name H or name HA )) or resid 287 through 302 or (resid 303 and (nam \ 
e N or name CA or name C or name O or name CB or name CG or name CD or name OE1  \ 
or name OE2 or name H or name HA )) or resid 304 through 383 or (resid 384 and ( \ 
name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ 
d 385 through 407 or (resid 408 and (name N or name CA or name C or name O or na \ 
me CB or name H or name HA )) or resid 409 through 425 or resid 1101))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.210
  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:             0.230
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     32.890
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
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   0.064   7120  Z= 0.422
  Angle     :  0.713  10.666   9701  Z= 0.375
  Chirality :  0.067   1.437   1075
  Planarity :  0.006   0.103   1257
  Dihedral  : 14.486 115.542   2697
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.13 %
  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: 868
  helix: -0.33 (0.29), residues: 300
  sheet: -0.41 (0.44), residues: 148
  loop : -1.13 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 146 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.015   0.002   PHE B 172 
 TYR   0.008   0.001   TYR A 154 
 ARG   0.011   0.001   ARG B 389 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.5385
  time to fit residues: 47.7308
Evaluate side-chains
  58 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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: 0.8334
moved from start:          0.0583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7120  Z= 0.329
  Angle     :  0.650  10.613   9701  Z= 0.329
  Chirality :  0.064   1.375   1075
  Planarity :  0.006   0.076   1257
  Dihedral  :  9.116 102.550   1167
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  2.72 %
    Favored  : 96.71 %
  Cbeta Deviations :  0.13 %
  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: -0.93 (0.28), residues: 868
  helix:  0.28 (0.29), residues: 300
  sheet: -0.88 (0.40), residues: 164
  loop : -1.11 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 146 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.019   0.001   PHE B 219 
 TYR   0.019   0.001   TYR B 154 
 ARG   0.003   0.000   ARG A 208 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 66
  average time/residue: 0.5906
  time to fit residues: 49.5854
Evaluate side-chains
  65 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0030
   chunk 21 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.5796

-------------------------------------------------------------------------------
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: 0.8313
moved from start:          0.0884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7120  Z= 0.222
  Angle     :  0.589  10.464   9701  Z= 0.294
  Chirality :  0.062   1.365   1075
  Planarity :  0.005   0.060   1257
  Dihedral  :  8.483  98.944   1167
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  4.72 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.13 %
  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: -0.66 (0.28), residues: 868
  helix:  0.70 (0.30), residues: 300
  sheet: -1.02 (0.39), residues: 164
  loop : -0.98 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 146 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.010   0.001   PHE B 219 
 TYR   0.015   0.001   TYR B 154 
 ARG   0.002   0.000   ARG A 148 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: B   55 ASN cc_start: 0.8144 (m-40) cc_final: 0.7926 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 68
  average time/residue: 0.5057
  time to fit residues: 44.5890
Evaluate side-chains
  68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   chunk 37 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 393 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7120  Z= 0.147
  Angle     :  0.547  10.733   9701  Z= 0.269
  Chirality :  0.060   1.371   1075
  Planarity :  0.004   0.051   1257
  Dihedral  :  7.876  99.109   1167
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.29 %
    Favored  : 93.42 %
  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: -0.40 (0.29), residues: 868
  helix:  1.08 (0.30), residues: 304
  sheet: -1.08 (0.39), residues: 164
  loop : -0.89 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 146 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.009   0.001   PHE B 219 
 TYR   0.017   0.001   TYR B 154 
 ARG   0.002   0.000   ARG A 157 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7598 (tt0) cc_final: 0.7036 (mt-10)
  outliers start: 2
  outliers final: 1
  residues processed: 66
  average time/residue: 0.5135
  time to fit residues: 44.9414
Evaluate side-chains
  63 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  235 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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: 0.8325
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7120  Z= 0.347
  Angle     :  0.602  10.709   9701  Z= 0.299
  Chirality :  0.064   1.412   1075
  Planarity :  0.005   0.055   1257
  Dihedral  :  8.131  90.889   1167
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  6.44 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.51 (0.29), residues: 868
  helix:  0.96 (0.30), residues: 304
  sheet: -1.11 (0.39), residues: 164
  loop : -0.96 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 146 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.015   0.001   PHE B 219 
 TYR   0.013   0.001   TYR B 154 
 ARG   0.004   0.000   ARG B  22 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 64
  average time/residue: 0.5260
  time to fit residues: 43.4567
Evaluate side-chains
  67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  235 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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: 0.8320
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7120  Z= 0.275
  Angle     :  0.579  10.443   9701  Z= 0.287
  Chirality :  0.063   1.384   1075
  Planarity :  0.005   0.053   1257
  Dihedral  :  7.977  90.024   1167
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.44 %
    Favored  : 91.70 %
  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: -0.41 (0.29), residues: 868
  helix:  1.09 (0.30), residues: 300
  sheet: -1.14 (0.39), residues: 164
  loop : -0.87 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 146 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.014   0.001   PHE B 219 
 TYR   0.014   0.001   TYR B 154 
 ARG   0.001   0.000   ARG C  11 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7632 (tt0) cc_final: 0.7072 (mt-10)
  outliers start: 6
  outliers final: 4
  residues processed: 65
  average time/residue: 0.5272
  time to fit residues: 44.4690
Evaluate side-chains
  66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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: 0.8312
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7120  Z= 0.233
  Angle     :  0.563  10.443   9701  Z= 0.279
  Chirality :  0.061   1.359   1075
  Planarity :  0.005   0.052   1257
  Dihedral  :  7.708  87.277   1167
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  8.30 %
    Favored  : 90.99 %
  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: -0.30 (0.29), residues: 868
  helix:  1.23 (0.30), residues: 300
  sheet: -1.16 (0.40), residues: 164
  loop : -0.81 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 146 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.011   0.001   PHE B 219 
 TYR   0.014   0.001   TYR B 154 
 ARG   0.002   0.000   ARG C  11 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  69 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7629 (tt0) cc_final: 0.7061 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 67
  average time/residue: 0.5105
  time to fit residues: 44.6164
Evaluate side-chains
  65 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  235 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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: 0.8330
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7120  Z= 0.325
  Angle     :  0.596  10.614   9701  Z= 0.296
  Chirality :  0.064   1.398   1075
  Planarity :  0.005   0.053   1257
  Dihedral  :  7.842  83.677   1167
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.30 %
    Favored  : 90.56 %
  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: -0.40 (0.29), residues: 868
  helix:  1.13 (0.30), residues: 300
  sheet: -1.15 (0.40), residues: 164
  loop : -0.89 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 146 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.015   0.001   PHE B 219 
 TYR   0.012   0.001   TYR B 154 
 ARG   0.001   0.000   ARG B 201 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7629 (tt0) cc_final: 0.7063 (mt-10)
REVERT: B  373 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8212 (mm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 67
  average time/residue: 0.5060
  time to fit residues: 43.9092
Evaluate side-chains
  68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  295 LYS
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 73 optimal weight:    0.3980
   chunk 76 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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: 0.8304
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7120  Z= 0.185
  Angle     :  0.552  10.485   9701  Z= 0.273
  Chirality :  0.061   1.363   1075
  Planarity :  0.005   0.051   1257
  Dihedral  :  7.448  83.869   1167
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.73 %
    Favored  : 90.41 %
  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: -0.32 (0.29), residues: 868
  helix:  1.15 (0.30), residues: 308
  sheet: -1.15 (0.40), residues: 164
  loop : -0.82 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  18 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.011   0.001   PHE B 172 
 TYR   0.014   0.001   TYR B 154 
 ARG   0.001   0.000   ARG C  11 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7526 (tt0) cc_final: 0.6980 (mt-10)
  outliers start: 6
  outliers final: 6
  residues processed: 66
  average time/residue: 0.5263
  time to fit residues: 45.2315
Evaluate side-chains
  68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  295 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 56 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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: 0.8307
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7120  Z= 0.219
  Angle     :  0.558  10.640   9701  Z= 0.275
  Chirality :  0.062   1.389   1075
  Planarity :  0.005   0.052   1257
  Dihedral  :  7.352  80.578   1167
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.73 %
    Favored  : 90.41 %
  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: -0.30 (0.29), residues: 868
  helix:  1.17 (0.30), residues: 308
  sheet: -1.12 (0.40), residues: 164
  loop : -0.81 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 146 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.011   0.001   PHE B 219 
 TYR   0.014   0.001   TYR B 154 
 ARG   0.002   0.000   ARG C  11 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  408 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Residue LYS   35 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  422 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7528 (tt0) cc_final: 0.6979 (mt-10)
  outliers start: 6
  outliers final: 5
  residues processed: 66
  average time/residue: 0.5096
  time to fit residues: 43.9531
Evaluate side-chains
  66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  235 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.2943 r_free = 0.2943 target = 0.096911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.081266 restraints weight = 25968.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 1.71
r_work: 0.2623 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2509 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7120  Z= 0.185
  Angle     :  0.547  10.656   9701  Z= 0.269
  Chirality :  0.061   1.394   1075
  Planarity :  0.004   0.051   1257
  Dihedral  :  6.942  73.732   1167
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  8.73 %
    Favored  : 90.56 %
  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: -0.23 (0.30), residues: 868
  helix:  1.23 (0.30), residues: 308
  sheet: -1.12 (0.40), residues: 164
  loop : -0.76 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  18 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.010   0.001   PHE B 172 
 TYR   0.014   0.001   TYR B 154 
 ARG   0.002   0.000   ARG C  11 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3277.07 seconds
wall clock time: 59 minutes 7.43 seconds (3547.43 seconds total)