Starting phenix.real_space_refine
on Sun Jan 19 01:07:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bcq_44434/01_2025/9bcq_44434_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bcq_44434/01_2025/9bcq_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_44434/01_2025/9bcq_44434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bcq_44434/01_2025/9bcq_44434.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bcq_44434/01_2025/9bcq_44434_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bcq_44434/01_2025/9bcq_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-5571/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: 6.99, per 1000 atoms: 0.52
  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: 4.17
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.23
  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: 4.80

  Time building geometry restraints manager: 4.48 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:             0.250
  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:             0.240
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     32.510
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.100
-------------------------------------------------------------------------------
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  : 1.089 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.5501
  time to fit residues: 48.6883
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  : 1.093 
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.093732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.079105 restraints weight = 26859.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.2688 rms_B_bonded: 1.61
r_work: 0.2583 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2465 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
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  : 1.050 
Fit side-chains
   revert: symmetry clash
REVERT: B  373 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8730 (mm-30)
  outliers start: 4
  outliers final: 4
  residues processed: 66
  average time/residue: 0.5683
  time to fit residues: 47.5279
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  : 1.125 
-------------------------------------------------------------------------------
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 44 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.2925 r_free = 0.2925 target = 0.095698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.080477 restraints weight = 27121.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.2715 rms_B_bonded: 1.72
r_work: 0.2614 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2497 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7120  Z= 0.172
  Angle     :  0.573  10.501   9701  Z= 0.286
  Chirality :  0.061   1.355   1075
  Planarity :  0.005   0.060   1257
  Dihedral  :  8.401 100.701   1167
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.58 %
    Favored  : 94.99 %
  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: 304
  sheet: -0.99 (0.39), residues: 164
  loop : -1.02 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 146 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.010   0.001   PHE B 219 
 TYR   0.017   0.001   TYR B 154 
 ARG   0.002   0.000   ARG A 355 

*********************** 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
  67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
REVERT: B   55 ASN cc_start: 0.8269 (m-40) cc_final: 0.7960 (m-40)
REVERT: B  373 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8549 (mm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 65
  average time/residue: 0.5255
  time to fit residues: 43.7181
Evaluate side-chains
  66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0570
   chunk 68 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0770
   chunk 70 optimal weight:    0.4980
   overall best weight:    0.8658

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.096482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.081311 restraints weight = 26313.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 1.68
r_work: 0.2664 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2550 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7120  Z= 0.160
  Angle     :  0.547  10.745   9701  Z= 0.270
  Chirality :  0.061   1.366   1075
  Planarity :  0.004   0.053   1257
  Dihedral  :  7.916  98.131   1167
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.01 %
    Favored  : 93.56 %
  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: -0.38 (0.29), residues: 868
  helix:  1.11 (0.30), residues: 304
  sheet: -1.09 (0.39), residues: 164
  loop : -0.89 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 146 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.011   0.001   PHE B 219 
 TYR   0.017   0.001   TYR B 154 
 ARG   0.001   0.000   ARG B 351 

*********************** 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
  68 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7913 (tt0) cc_final: 0.7130 (mt-10)
REVERT: B   55 ASN cc_start: 0.8096 (m-40) cc_final: 0.7837 (m-40)
REVERT: B  373 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8471 (mm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 66
  average time/residue: 0.5157
  time to fit residues: 44.1610
Evaluate side-chains
  66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 THR
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 43 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0070
   chunk 71 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.0600

-------------------------------------------------------------------------------
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 = 0.2944 r_free = 0.2944 target = 0.096956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.081591 restraints weight = 26345.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2725 rms_B_bonded: 1.70
r_work: 0.2630 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2516 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1265

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= 0.169
  Angle     :  0.542  10.725   9701  Z= 0.267
  Chirality :  0.061   1.375   1075
  Planarity :  0.004   0.053   1257
  Dihedral  :  7.719  95.946   1167
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  6.58 %
    Favored  : 92.56 %
  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: -0.29 (0.29), residues: 868
  helix:  1.16 (0.30), residues: 308
  sheet: -1.10 (0.39), residues: 164
  loop : -0.80 (0.32), 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   0.009   0.001   PHE B 172 
 TYR   0.015   0.001   TYR B 154 
 ARG   0.001   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
  72 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7941 (tt0) cc_final: 0.7174 (mt-10)
REVERT: B   55 ASN cc_start: 0.8080 (m-40) cc_final: 0.7835 (m-40)
REVERT: B  334 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7775 (mt-10)
REVERT: B  373 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8637 (mm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 68
  average time/residue: 0.5469
  time to fit residues: 47.8849
Evaluate side-chains
  66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0570
   chunk 74 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.2106

-------------------------------------------------------------------------------
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 = 0.2938 r_free = 0.2938 target = 0.096355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.081092 restraints weight = 26455.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2715 rms_B_bonded: 1.68
r_work: 0.2621 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2508 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7120  Z= 0.286
  Angle     :  0.579  10.619   9701  Z= 0.287
  Chirality :  0.063   1.375   1075
  Planarity :  0.005   0.054   1257
  Dihedral  :  7.865  89.772   1167
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.87 %
    Favored  : 91.27 %
  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: -0.35 (0.29), residues: 868
  helix:  1.17 (0.30), residues: 304
  sheet: -1.13 (0.39), residues: 164
  loop : -0.88 (0.32), residues: 400

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   0.013   0.001   TYR B 154 
 ARG   0.002   0.000   ARG B 201 

*********************** 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
  67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7971 (tt0) cc_final: 0.7191 (mt-10)
REVERT: B   55 ASN cc_start: 0.8127 (m-40) cc_final: 0.7864 (m-40)
  outliers start: 6
  outliers final: 4
  residues processed: 64
  average time/residue: 0.5244
  time to fit residues: 43.6022
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  : 1.241 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.2945 r_free = 0.2945 target = 0.096849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.081450 restraints weight = 26359.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.2719 rms_B_bonded: 1.69
r_work: 0.2625 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2512 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1326

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= 0.174
  Angle     :  0.543  10.548   9701  Z= 0.269
  Chirality :  0.061   1.375   1075
  Planarity :  0.004   0.051   1257
  Dihedral  :  7.553  90.591   1167
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.44 %
    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: -0.25 (0.29), residues: 868
  helix:  1.22 (0.30), residues: 308
  sheet: -1.15 (0.39), residues: 164
  loop : -0.77 (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   0.010   0.001   PHE B 219 
 TYR   0.014   0.001   TYR B 154 
 ARG   0.001   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
  65 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7938 (tt0) cc_final: 0.7175 (mt-10)
REVERT: B  334 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7576 (mt-10)
  outliers start: 4
  outliers final: 4
  residues processed: 64
  average time/residue: 0.5153
  time to fit residues: 42.5541
Evaluate side-chains
  64 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
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  295 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 = 0.2911 r_free = 0.2911 target = 0.094728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.079191 restraints weight = 26527.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2684 rms_B_bonded: 1.71
r_work: 0.2579 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2461 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.1283

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= 0.304
  Angle     :  0.588  10.565   9701  Z= 0.291
  Chirality :  0.063   1.378   1075
  Planarity :  0.005   0.053   1257
  Dihedral  :  7.721  84.487   1167
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.73 %
    Favored  : 90.70 %
  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: -0.38 (0.29), residues: 868
  helix:  1.11 (0.30), residues: 308
  sheet: -1.16 (0.39), residues: 164
  loop : -0.86 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   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   0.002   0.000   ARG B  22 

*********************** 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
  65 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7952 (tt0) cc_final: 0.7178 (mt-10)
REVERT: B   55 ASN cc_start: 0.8136 (m-40) cc_final: 0.7874 (m-40)
  outliers start: 4
  outliers final: 4
  residues processed: 64
  average time/residue: 0.5184
  time to fit residues: 43.1177
Evaluate side-chains
  64 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
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  295 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    0.2980
   chunk 61 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.2946 r_free = 0.2946 target = 0.097175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.081511 restraints weight = 26012.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 1.71
r_work: 0.2614 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2499 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1395

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= 0.168
  Angle     :  0.542  10.646   9701  Z= 0.268
  Chirality :  0.061   1.384   1075
  Planarity :  0.004   0.050   1257
  Dihedral  :  7.348  85.721   1167
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  8.58 %
    Favored  : 90.70 %
  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: -0.21 (0.29), residues: 868
  helix:  1.27 (0.30), residues: 308
  sheet: -1.17 (0.39), residues: 164
  loop : -0.74 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  18 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.009   0.001   PHE B 172 
 TYR   0.013   0.001   TYR B 154 
 ARG   0.002   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
  67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7857 (tt0) cc_final: 0.7087 (mt-10)
REVERT: B   55 ASN cc_start: 0.8072 (m-40) cc_final: 0.7844 (m-40)
REVERT: B  334 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7576 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 65
  average time/residue: 0.5111
  time to fit residues: 43.0673
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  : 1.197 
-------------------------------------------------------------------------------
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  295 LYS
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 47 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0030
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.5796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.096733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.081470 restraints weight = 26425.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 1.69
r_work: 0.2609 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2496 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1397

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= 0.216
  Angle     :  0.553  10.524   9701  Z= 0.272
  Chirality :  0.061   1.365   1075
  Planarity :  0.005   0.052   1257
  Dihedral  :  7.307  82.620   1167
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  8.58 %
    Favored  : 90.70 %
  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: -0.22 (0.29), residues: 868
  helix:  1.25 (0.30), residues: 308
  sheet: -1.15 (0.39), residues: 164
  loop : -0.74 (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   0.013   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
  67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7869 (tt0) cc_final: 0.7121 (mt-10)
REVERT: B  334 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7594 (mt-10)
  outliers start: 5
  outliers final: 5
  residues processed: 66
  average time/residue: 0.5498
  time to fit residues: 47.4216
Evaluate side-chains
  67 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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
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 4 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.4388

-------------------------------------------------------------------------------
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 = 0.2939 r_free = 0.2939 target = 0.096777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.081038 restraints weight = 26184.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.2701 rms_B_bonded: 1.72
r_work: 0.2606 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2493 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1441

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= 0.201
  Angle     :  0.550  10.556   9701  Z= 0.270
  Chirality :  0.061   1.377   1075
  Planarity :  0.004   0.052   1257
  Dihedral  :  7.033  76.630   1167
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  8.44 %
    Favored  : 90.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.30), residues: 868
  helix:  1.28 (0.30), residues: 308
  sheet: -1.15 (0.39), residues: 164
  loop : -0.70 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 146 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.010   0.001   PHE B 219 
 TYR   0.013   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: 5840.10 seconds
wall clock time: 103 minutes 45.73 seconds (6225.73 seconds total)