Starting phenix.real_space_refine
on Sat Jun 14 15:23:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rl7_19333/06_2025/8rl7_19333_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rl7_19333/06_2025/8rl7_19333.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rl7_19333/06_2025/8rl7_19333.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rl7_19333/06_2025/8rl7_19333.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rl7_19333/06_2025/8rl7_19333_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rl7_19333/06_2025/8rl7_19333_trim.cif"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    5340      2.51       5
     N    1376      2.21       5
     O    1464      1.98       5
     H    8042      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16262
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1824
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 2, 'TRANS': 124}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1824
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 2, 'TRANS': 124}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 6283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 6283
          Classifications: {'peptide': 423}
          Link IDs: {'PTRANS': 12, 'TRANS': 410}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 28
    Chain: "C"
      Number of atoms: 6283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 6283
          Classifications: {'peptide': 423}
          Link IDs: {'PTRANS': 12, 'TRANS': 410}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 28
    Chain: "A"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 5
    Chain: "C"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 8.30, per 1000 atoms: 0.51
  Number of scatterers: 16262
  At special positions: 0
  Unit cell: (189.841, 72.123, 85.387, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     O    1464      8.00
     N    1376      7.00
     C    5340      6.00
     H    8042      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  11 " - pdb=" SG  CYS D  11 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " 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
  Time building additional restraints: 4.56
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1992

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      73.8% alpha, 11.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 30
      No H-bonds generated for 'chain 'B' and resid 28 through 30'
    Processing helix  chain 'B' and resid 87 through 91
    Processing helix  chain 'D' and resid 28 through 30
      No H-bonds generated for 'chain 'D' and resid 28 through 30'
    Processing helix  chain 'D' and resid 87 through 91
    Processing helix  chain 'A' and resid 101 through 125
      removed outlier: 4.366A  pdb=" N   VAL A 122 " --> pdb=" O   ASP A 118 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   ALA A 123 " --> pdb=" O   ARG A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 136 through 165
      removed outlier: 4.031A  pdb=" N   GLN A 144 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
    Processing helix  chain 'A' and resid 166 through 186
      removed outlier: 3.907A  pdb=" N   ILE A 170 " --> pdb=" O   ASN A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 222
      Proline residue:  A 215  - end of helix
      removed outlier: 3.574A  pdb=" N   PHE A 222 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 257
      removed outlier: 4.166A  pdb=" N   ILE A 238 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
    Processing helix  chain 'A' and resid 259 through 281
      removed outlier: 3.744A  pdb=" N   LEU A 263 " --> pdb=" O   TRP A 259 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   SER A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
    Processing helix  chain 'A' and resid 298 through 312
    Processing helix  chain 'A' and resid 312 through 347
      removed outlier: 3.822A  pdb=" N   VAL A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      Proline residue:  A 337  - end of helix
    Processing helix  chain 'A' and resid 360 through 390
      removed outlier: 4.016A  pdb=" N   LEU A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 394 through 421
      removed outlier: 3.900A  pdb=" N   CYS A 400 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   PHE A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL A 416 " --> pdb=" O   CYS A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.844A  pdb=" N   ALA A 425 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 451
      removed outlier: 3.613A  pdb=" N   ALA A 444 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP A 445 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 471
    Processing helix  chain 'A' and resid 474 through 490
    Processing helix  chain 'A' and resid 493 through 539
      removed outlier: 4.055A  pdb=" N   CYS A 508 " --> pdb=" O   ALA A 504 " (cutoff:3.500A)
      Proline residue:  A 509  - end of helix
      removed outlier: 4.632A  pdb=" N   VAL A 527 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   SER A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 125
      removed outlier: 4.365A  pdb=" N   VAL C 122 " --> pdb=" O   ASP C 118 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   ALA C 123 " --> pdb=" O   ARG C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 134
    Processing helix  chain 'C' and resid 136 through 165
      removed outlier: 4.026A  pdb=" N   GLN C 144 " --> pdb=" O   ALA C 140 " (cutoff:3.500A)
      Proline residue:  C 156  - end of helix
    Processing helix  chain 'C' and resid 166 through 186
      removed outlier: 3.906A  pdb=" N   ILE C 170 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 222
      Proline residue:  C 215  - end of helix
      removed outlier: 3.588A  pdb=" N   PHE C 222 " --> pdb=" O   ILE C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 257
      removed outlier: 4.245A  pdb=" N   ILE C 238 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      Proline residue:  C 239  - end of helix
    Processing helix  chain 'C' and resid 259 through 281
      removed outlier: 3.748A  pdb=" N   LEU C 263 " --> pdb=" O   TRP C 259 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   SER C 266 " --> pdb=" O   ALA C 262 " (cutoff:3.500A)
      Proline residue:  C 267  - end of helix
    Processing helix  chain 'C' and resid 298 through 312
    Processing helix  chain 'C' and resid 312 through 347
      removed outlier: 3.826A  pdb=" N   VAL C 316 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
      Proline residue:  C 337  - end of helix
    Processing helix  chain 'C' and resid 360 through 390
      removed outlier: 3.929A  pdb=" N   LEU C 390 " --> pdb=" O   ARG C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 393
      No H-bonds generated for 'chain 'C' and resid 391 through 393'
    Processing helix  chain 'C' and resid 394 through 421
      removed outlier: 3.520A  pdb=" N   LEU C 398 " --> pdb=" O   ARG C 394 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   CYS C 400 " --> pdb=" O   ASP C 396 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   PHE C 415 " --> pdb=" O   ILE C 411 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL C 416 " --> pdb=" O   CYS C 412 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 438
      removed outlier: 3.836A  pdb=" N   ALA C 425 " --> pdb=" O   SER C 421 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 451
      removed outlier: 3.622A  pdb=" N   ALA C 444 " --> pdb=" O   TRP C 440 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ASP C 445 " --> pdb=" O   ALA C 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 455 through 471
    Processing helix  chain 'C' and resid 474 through 490
    Processing helix  chain 'C' and resid 493 through 539
      removed outlier: 4.031A  pdb=" N   CYS C 508 " --> pdb=" O   ALA C 504 " (cutoff:3.500A)
      Proline residue:  C 509  - end of helix
      removed outlier: 4.591A  pdb=" N   VAL C 527 " --> pdb=" O   ALA C 523 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   SER C 528 " --> pdb=" O   LEU C 524 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.938A  pdb=" N   MET B  34 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ALA B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 60
      removed outlier: 6.597A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   ALA D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   MET D  34 " --> pdb=" O   ALA D  50 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   CYS D  96 " --> pdb=" O   GLY D 119 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   LEU D   4 " --> pdb=" O   TRP D 118 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LYS D 120 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLU D   6 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 60
      removed outlier: 6.597A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   ALA D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   MET D  34 " --> pdb=" O   ALA D  50 " (cutoff:3.500A)

    681 hydrogen bonds defined for protein.
    1992 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: 6.68

  Time building geometry restraints manager: 5.51 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8028
        1.03 -     1.23: 32
        1.23 -     1.43: 3592
        1.43 -     1.62: 4736
        1.62 -     1.82: 60
  Bond restraints: 16448
  Sorted by residual:
  bond pdb=" C   SER C 528 "
       pdb=" N   ASP C 529 "
    ideal  model  delta    sigma   weight residual
    1.334  1.276  0.058 1.46e-02 4.69e+03 1.60e+01
  bond pdb=" C   LYS C 224 "
       pdb=" O   LYS C 224 "
    ideal  model  delta    sigma   weight residual
    1.235  1.271 -0.035 9.00e-03 1.23e+04 1.55e+01
  bond pdb=" C   TYR A 246 "
       pdb=" N   ILE A 247 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 1.26e-02 6.30e+03 1.13e+01
  bond pdb=" C   TYR C 246 "
       pdb=" N   ILE C 247 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 1.26e-02 6.30e+03 1.10e+01
  bond pdb=" C   GLY A 245 "
       pdb=" N   TYR A 246 "
    ideal  model  delta    sigma   weight residual
    1.335  1.293  0.042 1.31e-02 5.83e+03 1.02e+01
  ... (remaining 16443 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 29096
        1.87 -     3.74: 364
        3.74 -     5.62: 48
        5.62 -     7.49: 4
        7.49 -     9.36: 6
  Bond angle restraints: 29518
  Sorted by residual:
  angle pdb=" CA  GLY B 121 "
        pdb=" C   GLY B 121 "
        pdb=" O   GLY B 121 "
      ideal   model   delta    sigma   weight residual
     122.29  117.45    4.84 8.10e-01 1.52e+00 3.58e+01
  angle pdb=" CA  SER C 528 "
        pdb=" C   SER C 528 "
        pdb=" N   ASP C 529 "
      ideal   model   delta    sigma   weight residual
     117.30  123.09   -5.79 1.16e+00 7.43e-01 2.49e+01
  angle pdb=" CA  SER C 232 "
        pdb=" C   SER C 232 "
        pdb=" O   SER C 232 "
      ideal   model   delta    sigma   weight residual
     121.07  115.88    5.19 1.10e+00 8.26e-01 2.23e+01
  angle pdb=" CA  GLY D 121 "
        pdb=" C   GLY D 121 "
        pdb=" O   GLY D 121 "
      ideal   model   delta    sigma   weight residual
     121.58  117.34    4.24 9.00e-01 1.23e+00 2.22e+01
  angle pdb=" C   SER C 232 "
        pdb=" N   VAL C 233 "
        pdb=" CA  VAL C 233 "
      ideal   model   delta    sigma   weight residual
     120.46  126.88   -6.42 1.37e+00 5.33e-01 2.20e+01
  ... (remaining 29513 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 7046
       16.59 -    33.19: 540
       33.19 -    49.78: 133
       49.78 -    66.37: 132
       66.37 -    82.97: 2
  Dihedral angle restraints: 7853
    sinusoidal: 4063
      harmonic: 3790
  Sorted by residual:
  dihedral pdb=" CG  ARG D  72 "
           pdb=" CD  ARG D  72 "
           pdb=" NE  ARG D  72 "
           pdb=" CZ  ARG D  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.59  -41.59     2      1.50e+01 4.44e-03 9.40e+00
  dihedral pdb=" CA  LYS A 224 "
           pdb=" CB  LYS A 224 "
           pdb=" CG  LYS A 224 "
           pdb=" CD  LYS A 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.60  -54.40     3      1.50e+01 4.44e-03 9.28e+00
  dihedral pdb=" CA  CYS B  11 "
           pdb=" CB  CYS B  11 "
           pdb=" SG  CYS B  11 "
           pdb=" SG  CYS D  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00 -123.97   50.97     1      2.00e+01 2.50e-03 8.89e+00
  ... (remaining 7850 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1024
       0.041 -    0.082: 220
       0.082 -    0.124: 83
       0.124 -    0.165: 16
       0.165 -    0.206: 9
  Chirality restraints: 1352
  Sorted by residual:
  chirality pdb=" C4' LMT A 601 "
            pdb=" C3' LMT A 601 "
            pdb=" C5' LMT A 601 "
            pdb=" O1B LMT A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.76    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" C5' LMT C 601 "
            pdb=" C4' LMT C 601 "
            pdb=" C6' LMT C 601 "
            pdb=" O5' LMT C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.30   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" C4' LMT C 601 "
            pdb=" C3' LMT C 601 "
            pdb=" C5' LMT C 601 "
            pdb=" O1B LMT C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.76    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1349 not shown)

  Planarity restraints: 2480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 526 "   -0.013 2.00e-02 2.50e+03   2.65e-02 7.05e+00
        pdb=" C   PHE C 526 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PHE C 526 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL C 527 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 223 "   -0.012 2.00e-02 2.50e+03   2.50e-02 6.27e+00
        pdb=" C   THR C 223 "    0.043 2.00e-02 2.50e+03
        pdb=" O   THR C 223 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LYS C 224 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  72 "   -0.199 9.50e-02 1.11e+02   6.65e-02 4.97e+00
        pdb=" NE  ARG D  72 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  72 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  72 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  72 "   -0.006 2.00e-02 2.50e+03
        pdb="HH11 ARG D  72 "    0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG D  72 "   -0.006 2.00e-02 2.50e+03
        pdb="HH21 ARG D  72 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG D  72 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2477 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 1714
        2.24 -     2.83: 36600
        2.83 -     3.42: 45245
        3.42 -     4.01: 60321
        4.01 -     4.60: 93143
  Nonbonded interactions: 237023
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 206 "
            pdb=" HG  SER A 209 "
     model   vdw
     1.649 2.450
  nonbonded pdb=" O   GLY C 206 "
            pdb=" HG  SER C 209 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" O   ILE C 369 "
            pdb=" HG1 THR C 373 "
     model   vdw
     1.663 2.450
  nonbonded pdb=" O   ILE A 369 "
            pdb=" HG1 THR A 373 "
     model   vdw
     1.665 2.450
  nonbonded pdb=" O   LEU A 117 "
            pdb=" HG1 THR A 121 "
     model   vdw
     1.677 2.450
  ... (remaining 237018 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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 group one per residue
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:             3.410
  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:             0.270
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     38.000
  Find NCS groups from input model:        0.410
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
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      :  0.005   0.058   8409  Z= 0.313
  Angle     :  0.705   9.362  11456  Z= 0.468
  Chirality :  0.044   0.206   1352
  Planarity :  0.006   0.087   1416
  Dihedral  : 12.701  82.966   2836
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  0.49 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.26), residues: 1084
  helix:  1.54 (0.19), residues: 766
  sheet:  1.12 (0.50), residues: 80
  loop :  0.59 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 496 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.011   0.001   PHE C 236 
 TYR   0.015   0.001   TYR C 246 
 ARG   0.008   0.000   ARG A 532 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12154 (  663)
  hydrogen bonds       : angle       6.22664 ( 1992)
  SS BOND              : bond        0.00186 (    3)
  SS BOND              : angle       0.55427 (    6)
  covalent geometry    : bond        0.00462 ( 8406)
  covalent geometry    : angle       0.70552 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  176 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 170
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 ASN cc_start: 0.7960 (t0) cc_final: 0.7741 (t0)
REVERT: D   74 ASN cc_start: 0.7258 (m-40) cc_final: 0.6517 (m-40)
REVERT: D  100 ASN cc_start: 0.8105 (t0) cc_final: 0.7806 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 173
  average time/residue: 0.4220
  time to fit residues: 100.6361
Evaluate side-chains
  134 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  528 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
D 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.188913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.179037 restraints weight = 28743.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.181213 restraints weight = 21232.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.182422 restraints weight = 16049.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8409  Z= 0.186
  Angle     :  0.533   5.102  11456  Z= 0.300
  Chirality :  0.037   0.126   1352
  Planarity :  0.005   0.044   1416
  Dihedral  :  5.495  49.784   1258
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  9.07 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.25), residues: 1084
  helix:  1.72 (0.19), residues: 786
  sheet:  0.79 (0.46), residues: 96
  loop :  0.30 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 178 
 HIS   0.007   0.001   HIS A 468 
 PHE   0.016   0.002   PHE A 415 
 TYR   0.011   0.001   TYR C 116 
 ARG   0.005   0.001   ARG C 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05226 (  663)
  hydrogen bonds       : angle       4.83375 ( 1992)
  SS BOND              : bond        0.00895 (    3)
  SS BOND              : angle       0.69838 (    6)
  covalent geometry    : bond        0.00410 ( 8406)
  covalent geometry    : angle       0.53328 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 ASN cc_start: 0.8241 (t0) cc_final: 0.7874 (t0)
REVERT: D   74 ASN cc_start: 0.7516 (m-40) cc_final: 0.6601 (m-40)
REVERT: D  100 ASN cc_start: 0.8269 (t0) cc_final: 0.8014 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 144
  average time/residue: 0.4272
  time to fit residues: 86.6615
Evaluate side-chains
  134 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  265 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 95 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
C 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.183758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.173375 restraints weight = 28745.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.175691 restraints weight = 21839.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.176813 restraints weight = 16990.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8409  Z= 0.189
  Angle     :  0.521   5.015  11456  Z= 0.293
  Chirality :  0.038   0.148   1352
  Planarity :  0.005   0.058   1416
  Dihedral  :  5.528  42.905   1257
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 10.42 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.25), residues: 1084
  helix:  1.87 (0.19), residues: 776
  sheet:  0.51 (0.49), residues: 80
  loop :  0.59 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 178 
 HIS   0.005   0.002   HIS A 468 
 PHE   0.016   0.002   PHE C 526 
 TYR   0.012   0.001   TYR A 116 
 ARG   0.003   0.001   ARG D  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05319 (  663)
  hydrogen bonds       : angle       4.74833 ( 1992)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.75391 (    6)
  covalent geometry    : bond        0.00416 ( 8406)
  covalent geometry    : angle       0.52048 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  142 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 ASN cc_start: 0.8322 (t0) cc_final: 0.8091 (t0)
REVERT: C  126 LEU cc_start: 0.7524 (tt) cc_final: 0.7283 (tt)
  outliers start: 19
  outliers final: 15
  residues processed: 133
  average time/residue: 0.4098
  time to fit residues: 76.3959
Evaluate side-chains
  130 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain C residue  178 TRP
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  265 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  407 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   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 = 0.4045 r_free = 0.4045 target = 0.181615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.171471 restraints weight = 28795.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.173626 restraints weight = 21188.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.174721 restraints weight = 16492.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8409  Z= 0.175
  Angle     :  0.514   6.571  11456  Z= 0.286
  Chirality :  0.037   0.118   1352
  Planarity :  0.004   0.057   1416
  Dihedral  :  5.192  37.416   1257
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 10.66 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.25), residues: 1084
  helix:  2.10 (0.19), residues: 752
  sheet:  0.28 (0.47), residues: 80
  loop :  0.74 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 178 
 HIS   0.005   0.002   HIS A 468 
 PHE   0.015   0.002   PHE C 222 
 TYR   0.011   0.001   TYR A 116 
 ARG   0.003   0.000   ARG D 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05132 (  663)
  hydrogen bonds       : angle       4.64203 ( 1992)
  SS BOND              : bond        0.00057 (    3)
  SS BOND              : angle       0.25437 (    6)
  covalent geometry    : bond        0.00383 ( 8406)
  covalent geometry    : angle       0.51365 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  143 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.7634 (OUTLIER) cc_final: 0.6726 (p-90)
REVERT: C  126 LEU cc_start: 0.7503 (tt) cc_final: 0.7225 (tt)
REVERT: C  160 TYR cc_start: 0.5999 (t80) cc_final: 0.5714 (t80)
REVERT: C  178 TRP cc_start: 0.7649 (OUTLIER) cc_final: 0.6760 (p-90)
  outliers start: 23
  outliers final: 20
  residues processed: 131
  average time/residue: 0.4429
  time to fit residues: 79.0304
Evaluate side-chains
  137 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  178 TRP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  265 VAL
Chi-restraints excluded: chain C residue  342 ARG
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  407 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 103 optimal weight:    5.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.4005 r_free = 0.4005 target = 0.177606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.166895 restraints weight = 29156.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.169033 restraints weight = 21974.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.170448 restraints weight = 17460.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8409  Z= 0.229
  Angle     :  0.562   6.111  11456  Z= 0.317
  Chirality :  0.038   0.120   1352
  Planarity :  0.005   0.063   1416
  Dihedral  :  5.782  45.231   1257
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 12.01 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.25), residues: 1084
  helix:  1.90 (0.19), residues: 742
  sheet: -0.10 (0.47), residues: 80
  loop :  0.57 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 178 
 HIS   0.005   0.002   HIS C 468 
 PHE   0.024   0.002   PHE C 366 
 TYR   0.012   0.001   TYR B  60 
 ARG   0.004   0.001   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05492 (  663)
  hydrogen bonds       : angle       4.81610 ( 1992)
  SS BOND              : bond        0.00071 (    3)
  SS BOND              : angle       0.36277 (    6)
  covalent geometry    : bond        0.00516 ( 8406)
  covalent geometry    : angle       0.56250 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  144 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
REVERT: C  126 LEU cc_start: 0.7633 (tt) cc_final: 0.7372 (tt)
  outliers start: 27
  outliers final: 24
  residues processed: 132
  average time/residue: 0.4390
  time to fit residues: 79.2599
Evaluate side-chains
  138 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  178 TRP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  265 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  475 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 77 optimal weight:    0.4980
   chunk 47 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.177934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.154235 restraints weight = 29936.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.160483 restraints weight = 15272.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.164542 restraints weight = 9474.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8409  Z= 0.144
  Angle     :  0.481   4.984  11456  Z= 0.269
  Chirality :  0.036   0.124   1352
  Planarity :  0.004   0.058   1416
  Dihedral  :  5.107  35.876   1257
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 12.62 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.25), residues: 1084
  helix:  2.14 (0.19), residues: 742
  sheet: -0.04 (0.45), residues: 80
  loop :  0.61 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 468 
 PHE   0.013   0.001   PHE C 415 
 TYR   0.010   0.001   TYR C 116 
 ARG   0.003   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04955 (  663)
  hydrogen bonds       : angle       4.55471 ( 1992)
  SS BOND              : bond        0.00154 (    3)
  SS BOND              : angle       0.36644 (    6)
  covalent geometry    : bond        0.00301 ( 8406)
  covalent geometry    : angle       0.48064 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  134 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 1.241 
Fit side-chains
   revert: symmetry clash
REVERT: C  126 LEU cc_start: 0.7352 (tt) cc_final: 0.7042 (tt)
  outliers start: 22
  outliers final: 21
  residues processed: 125
  average time/residue: 0.4431
  time to fit residues: 77.1474
Evaluate side-chains
  128 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  178 TRP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  265 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  407 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 105 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.175768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152078 restraints weight = 30065.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.158049 restraints weight = 15732.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.161956 restraints weight = 9978.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8409  Z= 0.177
  Angle     :  0.512   4.935  11456  Z= 0.287
  Chirality :  0.037   0.124   1352
  Planarity :  0.004   0.060   1416
  Dihedral  :  5.466  44.117   1257
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 13.85 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.25), residues: 1084
  helix:  2.09 (0.19), residues: 740
  sheet: -0.18 (0.45), residues: 80
  loop :  0.49 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 178 
 HIS   0.004   0.002   HIS C 468 
 PHE   0.012   0.002   PHE A 526 
 TYR   0.011   0.001   TYR A 116 
 ARG   0.005   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05140 (  663)
  hydrogen bonds       : angle       4.62509 ( 1992)
  SS BOND              : bond        0.00079 (    3)
  SS BOND              : angle       0.36436 (    6)
  covalent geometry    : bond        0.00389 ( 8406)
  covalent geometry    : angle       0.51191 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  131 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
REVERT: C  126 LEU cc_start: 0.7446 (tt) cc_final: 0.7180 (tt)
  outliers start: 23
  outliers final: 22
  residues processed: 123
  average time/residue: 0.4306
  time to fit residues: 73.5316
Evaluate side-chains
  127 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain C residue  127 LEU
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  178 TRP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  475 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 103 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.177523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.153448 restraints weight = 29901.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.159666 restraints weight = 15445.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.163816 restraints weight = 9691.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8409  Z= 0.146
  Angle     :  0.483   4.862  11456  Z= 0.268
  Chirality :  0.036   0.124   1352
  Planarity :  0.004   0.058   1416
  Dihedral  :  5.084  39.840   1257
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.95 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.25), residues: 1084
  helix:  2.22 (0.19), residues: 740
  sheet: -0.17 (0.45), residues: 80
  loop :  0.55 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP C 178 
 HIS   0.003   0.001   HIS A 468 
 PHE   0.013   0.001   PHE C 415 
 TYR   0.010   0.001   TYR A 116 
 ARG   0.002   0.000   ARG C 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04875 (  663)
  hydrogen bonds       : angle       4.50781 ( 1992)
  SS BOND              : bond        0.00127 (    3)
  SS BOND              : angle       0.26124 (    6)
  covalent geometry    : bond        0.00311 ( 8406)
  covalent geometry    : angle       0.48262 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  131 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: C  126 LEU cc_start: 0.7232 (tt) cc_final: 0.6916 (tt)
  outliers start: 19
  outliers final: 19
  residues processed: 123
  average time/residue: 0.4291
  time to fit residues: 73.0225
Evaluate side-chains
  126 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain C residue  127 LEU
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  178 TRP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  475 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0970
   chunk 80 optimal weight:    0.3980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4036 r_free = 0.4036 target = 0.178316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.154082 restraints weight = 30070.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.160342 restraints weight = 15550.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.164491 restraints weight = 9751.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8409  Z= 0.137
  Angle     :  0.476   4.838  11456  Z= 0.264
  Chirality :  0.036   0.123   1352
  Planarity :  0.004   0.058   1416
  Dihedral  :  4.891  37.017   1257
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.93 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.25), residues: 1084
  helix:  2.31 (0.19), residues: 740
  sheet: -0.16 (0.46), residues: 80
  loop :  0.55 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.014   0.001   PHE C 415 
 TYR   0.019   0.001   TYR A 160 
 ARG   0.002   0.000   ARG C 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04740 (  663)
  hydrogen bonds       : angle       4.45898 ( 1992)
  SS BOND              : bond        0.00095 (    3)
  SS BOND              : angle       0.19145 (    6)
  covalent geometry    : bond        0.00289 ( 8406)
  covalent geometry    : angle       0.47630 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  129 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 1.060 
Fit side-chains
REVERT: C  126 LEU cc_start: 0.7355 (tt) cc_final: 0.7095 (tt)
  outliers start: 21
  outliers final: 19
  residues processed: 122
  average time/residue: 0.4227
  time to fit residues: 71.9642
Evaluate side-chains
  125 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  178 TRP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  475 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 78 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.176602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152466 restraints weight = 30364.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.158619 restraints weight = 15836.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.162674 restraints weight = 10006.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8409  Z= 0.160
  Angle     :  0.496   4.883  11456  Z= 0.276
  Chirality :  0.036   0.121   1352
  Planarity :  0.004   0.059   1416
  Dihedral  :  4.934  41.145   1253
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.69 %
    Favored  : 81.99 %
  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:  2.47 (0.25), residues: 1084
  helix:  2.26 (0.19), residues: 740
  sheet: -0.27 (0.47), residues: 80
  loop :  0.57 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP C 178 
 HIS   0.004   0.001   HIS C 468 
 PHE   0.013   0.002   PHE A 526 
 TYR   0.011   0.001   TYR A 116 
 ARG   0.003   0.000   ARG C 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04881 (  663)
  hydrogen bonds       : angle       4.51822 ( 1992)
  SS BOND              : bond        0.00090 (    3)
  SS BOND              : angle       0.25373 (    6)
  covalent geometry    : bond        0.00348 ( 8406)
  covalent geometry    : angle       0.49624 (11450)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS   43 is missing expected H atoms. Skipping.
Residue MET   83 is missing expected H atoms. Skipping.
Residue LYS   87 is missing expected H atoms. Skipping.
Residue LYS  120 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Residue LYS  136 is missing expected H atoms. Skipping.
Residue LYS  168 is missing expected H atoms. Skipping.
Residue LEU  229 is missing expected H atoms. Skipping.
Residue LYS  253 is missing expected H atoms. Skipping.
Residue MET  271 is missing expected H atoms. Skipping.
Residue LEU  276 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  284 is missing expected H atoms. Skipping.
Residue LYS  285 is missing expected H atoms. Skipping.
Residue LYS  297 is missing expected H atoms. Skipping.
Residue THR  300 is missing expected H atoms. Skipping.
Residue MET  306 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LEU  376 is missing expected H atoms. Skipping.
Residue LYS  491 is missing expected H atoms. Skipping.
Evaluate side-chains
  126 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 1.212 
Fit side-chains
REVERT: B  102 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7642 (mtm-85)
REVERT: C  126 LEU cc_start: 0.7379 (tt) cc_final: 0.7126 (tt)
  outliers start: 19
  outliers final: 19
  residues processed: 121
  average time/residue: 0.3967
  time to fit residues: 67.8785
Evaluate side-chains
  124 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  178 TRP
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  475 SER
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  178 TRP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  407 SER
Chi-restraints excluded: chain C residue  475 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.176340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.151920 restraints weight = 30394.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.158116 restraints weight = 15753.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.162212 restraints weight = 9929.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8409  Z= 0.165
  Angle     :  0.501   4.871  11456  Z= 0.279
  Chirality :  0.036   0.120   1352
  Planarity :  0.004   0.059   1416
  Dihedral  :  5.058  46.050   1253
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.56 %
    Favored  : 81.99 %
  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:  2.43 (0.25), residues: 1084
  helix:  2.24 (0.19), residues: 740
  sheet: -0.41 (0.47), residues: 80
  loop :  0.59 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP C 178 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.012   0.002   PHE C 415 
 TYR   0.012   0.001   TYR A 160 
 ARG   0.003   0.000   ARG C 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04911 (  663)
  hydrogen bonds       : angle       4.54526 ( 1992)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       0.24254 (    6)
  covalent geometry    : bond        0.00360 ( 8406)
  covalent geometry    : angle       0.50094 (11450)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5180.70 seconds
wall clock time: 89 minutes 31.31 seconds (5371.31 seconds total)