Starting phenix.real_space_refine
on Tue Mar  3 17:10:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ct2_26978/03_2026/8ct2_26978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ct2_26978/03_2026/8ct2_26978.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ct2_26978/03_2026/8ct2_26978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ct2_26978/03_2026/8ct2_26978.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ct2_26978/03_2026/8ct2_26978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ct2_26978/03_2026/8ct2_26978.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.169
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    4884      2.51       5
     N    1264      2.21       5
     O    1296      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7464
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "D"
      Number of atoms: 1838
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 247, 1827
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
      Conformer: "B"
        Number of residues, atoms: 247, 1827
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
          bond proxies already assigned to first conformer: 1850
    Chain: "B"
      Number of atoms: 1838
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 247, 1827
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
      Conformer: "B"
        Number of residues, atoms: 247, 1827
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
          bond proxies already assigned to first conformer: 1850
    Chain: "C"
      Number of atoms: 1838
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 247, 1827
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
      Conformer: "B"
        Number of residues, atoms: 247, 1827
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
          bond proxies already assigned to first conformer: 1850
    Chain: "A"
      Number of atoms: 1838
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 247, 1827
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
      Conformer: "B"
        Number of residues, atoms: 247, 1827
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
          bond proxies already assigned to first conformer: 1850
    Chain: "D"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AARG D 234 " occ=0.48
      ... (20 atoms not shown)
      pdb=" NH2BARG D 234 " occ=0.52
    residue:
      pdb=" N  AARG B 234 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 234 " occ=0.50
    residue:
      pdb=" N  AARG C 234 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C 234 " occ=0.50
    residue:
      pdb=" N  AARG A 234 " occ=0.51
      ... (20 atoms not shown)
      pdb=" NH2BARG A 234 " occ=0.49
  Time building chain proxies: 3.00, per 1000 atoms: 0.40
  Number of scatterers: 7464
  At special positions: 0
  Unit cell: (88.81, 89.64, 90.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1296      8.00
     N    1264      7.00
     C    4884      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 0.59
  Conformation dependent library (CDL) restraints added in 467.6 milliseconds
  

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      76.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'D' and resid 3 through 6
    Processing helix  chain 'D' and resid 7 through 33
      removed outlier: 3.575A  pdb=" N   TRP D  11 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 37
    Processing helix  chain 'D' and resid 48 through 72
      removed outlier: 5.754A  pdb=" N   HIS D  69 " --> pdb=" O   GLN D  65 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   ILE D  70 " --> pdb=" O   SER D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 86
    Processing helix  chain 'D' and resid 90 through 116
    Processing helix  chain 'D' and resid 134 through 157
    Processing helix  chain 'D' and resid 167 through 188
      removed outlier: 5.736A  pdb=" N   ASP D 185 " --> pdb=" O   LEU D 181 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   TYR D 186 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 192 through 204
      removed outlier: 3.511A  pdb=" N   SER D 199 " --> pdb=" O   ARG D 195 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 230
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 237 through 248
      removed outlier: 3.676A  pdb=" N   LYS D 243 " --> pdb=" O   THR D 239 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   VAL D 244 " --> pdb=" O   ASP D 240 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TRP D 245 " --> pdb=" O   ARG D 241 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   THR D 246 " --> pdb=" O   VAL D 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 6
      removed outlier: 3.603A  pdb=" N   LYS B   6 " --> pdb=" O   SER B   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 3 through 6'
    Processing helix  chain 'B' and resid 7 through 33
      removed outlier: 3.591A  pdb=" N   TRP B  11 " --> pdb=" O   LYS B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 37
    Processing helix  chain 'B' and resid 48 through 72
      removed outlier: 5.931A  pdb=" N   HIS B  69 " --> pdb=" O   GLN B  65 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   ILE B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 86
    Processing helix  chain 'B' and resid 90 through 116
    Processing helix  chain 'B' and resid 134 through 157
    Processing helix  chain 'B' and resid 167 through 188
      removed outlier: 5.706A  pdb=" N   ASP B 185 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   TYR B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 204
      removed outlier: 3.586A  pdb=" N   SER B 199 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 230
      Proline residue:  B 216  - end of helix
    Processing helix  chain 'B' and resid 237 through 248
      removed outlier: 4.231A  pdb=" N   VAL B 244 " --> pdb=" O   ASP B 240 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   TRP B 245 " --> pdb=" O   ARG B 241 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR B 246 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 6
      removed outlier: 3.501A  pdb=" N   LYS C   6 " --> pdb=" O   SER C   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 3 through 6'
    Processing helix  chain 'C' and resid 7 through 33
      removed outlier: 3.770A  pdb=" N   TRP C  11 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 37
    Processing helix  chain 'C' and resid 48 through 72
      removed outlier: 6.024A  pdb=" N   HIS C  69 " --> pdb=" O   GLN C  65 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   ILE C  70 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 86
    Processing helix  chain 'C' and resid 90 through 116
    Processing helix  chain 'C' and resid 134 through 157
    Processing helix  chain 'C' and resid 167 through 188
      removed outlier: 5.637A  pdb=" N   ASP C 185 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   TYR C 186 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 204
      removed outlier: 3.791A  pdb=" N   SER C 199 " --> pdb=" O   ARG C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 230
      Proline residue:  C 216  - end of helix
    Processing helix  chain 'C' and resid 237 through 248
      removed outlier: 3.728A  pdb=" N   LYS C 243 " --> pdb=" O   THR C 239 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   VAL C 244 " --> pdb=" O   ASP C 240 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   TRP C 245 " --> pdb=" O   ARG C 241 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   THR C 246 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3 through 6
    Processing helix  chain 'A' and resid 7 through 33
      removed outlier: 3.505A  pdb=" N   TRP A  11 " --> pdb=" O   LYS A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 37
    Processing helix  chain 'A' and resid 48 through 72
      removed outlier: 5.902A  pdb=" N   HIS A  69 " --> pdb=" O   GLN A  65 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   ILE A  70 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 86
    Processing helix  chain 'A' and resid 90 through 116
    Processing helix  chain 'A' and resid 134 through 157
    Processing helix  chain 'A' and resid 167 through 188
      removed outlier: 5.609A  pdb=" N   ASP A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   TYR A 186 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 204
      removed outlier: 3.557A  pdb=" N   SER A 199 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 230
      Proline residue:  A 216  - end of helix
    Processing helix  chain 'A' and resid 237 through 248
      removed outlier: 3.705A  pdb=" N   LYS A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   VAL A 244 " --> pdb=" O   ASP A 240 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   TRP A 245 " --> pdb=" O   ARG A 241 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   THR A 246 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)

    539 hydrogen bonds defined for protein.
    1599 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2372
        1.34 -     1.46: 1302
        1.46 -     1.57: 3918
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 7620
  Sorted by residual:
  bond pdb=" N   ASN C 192 "
       pdb=" CA  ASN C 192 "
    ideal  model  delta    sigma   weight residual
    1.463  1.450  0.013 8.80e-03 1.29e+04 2.09e+00
  bond pdb=" N   ASN A 192 "
       pdb=" CA  ASN A 192 "
    ideal  model  delta    sigma   weight residual
    1.463  1.451  0.012 8.80e-03 1.29e+04 1.78e+00
  bond pdb=" N   ASN B 192 "
       pdb=" CA  ASN B 192 "
    ideal  model  delta    sigma   weight residual
    1.463  1.452  0.010 8.80e-03 1.29e+04 1.39e+00
  bond pdb=" CG  LEU D 112 "
       pdb=" CD2 LEU D 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.62e-01
  bond pdb=" C   ALA C 168 "
       pdb=" N   PRO C 169 "
    ideal  model  delta    sigma   weight residual
    1.335  1.349 -0.013 1.36e-02 5.41e+03 9.49e-01
  ... (remaining 7615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 10197
        1.76 -     3.51: 150
        3.51 -     5.27: 37
        5.27 -     7.03: 6
        7.03 -     8.79: 2
  Bond angle restraints: 10392
  Sorted by residual:
  angle pdb=" C   ILE A 191 "
        pdb=" N   ASN A 192 "
        pdb=" CA  ASN A 192 "
      ideal   model   delta    sigma   weight residual
     122.26  126.52   -4.26 1.10e+00 8.26e-01 1.50e+01
  angle pdb=" CA  CYS D 189 "
        pdb=" CB  CYS D 189 "
        pdb=" SG  CYS D 189 "
      ideal   model   delta    sigma   weight residual
     114.40  105.61    8.79 2.30e+00 1.89e-01 1.46e+01
  angle pdb=" C   ILE B 191 "
        pdb=" N   ASN B 192 "
        pdb=" CA  ASN B 192 "
      ideal   model   delta    sigma   weight residual
     122.26  126.18   -3.92 1.10e+00 8.26e-01 1.27e+01
  angle pdb=" C   ILE C 191 "
        pdb=" N   ASN C 192 "
        pdb=" CA  ASN C 192 "
      ideal   model   delta    sigma   weight residual
     122.26  126.14   -3.88 1.10e+00 8.26e-01 1.24e+01
  angle pdb=" C   ASP D 158 "
        pdb=" N   ARG D 159 "
        pdb=" CA  ARG D 159 "
      ideal   model   delta    sigma   weight residual
     121.54  126.21   -4.67 1.91e+00 2.74e-01 5.99e+00
  ... (remaining 10387 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4293
       17.91 -    35.82: 225
       35.82 -    53.73: 46
       53.73 -    71.64: 14
       71.64 -    89.56: 6
  Dihedral angle restraints: 4584
    sinusoidal: 1808
      harmonic: 2776
  Sorted by residual:
  dihedral pdb=" CA  LEU B 182 "
           pdb=" C   LEU B 182 "
           pdb=" N   ALA B 183 "
           pdb=" CA  ALA B 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.02  -23.98     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  LEU A 182 "
           pdb=" C   LEU A 182 "
           pdb=" N   ALA A 183 "
           pdb=" CA  ALA A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.53  -22.47     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  LEU D 182 "
           pdb=" C   LEU D 182 "
           pdb=" N   ALA D 183 "
           pdb=" CA  ALA D 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.33  -21.67     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 4581 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 892
       0.042 -    0.083: 324
       0.083 -    0.125: 47
       0.125 -    0.166: 4
       0.166 -    0.208: 1
  Chirality restraints: 1268
  Sorted by residual:
  chirality pdb=" CA  CYS D 189 "
            pdb=" N   CYS D 189 "
            pdb=" C   CYS D 189 "
            pdb=" CB  CYS D 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CB  ILE D 191 "
            pdb=" CA  ILE D 191 "
            pdb=" CG1 ILE D 191 "
            pdb=" CG2 ILE D 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.25e-01
  chirality pdb=" CB  ILE B 191 "
            pdb=" CA  ILE B 191 "
            pdb=" CG1 ILE B 191 "
            pdb=" CG2 ILE B 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.03e-01
  ... (remaining 1265 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 215 "    0.036 5.00e-02 4.00e+02   5.43e-02 4.71e+00
        pdb=" N   PRO D 216 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO D 216 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D 216 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 215 "   -0.035 5.00e-02 4.00e+02   5.30e-02 4.50e+00
        pdb=" N   PRO C 216 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO C 216 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 216 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 215 "   -0.034 5.00e-02 4.00e+02   5.10e-02 4.15e+00
        pdb=" N   PRO A 216 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 216 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 216 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 841
        2.75 -     3.29: 7691
        3.29 -     3.82: 13489
        3.82 -     4.36: 16014
        4.36 -     4.90: 27417
  Nonbonded interactions: 65452
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 152 "
            pdb=" OG1 THR B 156 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   CYS C 152 "
            pdb=" OG1 THR C 156 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" NZ  LYS D  51 "
            pdb=" OD2 ASP B 185 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" O   ASN A  49 "
            pdb=" OG  SER A  53 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OD1 ASN C 127 "
            pdb=" OG  SER C 196 "
     model   vdw
     2.300 3.040
  ... (remaining 65447 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' and (resid 3 through 233 or resid 235 through 249))
  selection = (chain 'B' and (resid 3 through 233 or resid 235 through 249))
  selection = (chain 'C' and (resid 3 through 233 or resid 235 through 249))
  selection = (chain 'D' and (resid 3 through 233 or resid 235 through 249))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.790
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
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      :  0.004   0.033   7620  Z= 0.174
  Angle     :  0.611   8.785  10392  Z= 0.330
  Chirality :  0.041   0.208   1268
  Planarity :  0.005   0.054   1272
  Dihedral  : 12.297  89.556   2816
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.58 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  5.81 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.26), residues: 980
  helix:  1.64 (0.20), residues: 616
  sheet:  None (None), residues: 0
  loop : -0.04 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 160 
 TYR   0.010   0.002   TYR A 227 
 PHE   0.013   0.002   PHE A 212 
 TRP   0.011   0.001   TRP D  11 
 HIS   0.008   0.002   HIS D 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7620)
  covalent geometry    : angle       0.61080 (10392)
  hydrogen bonds       : bond        0.10342 (  539)
  hydrogen bonds       : angle       6.51744 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.285 
Fit side-chains
REVERT: D  123 SER cc_start: 0.8361 (p) cc_final: 0.8117 (t)
REVERT: B  172 ILE cc_start: 0.8790 (mm) cc_final: 0.8435 (mt)
REVERT: C   95 LEU cc_start: 0.8483 (tp) cc_final: 0.8039 (mp)
REVERT: A  123 SER cc_start: 0.7644 (p) cc_final: 0.7411 (m)
REVERT: A  159 ARG cc_start: 0.6977 (mtm180) cc_final: 0.6694 (mtm180)
  outliers start: 15
  outliers final: 6
  residues processed: 112
  average time/residue: 0.0602
  time to fit residues: 10.1806
Evaluate side-chains
  99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain A residue  191 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
D 127 ASN
A  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.129430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.104611 restraints weight = 39247.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 3.49
r_work: 0.2850 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.0714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7620  Z= 0.152
  Angle     :  0.558   8.662  10392  Z= 0.288
  Chirality :  0.040   0.194   1268
  Planarity :  0.005   0.050   1272
  Dihedral  :  8.275  59.550   1380
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.79 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  8.24 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.27), residues: 980
  helix:  1.93 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.04 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 241 
 TYR   0.009   0.001   TYR A 227 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.011   0.001   TRP B  11 
 HIS   0.006   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7620)
  covalent geometry    : angle       0.55795 (10392)
  hydrogen bonds       : bond        0.04477 (  539)
  hydrogen bonds       : angle       5.30716 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.257 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8348 (mp)
REVERT: B  172 ILE cc_start: 0.8798 (mm) cc_final: 0.8479 (mt)
REVERT: C   95 LEU cc_start: 0.8472 (tp) cc_final: 0.8018 (mp)
REVERT: A  123 SER cc_start: 0.7628 (p) cc_final: 0.7357 (m)
  outliers start: 12
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0621
  time to fit residues: 9.5069
Evaluate side-chains
  101 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue  246 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 8 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 78 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.133636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.109018 restraints weight = 33071.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 3.06
r_work: 0.2906 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7620  Z= 0.111
  Angle     :  0.512   7.853  10392  Z= 0.264
  Chirality :  0.038   0.183   1268
  Planarity :  0.004   0.047   1272
  Dihedral  :  7.335  57.903   1375
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.69 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.51 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.27), residues: 980
  helix:  2.27 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.15 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 160 
 TYR   0.006   0.001   TYR B 227 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.011   0.001   TRP B  11 
 HIS   0.005   0.001   HIS D 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7620)
  covalent geometry    : angle       0.51187 (10392)
  hydrogen bonds       : bond        0.03727 (  539)
  hydrogen bonds       : angle       5.00625 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.191 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7942 (mp)
REVERT: B   91 ILE cc_start: 0.8423 (mt) cc_final: 0.8026 (tt)
REVERT: C   95 LEU cc_start: 0.8381 (tp) cc_final: 0.7940 (mp)
REVERT: C  124 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8047 (mt)
REVERT: A  123 SER cc_start: 0.7604 (p) cc_final: 0.7344 (m)
  outliers start: 11
  outliers final: 4
  residues processed: 103
  average time/residue: 0.0519
  time to fit residues: 8.2376
Evaluate side-chains
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain A residue  246 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0370
   chunk 79 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 68 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.134466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.109368 restraints weight = 26307.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.72
r_work: 0.2946 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7620  Z= 0.110
  Angle     :  0.499   7.497  10392  Z= 0.259
  Chirality :  0.038   0.180   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  7.066  58.766   1374
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.69 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  8.38 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.27), residues: 980
  helix:  2.49 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.09 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 160 
 TYR   0.006   0.001   TYR A 227 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.010   0.001   TRP D  11 
 HIS   0.005   0.001   HIS D 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 7620)
  covalent geometry    : angle       0.49862 (10392)
  hydrogen bonds       : bond        0.03679 (  539)
  hydrogen bonds       : angle       4.90723 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.260 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7878 (mp)
REVERT: B   91 ILE cc_start: 0.8396 (mt) cc_final: 0.8030 (tt)
REVERT: C   95 LEU cc_start: 0.8330 (tp) cc_final: 0.7925 (mp)
REVERT: A  123 SER cc_start: 0.7624 (p) cc_final: 0.7361 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 98
  average time/residue: 0.0580
  time to fit residues: 8.7184
Evaluate side-chains
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue  246 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.133906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.108928 restraints weight = 30477.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.98
r_work: 0.2930 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7620  Z= 0.117
  Angle     :  0.512   7.553  10392  Z= 0.266
  Chirality :  0.038   0.182   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  7.030  57.829   1374
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.58 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  8.38 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.28), residues: 980
  helix:  2.51 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.11 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 160 
 TYR   0.007   0.001   TYR A 227 
 PHE   0.011   0.001   PHE A 212 
 TRP   0.009   0.001   TRP D  11 
 HIS   0.005   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 7620)
  covalent geometry    : angle       0.51182 (10392)
  hydrogen bonds       : bond        0.03768 (  539)
  hydrogen bonds       : angle       4.90593 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.254 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7867 (mp)
REVERT: B   91 ILE cc_start: 0.8416 (mt) cc_final: 0.8056 (tt)
REVERT: C   95 LEU cc_start: 0.8382 (tp) cc_final: 0.7969 (mp)
REVERT: A  123 SER cc_start: 0.7656 (p) cc_final: 0.7398 (m)
  outliers start: 13
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0578
  time to fit residues: 8.3069
Evaluate side-chains
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue  246 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.132218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.107546 restraints weight = 33721.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.11
r_work: 0.2895 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7620  Z= 0.132
  Angle     :  0.523   7.839  10392  Z= 0.272
  Chirality :  0.039   0.187   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  7.159  58.592   1374
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.58 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  8.51 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.28), residues: 980
  helix:  2.46 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.12 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 160 
 TYR   0.009   0.001   TYR A 227 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.009   0.001   TRP D  11 
 HIS   0.006   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7620)
  covalent geometry    : angle       0.52285 (10392)
  hydrogen bonds       : bond        0.04033 (  539)
  hydrogen bonds       : angle       4.95366 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.230 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7978 (mp)
REVERT: B   91 ILE cc_start: 0.8417 (mt) cc_final: 0.8032 (tt)
REVERT: C   95 LEU cc_start: 0.8418 (tp) cc_final: 0.7993 (mp)
REVERT: A  123 SER cc_start: 0.7651 (p) cc_final: 0.7408 (m)
  outliers start: 13
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0602
  time to fit residues: 8.4073
Evaluate side-chains
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue  246 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.131086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.105593 restraints weight = 32703.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 3.15
r_work: 0.2858 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7620  Z= 0.142
  Angle     :  0.534   8.030  10392  Z= 0.277
  Chirality :  0.039   0.190   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  7.305  59.266   1374
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.58 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  8.65 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.28), residues: 980
  helix:  2.38 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.16 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 160 
 TYR   0.010   0.001   TYR A 227 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.009   0.001   TRP D  11 
 HIS   0.006   0.001   HIS A 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7620)
  covalent geometry    : angle       0.53403 (10392)
  hydrogen bonds       : bond        0.04208 (  539)
  hydrogen bonds       : angle       5.00911 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.264 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8088 (mp)
REVERT: B   91 ILE cc_start: 0.8414 (mt) cc_final: 0.8007 (tt)
REVERT: B  172 ILE cc_start: 0.8798 (mm) cc_final: 0.8448 (mt)
REVERT: C   95 LEU cc_start: 0.8443 (tp) cc_final: 0.8010 (mp)
REVERT: A  123 SER cc_start: 0.7634 (p) cc_final: 0.7393 (m)
  outliers start: 14
  outliers final: 9
  residues processed: 91
  average time/residue: 0.0519
  time to fit residues: 7.0967
Evaluate side-chains
  95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue  191 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  246 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    0.0060
   chunk 22 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
D 127 ASN
A  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.134800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.110367 restraints weight = 34072.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 3.10
r_work: 0.2938 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7620  Z= 0.111
  Angle     :  0.507   8.778  10392  Z= 0.261
  Chirality :  0.038   0.181   1268
  Planarity :  0.004   0.045   1272
  Dihedral  :  6.808  57.401   1374
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.79 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.05 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.28), residues: 980
  helix:  2.62 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.17 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 160 
 TYR   0.006   0.001   TYR B 227 
 PHE   0.010   0.001   PHE A 212 
 TRP   0.009   0.001   TRP D  11 
 HIS   0.005   0.001   HIS D 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 7620)
  covalent geometry    : angle       0.50727 (10392)
  hydrogen bonds       : bond        0.03662 (  539)
  hydrogen bonds       : angle       4.87009 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B   91 ILE cc_start: 0.8408 (mt) cc_final: 0.8028 (tt)
REVERT: C   95 LEU cc_start: 0.8364 (tp) cc_final: 0.7948 (mp)
REVERT: A  123 SER cc_start: 0.7577 (p) cc_final: 0.7348 (m)
  outliers start: 11
  outliers final: 8
  residues processed: 95
  average time/residue: 0.0626
  time to fit residues: 8.8836
Evaluate side-chains
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  246 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 55 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 66 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.132257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.107644 restraints weight = 34463.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 3.10
r_work: 0.2895 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2872
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2872 r_free = 0.2872    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2872 r_free = 0.2872    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2872
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7620  Z= 0.133
  Angle     :  0.530   8.818  10392  Z= 0.272
  Chirality :  0.039   0.192   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  6.967  58.631   1372
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.58 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.46 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.28), residues: 980
  helix:  2.54 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.21 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 160 
 TYR   0.009   0.001   TYR A 227 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.009   0.001   TRP D  11 
 HIS   0.006   0.001   HIS D 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7620)
  covalent geometry    : angle       0.52969 (10392)
  hydrogen bonds       : bond        0.04049 (  539)
  hydrogen bonds       : angle       4.92860 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.245 
Fit side-chains
REVERT: B   91 ILE cc_start: 0.8420 (mt) cc_final: 0.8027 (tt)
REVERT: C   95 LEU cc_start: 0.8427 (tp) cc_final: 0.7999 (mp)
REVERT: A  123 SER cc_start: 0.7630 (p) cc_final: 0.7396 (m)
  outliers start: 9
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0701
  time to fit residues: 9.6896
Evaluate side-chains
  94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue   83 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0970
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.134460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.109039 restraints weight = 29226.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 3.04
r_work: 0.2919 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7620  Z= 0.111
  Angle     :  0.509   8.924  10392  Z= 0.261
  Chirality :  0.038   0.182   1268
  Planarity :  0.004   0.045   1272
  Dihedral  :  6.732  57.172   1372
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.89 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.73 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.28), residues: 980
  helix:  2.64 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.18 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 160 
 TYR   0.006   0.001   TYR A 227 
 PHE   0.011   0.001   PHE A 212 
 TRP   0.010   0.001   TRP D  11 
 HIS   0.005   0.001   HIS D 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 7620)
  covalent geometry    : angle       0.50902 (10392)
  hydrogen bonds       : bond        0.03713 (  539)
  hydrogen bonds       : angle       4.86343 ( 1599)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B   91 ILE cc_start: 0.8417 (mt) cc_final: 0.8037 (tt)
REVERT: C   95 LEU cc_start: 0.8374 (tp) cc_final: 0.7955 (mp)
REVERT: A  123 SER cc_start: 0.7585 (p) cc_final: 0.7361 (m)
  outliers start: 7
  outliers final: 7
  residues processed: 93
  average time/residue: 0.0648
  time to fit residues: 9.0266
Evaluate side-chains
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  246 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0770
   chunk 4 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.8142

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.135006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.109780 restraints weight = 32909.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 3.05
r_work: 0.2908 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7620  Z= 0.112
  Angle     :  0.509   9.042  10392  Z= 0.261
  Chirality :  0.038   0.181   1268
  Planarity :  0.004   0.045   1272
  Dihedral  :  6.628  57.677   1372
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.58 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.32 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.28), residues: 980
  helix:  2.70 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.17 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 160 
 TYR   0.007   0.001   TYR A 227 
 PHE   0.010   0.001   PHE A 212 
 TRP   0.009   0.001   TRP D  11 
 HIS   0.005   0.001   HIS D 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 7620)
  covalent geometry    : angle       0.50900 (10392)
  hydrogen bonds       : bond        0.03685 (  539)
  hydrogen bonds       : angle       4.82700 ( 1599)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2000.41 seconds
wall clock time: 34 minutes 57.47 seconds (2097.47 seconds total)