Starting phenix.real_space_refine
on Wed Mar 12 06:23:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ct2_26978/03_2025/8ct2_26978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ct2_26978/03_2025/8ct2_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ct2_26978/03_2025/8ct2_26978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ct2_26978/03_2025/8ct2_26978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ct2_26978/03_2025/8ct2_26978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ct2_26978/03_2025/8ct2_26978.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2}
          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: 11.23, per 1000 atoms: 1.50
  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: 2.23
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 0.67
  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: 2.04

  Time building geometry restraints manager: 2.59 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: 0.02
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:             1.700
  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:             0.000
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     29.570
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.110
-------------------------------------------------------------------------------
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= 0.249
  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 (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:  1.50 (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
 TRP   0.011   0.001   TRP D  11 
 HIS   0.008   0.002   HIS D 180 
 PHE   0.013   0.002   PHE A 212 
 TYR   0.010   0.002   TYR A 227 
 ARG   0.002   0.000   ARG C 160 

*********************** 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  : 0.690 
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: 0.1414
  time to fit residues: 23.4199
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  : 0.853 
-------------------------------------------------------------------------------
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 81 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3321 r_free = 0.3321 target = 0.127950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.102484 restraints weight = 25510.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.66
r_work: 0.2856 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.0708

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= 0.267
  Angle     :  0.585   8.635  10392  Z= 0.302
  Chirality :  0.041   0.200   1268
  Planarity :  0.005   0.051   1272
  Dihedral  :  8.495  59.288   1380
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.79 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  7.97 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  1.71 (0.28), residues: 980
  helix:  1.80 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.07 (0.38), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  11 
 HIS   0.007   0.001   HIS A 180 
 PHE   0.016   0.002   PHE A 212 
 TYR   0.010   0.002   TYR A 227 
 ARG   0.003   0.000   ARG C 241 

*********************** 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
  110 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.866 
Fit side-chains
REVERT: D  123 SER cc_start: 0.8315 (p) cc_final: 0.8088 (t)
REVERT: D  191 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8427 (mp)
REVERT: B  172 ILE cc_start: 0.8790 (mm) cc_final: 0.8486 (mt)
REVERT: C   95 LEU cc_start: 0.8474 (tp) cc_final: 0.8007 (mp)
REVERT: A  123 SER cc_start: 0.7633 (p) cc_final: 0.7364 (m)
  outliers start: 13
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1480
  time to fit residues: 22.4320
Evaluate side-chains
  104 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
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  187 THR
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 68 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 5 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3356 r_free = 0.3356 target = 0.131006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.106219 restraints weight = 23365.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.55
r_work: 0.2909 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2889
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.0919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7620  Z= 0.179
  Angle     :  0.525   8.013  10392  Z= 0.272
  Chirality :  0.039   0.190   1268
  Planarity :  0.004   0.049   1272
  Dihedral  :  7.704  59.983   1375
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.79 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  8.92 %
    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 (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:  1.99 (0.27), residues: 980
  helix:  2.09 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.18 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  11 
 HIS   0.006   0.001   HIS D 180 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.007   0.001   TYR A 227 
 ARG   0.003   0.000   ARG C 160 

*********************** 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
  107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.705 
Fit side-chains
REVERT: D  128 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8218 (m-30)
REVERT: D  191 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8257 (mp)
REVERT: B  172 ILE cc_start: 0.8764 (mm) cc_final: 0.8398 (mt)
REVERT: C   95 LEU cc_start: 0.8406 (tp) cc_final: 0.7971 (mp)
REVERT: C  124 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8030 (mt)
REVERT: A  123 SER cc_start: 0.7561 (p) cc_final: 0.7306 (m)
  outliers start: 13
  outliers final: 4
  residues processed: 101
  average time/residue: 0.1363
  time to fit residues: 20.9469
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  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  128 ASP
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  201 VAL
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 60 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0970
   chunk 82 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 = 0.134547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.109905 restraints weight = 24177.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.59
r_work: 0.2958 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7620  Z= 0.141
  Angle     :  0.497   7.512  10392  Z= 0.256
  Chirality :  0.038   0.181   1268
  Planarity :  0.004   0.047   1272
  Dihedral  :  7.125  57.596   1374
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.79 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  8.65 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  2.36 (0.28), residues: 980
  helix:  2.42 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.13 (0.37), residues: 336

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

*********************** 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
  104 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.759 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7875 (mp)
REVERT: B   91 ILE cc_start: 0.8376 (mt) cc_final: 0.8000 (tt)
REVERT: C   95 LEU cc_start: 0.8323 (tp) cc_final: 0.8004 (mp)
REVERT: A  123 SER cc_start: 0.7546 (p) cc_final: 0.7291 (m)
  outliers start: 13
  outliers final: 7
  residues processed: 99
  average time/residue: 0.1339
  time to fit residues: 20.2219
Evaluate side-chains
  94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 11 optimal weight:    0.0050
   chunk 32 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0980
   overall best weight:    3.0200

-------------------------------------------------------------------------------
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 = 0.3310 r_free = 0.3310 target = 0.127023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.101739 restraints weight = 25450.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 2.65
r_work: 0.2845 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    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 = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7620  Z= 0.321
  Angle     :  0.599   8.687  10392  Z= 0.312
  Chirality :  0.042   0.205   1268
  Planarity :  0.005   0.049   1272
  Dihedral  :  8.138  58.316   1374
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.48 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  8.24 %
    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 (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:  1.83 (0.28), residues: 980
  helix:  1.99 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.28 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  11 
 HIS   0.007   0.001   HIS A 180 
 PHE   0.017   0.002   PHE A 212 
 TYR   0.013   0.002   TYR A 227 
 ARG   0.002   0.000   ARG C 160 

*********************** 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
  107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.698 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8331 (mp)
REVERT: B  172 ILE cc_start: 0.8806 (mm) cc_final: 0.8487 (mt)
REVERT: C   95 LEU cc_start: 0.8493 (tp) cc_final: 0.8045 (mp)
REVERT: A  123 SER cc_start: 0.7670 (p) cc_final: 0.7422 (m)
  outliers start: 13
  outliers final: 8
  residues processed: 98
  average time/residue: 0.1571
  time to fit residues: 22.8397
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  : 0.747 
-------------------------------------------------------------------------------
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  246 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0870
   chunk 16 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.7560

-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.133545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.108618 restraints weight = 30220.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.81
r_work: 0.2911 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1267

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= 0.151
  Angle     :  0.509   7.589  10392  Z= 0.267
  Chirality :  0.038   0.185   1268
  Planarity :  0.004   0.047   1272
  Dihedral  :  7.203  59.414   1374
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.79 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.05 %
    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 (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:  2.33 (0.28), residues: 980
  helix:  2.45 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.24 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  11 
 HIS   0.005   0.001   HIS D 180 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.006   0.001   TYR B 227 
 ARG   0.004   0.000   ARG C 160 

*********************** 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
  98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.704 
Fit side-chains
REVERT: D  191 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7890 (mp)
REVERT: B   91 ILE cc_start: 0.8409 (mt) cc_final: 0.7997 (tt)
REVERT: C   95 LEU cc_start: 0.8381 (tp) cc_final: 0.8011 (mp)
REVERT: A  123 SER cc_start: 0.7566 (p) cc_final: 0.7329 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 94
  average time/residue: 0.1505
  time to fit residues: 21.2391
Evaluate side-chains
  95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
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  118 SER
Chi-restraints excluded: chain B residue  191 ILE
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 78 optimal weight:    5.9990
   chunk 22 optimal weight:    0.3980
   chunk 88 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0020
   chunk 76 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6588

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.135144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.109682 restraints weight = 27195.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.79
r_work: 0.2949 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7620  Z= 0.142
  Angle     :  0.505   9.385  10392  Z= 0.262
  Chirality :  0.037   0.180   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  6.803  57.502   1374
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.58 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  9.32 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  2.54 (0.28), residues: 980
  helix:  2.64 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.22 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  11 
 HIS   0.005   0.001   HIS D 180 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.006   0.001   TYR A 227 
 ARG   0.004   0.000   ARG C 160 

*********************** 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
  96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.751 
Fit side-chains
REVERT: B   91 ILE cc_start: 0.8383 (mt) cc_final: 0.8018 (tt)
REVERT: C   95 LEU cc_start: 0.8330 (tp) cc_final: 0.8001 (mp)
REVERT: A  123 SER cc_start: 0.7540 (p) cc_final: 0.7311 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1455
  time to fit residues: 19.7425
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  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 11 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 = 0.3338 r_free = 0.3338 target = 0.129126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.104077 restraints weight = 38341.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 3.55
r_work: 0.2844 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    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 = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7620  Z= 0.245
  Angle     :  0.566   8.468  10392  Z= 0.294
  Chirality :  0.040   0.202   1268
  Planarity :  0.004   0.047   1272
  Dihedral  :  7.502  59.665   1372
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.79 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.05 %
    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 (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:  2.14 (0.28), residues: 980
  helix:  2.27 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.27 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  11 
 HIS   0.006   0.001   HIS A 180 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A 227 
 ARG   0.004   0.000   ARG C 160 

*********************** 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
  101 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.736 
Fit side-chains
REVERT: B  172 ILE cc_start: 0.8803 (mm) cc_final: 0.8463 (mt)
REVERT: C   95 LEU cc_start: 0.8482 (tp) cc_final: 0.8038 (mp)
REVERT: A  123 SER cc_start: 0.7655 (p) cc_final: 0.7409 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 95
  average time/residue: 0.1511
  time to fit residues: 20.8628
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  : 0.685 
-------------------------------------------------------------------------------
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  201 VAL
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue   83 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3372 r_free = 0.3372 target = 0.132206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.106929 restraints weight = 31049.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.94
r_work: 0.2870 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7620  Z= 0.169
  Angle     :  0.523   8.516  10392  Z= 0.271
  Chirality :  0.038   0.190   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  7.080  58.110   1372
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.79 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.19 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  2.32 (0.28), residues: 980
  helix:  2.46 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.28 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  11 
 HIS   0.005   0.001   HIS D 180 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 227 
 ARG   0.003   0.000   ARG C 160 

*********************** 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
  97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.711 
Fit side-chains
REVERT: B   91 ILE cc_start: 0.8432 (mt) cc_final: 0.8015 (tt)
REVERT: C   95 LEU cc_start: 0.8423 (tp) cc_final: 0.7997 (mp)
REVERT: A  123 SER cc_start: 0.7586 (p) cc_final: 0.7349 (m)
  outliers start: 9
  outliers final: 8
  residues processed: 92
  average time/residue: 0.1487
  time to fit residues: 20.3404
Evaluate side-chains
  95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   83 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    0.2980
   chunk 81 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.131949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.106559 restraints weight = 31944.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 3.10
r_work: 0.2872 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1270

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= 0.177
  Angle     :  0.526   8.520  10392  Z= 0.273
  Chirality :  0.038   0.190   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  7.083  58.451   1372
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  2.69 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.05 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  2.32 (0.28), residues: 980
  helix:  2.47 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.29 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  11 
 HIS   0.006   0.001   HIS D 180 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 227 
 ARG   0.003   0.000   ARG C 160 

********************** 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
  98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.676 
Fit side-chains
REVERT: B   91 ILE cc_start: 0.8414 (mt) cc_final: 0.8007 (tt)
REVERT: C   95 LEU cc_start: 0.8416 (tp) cc_final: 0.8077 (mp)
REVERT: A  123 SER cc_start: 0.7588 (p) cc_final: 0.7344 (m)
  outliers start: 10
  outliers final: 10
  residues processed: 93
  average time/residue: 0.1417
  time to fit residues: 19.7308
Evaluate side-chains
  98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   60 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   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 89 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0000
   chunk 11 optimal weight:    6.9990
   chunk 90 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.3377 r_free = 0.3377 target = 0.132504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.108357 restraints weight = 36931.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 3.73
r_work: 0.2900 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7620  Z= 0.172
  Angle     :  0.522   8.443  10392  Z= 0.270
  Chirality :  0.038   0.188   1268
  Planarity :  0.004   0.046   1272
  Dihedral  :  7.027  58.190   1372
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  3.00 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.92 %
    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 (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:  2.35 (0.28), residues: 980
  helix:  2.49 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.29 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  11 
 HIS   0.006   0.001   HIS D 180 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 227 
 ARG   0.003   0.000   ARG C 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4141.17 seconds
wall clock time: 72 minutes 0.81 seconds (4320.81 seconds total)