Starting phenix.real_space_refine
on Fri Jun  6 01:38:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r0c_14221/06_2025/7r0c_14221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r0c_14221/06_2025/7r0c_14221.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r0c_14221/06_2025/7r0c_14221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r0c_14221/06_2025/7r0c_14221.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r0c_14221/06_2025/7r0c_14221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r0c_14221/06_2025/7r0c_14221.cif"
  }
  resolution = 4.73
  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=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      39      5.16       5
     C    4365      2.51       5
     N    1158      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6816
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2181
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 15, 'TRANS': 268}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 41
    Chain: "B"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 74
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 2810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2810
          Classifications: {'peptide': 353}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 324}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1750
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220}
          Chain breaks: 1
  Time building chain proxies: 5.66, per 1000 atoms: 0.83
  Number of scatterers: 6816
  At special positions: 0
  Unit cell: (83.2, 99.84, 139.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      39     16.00
     P       6     15.00
     O    1248      8.00
     N    1158      7.00
     C    4365      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 112 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   1 " - pdb=" SG  CYS B   6 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 103 " - pdb=" SG  CYS D 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 148 " - pdb=" SG  CYS D 222 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1660

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 11 sheets defined
      29.0% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 69
    Processing helix  chain 'A' and resid 72 through 103
      removed outlier: 3.924A  pdb=" N   ILE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LEU A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      Proline residue:  A  95  - end of helix
    Processing helix  chain 'A' and resid 109 through 140
      removed outlier: 4.001A  pdb=" N   ARG A 113 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   GLY A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   MET A 123 " --> pdb=" O   GLN A 119 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 171
    Processing helix  chain 'A' and resid 173 through 178
      removed outlier: 3.582A  pdb=" N   PHE A 178 " --> pdb=" O   GLN A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 228
      removed outlier: 5.019A  pdb=" N   ALA A 216 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      Proline residue:  A 217  - end of helix
      removed outlier: 3.938A  pdb=" N   ILE A 228 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 304 through 311
      removed outlier: 3.583A  pdb=" N   VAL A 308 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 310 " --> pdb=" O   PRO A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 319
      removed outlier: 5.570A  pdb=" N   SER A 315 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ASN A 317 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   CYS A 319 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 329
      removed outlier: 3.574A  pdb=" N   PHE A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'C' and resid 98 through 109
    Processing helix  chain 'C' and resid 159 through 161
      No H-bonds generated for 'chain 'C' and resid 159 through 161'
    Processing helix  chain 'C' and resid 277 through 282
      removed outlier: 3.663A  pdb=" N   ASN C 280 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ARG C 282 " --> pdb=" O   ALA C 279 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 86
      removed outlier: 3.529A  pdb=" N   PHE D  86 " --> pdb=" O   PRO D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 157
    Processing helix  chain 'D' and resid 188 through 191
    Processing helix  chain 'D' and resid 213 through 217
    Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363
    Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28
      removed outlier: 6.102A  pdb=" N   PHE C  27 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   LYS C 170 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   VAL C 142 " --> pdb=" O   LYS C 170 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   VAL C  53 " --> pdb=" O   SER C  86 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   PHE C  61 " --> pdb=" O   ASP C  78 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   ASP C  78 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67
    Processing sheet with id=AA4, first strand: chain 'C' and resid 127 through 129
    Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 188
    Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 208
      removed outlier: 4.128A  pdb=" N   TYR C 321 " --> pdb=" O   PHE C 349 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   LEU C 351 " --> pdb=" O   VAL C 319 " (cutoff:3.500A)
      removed outlier: 9.194A  pdb=" N   VAL C 319 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   ILE C 318 " --> pdb=" O   ALA C 239 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ALA C 239 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   SER C 320 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   GLN C 237 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   LYS C 322 " --> pdb=" O   VAL C 235 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   VAL C 235 " --> pdb=" O   LYS C 322 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LYS C 324 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ILE C 233 " --> pdb=" O   LYS C 324 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LYS C 326 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ILE C 231 " --> pdb=" O   LYS C 326 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL C 328 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ILE C 231 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLU C 257 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ILE C 233 " --> pdb=" O   MET C 255 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   MET C 255 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL C 235 " --> pdb=" O   VAL C 253 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN C 237 " --> pdb=" O   CYS C 251 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   CYS C 251 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA C 239 " --> pdb=" O   TYR C 249 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 7 through 9
    Processing sheet with id=AA8, first strand: chain 'D' and resid 56 through 57
      removed outlier: 6.413A  pdb=" N   TRP D  38 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   TYR D  52 " --> pdb=" O   VAL D  36 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL D  36 " --> pdb=" O   TYR D  52 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 129 through 133
    Processing sheet with id=AB1, first strand: chain 'D' and resid 136 through 138
      removed outlier: 6.376A  pdb=" N   GLY D 136 " --> pdb=" O   THR D 243 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE D 160 " --> pdb=" O   SER D 176 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   SER D 176 " --> pdb=" O   ILE D 160 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TRP D 162 " --> pdb=" O   VAL D 174 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU D 172 " --> pdb=" O   ARG D 164 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 136 through 138
      removed outlier: 6.376A  pdb=" N   GLY D 136 " --> pdb=" O   THR D 243 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   TYR D 235 " --> pdb=" O   ARG D 224 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    828 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: 2.33

  Time building geometry restraints manager: 2.62 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1179
        1.32 -     1.45: 1796
        1.45 -     1.57: 3926
        1.57 -     1.69: 22
        1.69 -     1.81: 52
  Bond restraints: 6975
  Sorted by residual:
  bond pdb=" OG1 TPO A 360 "
       pdb=" P   TPO A 360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" OG1 TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.620  0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" O1P TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.525  1.610 -0.085 2.00e-02 2.50e+03 1.80e+01
  bond pdb=" O1P TPO A 360 "
       pdb=" P   TPO A 360 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" O3P TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.70e+01
  ... (remaining 6970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 9271
        2.56 -     5.11: 193
        5.11 -     7.67: 27
        7.67 -    10.23: 6
       10.23 -    12.78: 1
  Bond angle restraints: 9498
  Sorted by residual:
  angle pdb=" N   ILE A  74 "
        pdb=" CA  ILE A  74 "
        pdb=" C   ILE A  74 "
      ideal   model   delta    sigma   weight residual
     110.42  101.79    8.63 9.60e-01 1.09e+00 8.08e+01
  angle pdb=" N   VAL A  76 "
        pdb=" CA  VAL A  76 "
        pdb=" C   VAL A  76 "
      ideal   model   delta    sigma   weight residual
     110.62  104.23    6.39 1.02e+00 9.61e-01 3.93e+01
  angle pdb=" N   PRO A  73 "
        pdb=" CA  PRO A  73 "
        pdb=" C   PRO A  73 "
      ideal   model   delta    sigma   weight residual
     113.84  107.29    6.55 1.30e+00 5.92e-01 2.53e+01
  angle pdb=" CA  LYS D 202 "
        pdb=" CB  LYS D 202 "
        pdb=" CG  LYS D 202 "
      ideal   model   delta    sigma   weight residual
     114.10  122.95   -8.85 2.00e+00 2.50e-01 1.96e+01
  angle pdb=" C   LEU C  68 "
        pdb=" N   ASP C  69 "
        pdb=" CA  ASP C  69 "
      ideal   model   delta    sigma   weight residual
     122.61  129.40   -6.79 1.56e+00 4.11e-01 1.89e+01
  ... (remaining 9493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.88: 3812
       16.88 -    33.77: 308
       33.77 -    50.65: 54
       50.65 -    67.54: 9
       67.54 -    84.42: 8
  Dihedral angle restraints: 4191
    sinusoidal: 1628
      harmonic: 2563
  Sorted by residual:
  dihedral pdb=" CB  CYS A 112 "
           pdb=" SG  CYS A 112 "
           pdb=" SG  CYS A 192 "
           pdb=" CB  CYS A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.74   55.74     1      1.00e+01 1.00e-02 4.20e+01
  dihedral pdb=" CB  CYS B   1 "
           pdb=" SG  CYS B   1 "
           pdb=" SG  CYS B   6 "
           pdb=" CB  CYS B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.16   47.84     1      1.00e+01 1.00e-02 3.16e+01
  dihedral pdb=" CA  ARG D 226 "
           pdb=" C   ARG D 226 "
           pdb=" N   GLN D 227 "
           pdb=" CA  GLN D 227 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.86  -27.14     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 4188 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 1040
       0.108 -    0.215: 43
       0.215 -    0.323: 1
       0.323 -    0.430: 1
       0.430 -    0.538: 1
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CA  ILE A  74 "
            pdb=" N   ILE A  74 "
            pdb=" C   ILE A  74 "
            pdb=" CB  ILE A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.97   -0.54 2.00e-01 2.50e+01 7.24e+00
  chirality pdb=" CA  TRP A  71 "
            pdb=" N   TRP A  71 "
            pdb=" C   TRP A  71 "
            pdb=" CB  TRP A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" CA  VAL A  76 "
            pdb=" N   VAL A  76 "
            pdb=" C   VAL A  76 "
            pdb=" CB  VAL A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 1083 not shown)

  Planarity restraints: 1191
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  99 "    0.015 2.00e-02 2.50e+03   1.55e-02 6.01e+00
        pdb=" CG  TRP A  99 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  99 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  99 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  99 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  99 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  99 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  94 "    0.040 5.00e-02 4.00e+02   6.03e-02 5.82e+00
        pdb=" N   PRO A  95 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 359 "    0.039 5.00e-02 4.00e+02   5.92e-02 5.60e+00
        pdb=" N   PRO C 360 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO C 360 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 360 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1188 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 180
        2.66 -     3.22: 7059
        3.22 -     3.78: 11171
        3.78 -     4.34: 14375
        4.34 -     4.90: 22454
  Nonbonded interactions: 55239
  Sorted by model distance:
  nonbonded pdb=" O   ASN C 222 "
            pdb=" N   SER C 265 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" OE1 GLN D   9 "
            pdb=" OG1 THR D 105 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OG1 THR C  56 "
            pdb=" O   ALA C  82 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" NZ  LYS C  11 "
            pdb=" O   ARG C 165 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OD1 ASP C 204 "
            pdb=" OH  TYR C 208 "
     model   vdw
     2.210 3.040
  ... (remaining 55234 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  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:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.970
  Find NCS groups from input model:        0.080
  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:             0.000
  Load rotamer database and sin/cos tables:3.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110   6981  Z= 0.290
  Angle     :  0.909  12.782   9508  Z= 0.523
  Chirality :  0.052   0.538   1086
  Planarity :  0.005   0.060   1191
  Dihedral  : 13.187  84.422   2516
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 26.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.55 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.28), residues: 846
  helix: -0.59 (0.32), residues: 209
  sheet: -0.36 (0.34), residues: 245
  loop : -0.59 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A  99 
 HIS   0.006   0.002   HIS C 159 
 PHE   0.023   0.002   PHE D 228 
 TYR   0.020   0.002   TYR A 128 
 ARG   0.008   0.001   ARG D  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15121 (  301)
  hydrogen bonds       : angle       6.94444 (  828)
  SS BOND              : bond        0.00161 (    5)
  SS BOND              : angle       1.12490 (   10)
  covalent geometry    : bond        0.00501 ( 6975)
  covalent geometry    : angle       0.90892 ( 9498)
  Misc. bond           : bond        0.10138 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9158 (ppp) cc_final: 0.8925 (ppp)
REVERT: A  288 PHE cc_start: 0.8903 (m-80) cc_final: 0.8337 (m-80)
REVERT: C   75 PHE cc_start: 0.6481 (m-80) cc_final: 0.5776 (m-10)
REVERT: C  129 LEU cc_start: 0.9301 (mt) cc_final: 0.9092 (mt)
REVERT: D   48 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8827 (tmtt)
REVERT: D   49 LEU cc_start: 0.8528 (tp) cc_final: 0.8280 (tp)
REVERT: D   50 LEU cc_start: 0.8422 (mt) cc_final: 0.7655 (mt)
REVERT: D   74 PHE cc_start: 0.9063 (m-80) cc_final: 0.8473 (m-80)
REVERT: D  195 THR cc_start: 0.8680 (m) cc_final: 0.8416 (p)
REVERT: D  209 MET cc_start: 0.6815 (mpp) cc_final: 0.6419 (mpp)
  outliers start: 1
  outliers final: 1
  residues processed: 131
  average time/residue: 0.2456
  time to fit residues: 42.4215
Evaluate side-chains
  95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   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  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 GLN
C 122 ASN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 237 GLN
C 281 ASN
D   9 GLN
D 165 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.112344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.090603 restraints weight = 27389.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.093662 restraints weight = 17211.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.095836 restraints weight = 12341.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6981  Z= 0.140
  Angle     :  0.647   7.261   9508  Z= 0.331
  Chirality :  0.044   0.170   1086
  Planarity :  0.005   0.057   1191
  Dihedral  :  6.290  73.102    965
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.29), residues: 846
  helix: -0.05 (0.33), residues: 211
  sheet: -0.20 (0.34), residues: 242
  loop : -0.66 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  99 
 HIS   0.006   0.001   HIS A  75 
 PHE   0.021   0.002   PHE D 228 
 TYR   0.013   0.001   TYR A 128 
 ARG   0.003   0.000   ARG D 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  301)
  hydrogen bonds       : angle       5.90434 (  828)
  SS BOND              : bond        0.00383 (    5)
  SS BOND              : angle       1.05508 (   10)
  covalent geometry    : bond        0.00301 ( 6975)
  covalent geometry    : angle       0.64691 ( 9498)
  Misc. bond           : bond        0.00006 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 2.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9089 (ppp) cc_final: 0.8806 (ppp)
REVERT: A  272 MET cc_start: 0.8516 (ppp) cc_final: 0.8266 (ppp)
REVERT: A  288 PHE cc_start: 0.8998 (m-80) cc_final: 0.8526 (m-80)
REVERT: C   10 LYS cc_start: 0.7628 (pttt) cc_final: 0.7089 (pmtt)
REVERT: C   75 PHE cc_start: 0.6465 (m-80) cc_final: 0.5695 (m-10)
REVERT: C  172 GLN cc_start: 0.8731 (mp-120) cc_final: 0.8068 (mp-120)
REVERT: C  315 LEU cc_start: 0.9210 (mm) cc_final: 0.9008 (mm)
REVERT: D   74 PHE cc_start: 0.9100 (m-80) cc_final: 0.8487 (m-80)
REVERT: D   75 THR cc_start: 0.8628 (p) cc_final: 0.8316 (p)
REVERT: D  195 THR cc_start: 0.8811 (m) cc_final: 0.8584 (p)
REVERT: D  209 MET cc_start: 0.7161 (mpp) cc_final: 0.6616 (mpp)
REVERT: D  234 ASP cc_start: 0.8646 (p0) cc_final: 0.8344 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.3134
  time to fit residues: 58.0359
Evaluate side-chains
  96 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 2.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0970
   chunk 14 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 122 ASN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.113314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.091242 restraints weight = 27387.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.094333 restraints weight = 16952.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.096496 restraints weight = 12065.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6981  Z= 0.126
  Angle     :  0.625   6.612   9508  Z= 0.318
  Chirality :  0.044   0.169   1086
  Planarity :  0.005   0.057   1191
  Dihedral  :  6.129  73.589    965
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.29), residues: 846
  helix:  0.20 (0.34), residues: 211
  sheet: -0.21 (0.34), residues: 255
  loop : -0.62 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A  99 
 HIS   0.005   0.001   HIS C 159 
 PHE   0.020   0.001   PHE D 228 
 TYR   0.023   0.001   TYR D  52 
 ARG   0.004   0.000   ARG D 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  301)
  hydrogen bonds       : angle       5.64802 (  828)
  SS BOND              : bond        0.00129 (    5)
  SS BOND              : angle       1.13583 (   10)
  covalent geometry    : bond        0.00272 ( 6975)
  covalent geometry    : angle       0.62381 ( 9498)
  Misc. bond           : bond        0.00003 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9123 (ppp) cc_final: 0.8800 (ppp)
REVERT: A  134 THR cc_start: 0.9119 (p) cc_final: 0.8880 (p)
REVERT: A  272 MET cc_start: 0.8574 (ppp) cc_final: 0.8341 (ppp)
REVERT: A  288 PHE cc_start: 0.8859 (m-80) cc_final: 0.8642 (m-80)
REVERT: C  172 GLN cc_start: 0.8721 (mp-120) cc_final: 0.8135 (mp10)
REVERT: C  315 LEU cc_start: 0.9111 (mm) cc_final: 0.8875 (mm)
REVERT: D   49 LEU cc_start: 0.8561 (tp) cc_final: 0.8050 (tp)
REVERT: D   50 LEU cc_start: 0.8870 (mt) cc_final: 0.8134 (mt)
REVERT: D   51 ILE cc_start: 0.8704 (tp) cc_final: 0.8502 (tp)
REVERT: D   65 PHE cc_start: 0.8219 (m-10) cc_final: 0.8011 (m-80)
REVERT: D   74 PHE cc_start: 0.9076 (m-80) cc_final: 0.8806 (m-80)
REVERT: D  195 THR cc_start: 0.8776 (m) cc_final: 0.8513 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2285
  time to fit residues: 37.6831
Evaluate side-chains
  94 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0870
   chunk 25 optimal weight:    0.0770
   chunk 11 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 80 optimal weight:    0.0040
   chunk 65 optimal weight:    6.9990
   overall best weight:    0.3930

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

Flipped N/Q/H residues before XYZ refinement:
C 122 ASN
C 159 HIS
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.114705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.092672 restraints weight = 27868.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.095905 restraints weight = 17152.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.098188 restraints weight = 12092.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6981  Z= 0.115
  Angle     :  0.618   6.546   9508  Z= 0.311
  Chirality :  0.044   0.154   1086
  Planarity :  0.005   0.056   1191
  Dihedral  :  5.973  74.035    965
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.29), residues: 846
  helix:  0.38 (0.34), residues: 211
  sheet: -0.11 (0.35), residues: 258
  loop : -0.60 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 173 
 HIS   0.004   0.001   HIS C 159 
 PHE   0.018   0.001   PHE D 228 
 TYR   0.009   0.001   TYR D  52 
 ARG   0.005   0.000   ARG D 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  301)
  hydrogen bonds       : angle       5.36869 (  828)
  SS BOND              : bond        0.00204 (    5)
  SS BOND              : angle       1.44676 (   10)
  covalent geometry    : bond        0.00252 ( 6975)
  covalent geometry    : angle       0.61691 ( 9498)
  Misc. bond           : bond        0.00003 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ILE cc_start: 0.9708 (mm) cc_final: 0.9483 (mm)
REVERT: C   29 ASP cc_start: 0.7845 (t0) cc_final: 0.7402 (t0)
REVERT: C  172 GLN cc_start: 0.8676 (mp-120) cc_final: 0.7811 (mp-120)
REVERT: C  203 LEU cc_start: 0.8914 (mm) cc_final: 0.8613 (mt)
REVERT: C  223 ASN cc_start: 0.7988 (m-40) cc_final: 0.7621 (p0)
REVERT: C  315 LEU cc_start: 0.9158 (mm) cc_final: 0.8946 (mm)
REVERT: D   50 LEU cc_start: 0.8807 (mt) cc_final: 0.8582 (mt)
REVERT: D   57 LEU cc_start: 0.8661 (pp) cc_final: 0.8454 (pp)
REVERT: D   74 PHE cc_start: 0.8877 (m-80) cc_final: 0.8667 (m-80)
REVERT: D  195 THR cc_start: 0.8553 (m) cc_final: 0.8316 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.3666
  time to fit residues: 66.0402
Evaluate side-chains
  98 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0030
   chunk 63 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.3394

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.112949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.090676 restraints weight = 28355.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.093910 restraints weight = 17292.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.096082 restraints weight = 12174.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6981  Z= 0.137
  Angle     :  0.632   6.742   9508  Z= 0.320
  Chirality :  0.044   0.169   1086
  Planarity :  0.005   0.058   1191
  Dihedral  :  6.020  75.894    965
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.29), residues: 846
  helix:  0.34 (0.34), residues: 208
  sheet: -0.22 (0.34), residues: 264
  loop : -0.44 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP A  99 
 HIS   0.003   0.001   HIS A  75 
 PHE   0.017   0.001   PHE D 228 
 TYR   0.020   0.001   TYR D  52 
 ARG   0.006   0.001   ARG D 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  301)
  hydrogen bonds       : angle       5.33818 (  828)
  SS BOND              : bond        0.00163 (    5)
  SS BOND              : angle       1.22199 (   10)
  covalent geometry    : bond        0.00298 ( 6975)
  covalent geometry    : angle       0.63128 ( 9498)
  Misc. bond           : bond        0.00004 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ILE cc_start: 0.9711 (mm) cc_final: 0.9500 (mm)
REVERT: A  133 MET cc_start: 0.9133 (ppp) cc_final: 0.8860 (ppp)
REVERT: A  272 MET cc_start: 0.8336 (ppp) cc_final: 0.8093 (ppp)
REVERT: A  288 PHE cc_start: 0.8796 (m-80) cc_final: 0.8391 (m-80)
REVERT: C   29 ASP cc_start: 0.8082 (t0) cc_final: 0.7604 (t0)
REVERT: C  172 GLN cc_start: 0.8585 (mp-120) cc_final: 0.8039 (mm-40)
REVERT: C  212 GLU cc_start: 0.8507 (mp0) cc_final: 0.8214 (mp0)
REVERT: C  223 ASN cc_start: 0.8064 (m-40) cc_final: 0.7736 (p0)
REVERT: C  232 LYS cc_start: 0.8931 (tppt) cc_final: 0.8466 (tppt)
REVERT: D   65 PHE cc_start: 0.7920 (m-80) cc_final: 0.7622 (m-80)
REVERT: D  193 ARG cc_start: 0.8094 (ttt180) cc_final: 0.7849 (ttt180)
REVERT: D  195 THR cc_start: 0.8653 (m) cc_final: 0.8410 (p)
REVERT: D  209 MET cc_start: 0.7243 (mpp) cc_final: 0.6702 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2009
  time to fit residues: 33.7290
Evaluate side-chains
  96 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 27 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 67 optimal weight:   20.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  41 GLN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.105596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.084301 restraints weight = 29406.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.087193 restraints weight = 18373.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.089098 restraints weight = 13140.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   6981  Z= 0.270
  Angle     :  0.763   8.289   9508  Z= 0.398
  Chirality :  0.048   0.169   1086
  Planarity :  0.006   0.059   1191
  Dihedral  :  6.709  80.978    965
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 24.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.30), residues: 846
  helix:  0.18 (0.35), residues: 202
  sheet: -0.59 (0.34), residues: 251
  loop : -0.26 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 284 
 HIS   0.007   0.002   HIS C  30 
 PHE   0.034   0.003   PHE C  27 
 TYR   0.017   0.002   TYR D 181 
 ARG   0.014   0.001   ARG C 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04574 (  301)
  hydrogen bonds       : angle       6.04407 (  828)
  SS BOND              : bond        0.00433 (    5)
  SS BOND              : angle       1.62489 (   10)
  covalent geometry    : bond        0.00561 ( 6975)
  covalent geometry    : angle       0.76200 ( 9498)
  Misc. bond           : bond        0.00001 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.6957 (pt) cc_final: 0.6439 (pt)
REVERT: A  123 MET cc_start: 0.7569 (mmp) cc_final: 0.7291 (mmp)
REVERT: A  134 THR cc_start: 0.9486 (p) cc_final: 0.9254 (p)
REVERT: A  145 MET cc_start: 0.7571 (mmp) cc_final: 0.7286 (mmp)
REVERT: A  288 PHE cc_start: 0.8909 (m-80) cc_final: 0.8321 (m-80)
REVERT: C   29 ASP cc_start: 0.8084 (t0) cc_final: 0.7415 (t0)
REVERT: D   65 PHE cc_start: 0.7707 (m-80) cc_final: 0.7502 (m-80)
REVERT: D  195 THR cc_start: 0.8838 (m) cc_final: 0.8613 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1723
  time to fit residues: 27.7108
Evaluate side-chains
  90 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 28 optimal weight:    8.9990
   chunk 10 optimal weight:    0.0070
   chunk 8 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 299 ASN
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.112799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.091616 restraints weight = 28814.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.094617 restraints weight = 18042.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.096658 restraints weight = 12911.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6981  Z= 0.125
  Angle     :  0.653   6.835   9508  Z= 0.327
  Chirality :  0.046   0.173   1086
  Planarity :  0.005   0.062   1191
  Dihedral  :  6.175  77.627    965
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.19 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.30), residues: 846
  helix:  0.45 (0.35), residues: 202
  sheet: -0.29 (0.34), residues: 251
  loop : -0.39 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 284 
 HIS   0.015   0.001   HIS A  80 
 PHE   0.011   0.001   PHE D 228 
 TYR   0.025   0.002   TYR D  52 
 ARG   0.004   0.000   ARG C 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  301)
  hydrogen bonds       : angle       5.38829 (  828)
  SS BOND              : bond        0.00710 (    5)
  SS BOND              : angle       1.35233 (   10)
  covalent geometry    : bond        0.00276 ( 6975)
  covalent geometry    : angle       0.65155 ( 9498)
  Misc. bond           : bond        0.00001 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7479 (mmp) cc_final: 0.7129 (mmp)
REVERT: A  133 MET cc_start: 0.9083 (ppp) cc_final: 0.8747 (ppp)
REVERT: A  272 MET cc_start: 0.8522 (ppp) cc_final: 0.8264 (ppp)
REVERT: A  288 PHE cc_start: 0.8957 (m-80) cc_final: 0.8703 (m-80)
REVERT: A  325 TYR cc_start: 0.9070 (t80) cc_final: 0.8705 (t80)
REVERT: C   29 ASP cc_start: 0.8115 (t0) cc_final: 0.7730 (t0)
REVERT: C  172 GLN cc_start: 0.8508 (mp-120) cc_final: 0.7865 (mp-120)
REVERT: C  212 GLU cc_start: 0.8476 (mp0) cc_final: 0.8119 (mp0)
REVERT: C  315 LEU cc_start: 0.9143 (mm) cc_final: 0.8919 (mm)
REVERT: D   39 TYR cc_start: 0.6992 (m-10) cc_final: 0.6768 (m-10)
REVERT: D   50 LEU cc_start: 0.8740 (mm) cc_final: 0.8269 (mp)
REVERT: D   65 PHE cc_start: 0.7600 (m-80) cc_final: 0.7376 (m-80)
REVERT: D   74 PHE cc_start: 0.8996 (m-80) cc_final: 0.8582 (m-80)
REVERT: D  169 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8694 (ptpp)
REVERT: D  193 ARG cc_start: 0.8252 (ttt180) cc_final: 0.8022 (ttt180)
REVERT: D  195 THR cc_start: 0.8803 (m) cc_final: 0.8602 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1996
  time to fit residues: 34.5676
Evaluate side-chains
  100 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 223 ASN
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.107790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.086328 restraints weight = 28628.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.089148 restraints weight = 18152.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.091031 restraints weight = 13129.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6981  Z= 0.210
  Angle     :  0.710   7.494   9508  Z= 0.367
  Chirality :  0.046   0.152   1086
  Planarity :  0.006   0.059   1191
  Dihedral  :  6.462  79.784    965
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 22.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.30), residues: 846
  helix:  0.22 (0.35), residues: 205
  sheet: -0.34 (0.35), residues: 240
  loop : -0.49 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.004   TRP A  99 
 HIS   0.005   0.001   HIS C  30 
 PHE   0.022   0.002   PHE D  74 
 TYR   0.017   0.002   TYR A 280 
 ARG   0.017   0.001   ARG D 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04240 (  301)
  hydrogen bonds       : angle       5.71640 (  828)
  SS BOND              : bond        0.00305 (    5)
  SS BOND              : angle       1.71300 (   10)
  covalent geometry    : bond        0.00443 ( 6975)
  covalent geometry    : angle       0.70847 ( 9498)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 TYR cc_start: 0.6000 (t80) cc_final: 0.5747 (t80)
REVERT: A  123 MET cc_start: 0.7504 (mmp) cc_final: 0.7206 (mmp)
REVERT: A  133 MET cc_start: 0.9012 (ppp) cc_final: 0.8773 (ppp)
REVERT: A  280 TYR cc_start: 0.8880 (t80) cc_final: 0.8637 (t80)
REVERT: A  284 TRP cc_start: 0.8521 (m-10) cc_final: 0.7924 (m-10)
REVERT: A  288 PHE cc_start: 0.8939 (m-80) cc_final: 0.8618 (m-80)
REVERT: A  325 TYR cc_start: 0.9220 (t80) cc_final: 0.8874 (t80)
REVERT: C   29 ASP cc_start: 0.8100 (t0) cc_final: 0.7688 (t0)
REVERT: C  172 GLN cc_start: 0.8498 (mp-120) cc_final: 0.7721 (mp-120)
REVERT: C  223 ASN cc_start: 0.8701 (m-40) cc_final: 0.8305 (p0)
REVERT: C  315 LEU cc_start: 0.9176 (mm) cc_final: 0.8965 (mm)
REVERT: D   48 LYS cc_start: 0.8574 (tmtt) cc_final: 0.8347 (tptt)
REVERT: D   73 ASP cc_start: 0.8892 (m-30) cc_final: 0.8481 (m-30)
REVERT: D   74 PHE cc_start: 0.9098 (m-80) cc_final: 0.8464 (m-80)
REVERT: D  193 ARG cc_start: 0.8062 (ttt180) cc_final: 0.7815 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1804
  time to fit residues: 28.8601
Evaluate side-chains
  94 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 210 HIS
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.110483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.089164 restraints weight = 29012.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.092142 restraints weight = 18339.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.094140 restraints weight = 13090.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6981  Z= 0.150
  Angle     :  0.673   6.981   9508  Z= 0.342
  Chirality :  0.046   0.207   1086
  Planarity :  0.005   0.058   1191
  Dihedral  :  6.325  79.418    965
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.30), residues: 846
  helix:  0.28 (0.35), residues: 205
  sheet: -0.26 (0.35), residues: 234
  loop : -0.52 (0.33), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP A  99 
 HIS   0.005   0.001   HIS C 353 
 PHE   0.016   0.002   PHE D 228 
 TYR   0.028   0.002   TYR D  52 
 ARG   0.008   0.001   ARG D 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03875 (  301)
  hydrogen bonds       : angle       5.55137 (  828)
  SS BOND              : bond        0.00183 (    5)
  SS BOND              : angle       1.64740 (   10)
  covalent geometry    : bond        0.00325 ( 6975)
  covalent geometry    : angle       0.67077 ( 9498)
  Misc. bond           : bond        0.00002 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7550 (mmp) cc_final: 0.7291 (mmm)
REVERT: A  133 MET cc_start: 0.9085 (ppp) cc_final: 0.8843 (ppp)
REVERT: A  145 MET cc_start: 0.6167 (mmp) cc_final: 0.4441 (tmm)
REVERT: A  212 MET cc_start: 0.8911 (ppp) cc_final: 0.8685 (ppp)
REVERT: A  272 MET cc_start: 0.8531 (ppp) cc_final: 0.8281 (ppp)
REVERT: A  288 PHE cc_start: 0.9013 (m-80) cc_final: 0.8621 (m-80)
REVERT: A  325 TYR cc_start: 0.9198 (t80) cc_final: 0.8857 (t80)
REVERT: C   29 ASP cc_start: 0.8249 (t0) cc_final: 0.7874 (t0)
REVERT: C  172 GLN cc_start: 0.8603 (mp-120) cc_final: 0.7958 (mp-120)
REVERT: C  223 ASN cc_start: 0.8563 (m-40) cc_final: 0.8119 (p0)
REVERT: C  315 LEU cc_start: 0.9144 (mm) cc_final: 0.8924 (mm)
REVERT: D   48 LYS cc_start: 0.8442 (tmtt) cc_final: 0.8232 (tptt)
REVERT: D   73 ASP cc_start: 0.8935 (m-30) cc_final: 0.8555 (m-30)
REVERT: D   74 PHE cc_start: 0.9298 (m-80) cc_final: 0.8540 (m-80)
REVERT: D   90 TYR cc_start: 0.7742 (m-10) cc_final: 0.7339 (m-80)
REVERT: D  169 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8656 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1795
  time to fit residues: 29.3034
Evaluate side-chains
  97 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0050
   chunk 21 optimal weight:    0.9990
   overall best weight:    2.8002

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.107267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.085902 restraints weight = 30069.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.088920 restraints weight = 18640.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.090969 restraints weight = 13212.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6981  Z= 0.220
  Angle     :  0.729   7.824   9508  Z= 0.375
  Chirality :  0.048   0.202   1086
  Planarity :  0.006   0.059   1191
  Dihedral  :  6.638  80.223    965
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 23.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.30), residues: 846
  helix:  0.07 (0.35), residues: 205
  sheet: -0.42 (0.35), residues: 234
  loop : -0.48 (0.34), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP D  38 
 HIS   0.006   0.002   HIS C 210 
 PHE   0.025   0.002   PHE D 228 
 TYR   0.017   0.002   TYR D 181 
 ARG   0.008   0.001   ARG C 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04242 (  301)
  hydrogen bonds       : angle       5.89920 (  828)
  SS BOND              : bond        0.00160 (    5)
  SS BOND              : angle       1.69321 (   10)
  covalent geometry    : bond        0.00463 ( 6975)
  covalent geometry    : angle       0.72705 ( 9498)
  Misc. bond           : bond        0.00006 (    1)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9070 (ppp) cc_final: 0.8773 (ppp)
REVERT: A  134 THR cc_start: 0.9477 (p) cc_final: 0.9267 (p)
REVERT: A  272 MET cc_start: 0.8573 (ppp) cc_final: 0.8301 (ppp)
REVERT: A  280 TYR cc_start: 0.9012 (t80) cc_final: 0.8692 (t80)
REVERT: A  284 TRP cc_start: 0.8621 (m-10) cc_final: 0.8016 (m-10)
REVERT: A  288 PHE cc_start: 0.9005 (m-80) cc_final: 0.8676 (m-80)
REVERT: A  325 TYR cc_start: 0.9282 (t80) cc_final: 0.8939 (t80)
REVERT: C  172 GLN cc_start: 0.8491 (mp-120) cc_final: 0.7651 (mp-120)
REVERT: C  223 ASN cc_start: 0.8510 (m-40) cc_final: 0.8172 (p0)
REVERT: D   73 ASP cc_start: 0.8926 (m-30) cc_final: 0.8465 (m-30)
REVERT: D   74 PHE cc_start: 0.9117 (m-80) cc_final: 0.8373 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1665
  time to fit residues: 25.9570
Evaluate side-chains
  93 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 69 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B   4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 ASN
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.107988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.086778 restraints weight = 28704.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.089661 restraints weight = 18129.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.091615 restraints weight = 13052.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6981  Z= 0.183
  Angle     :  0.709   8.278   9508  Z= 0.361
  Chirality :  0.047   0.195   1086
  Planarity :  0.005   0.058   1191
  Dihedral  :  6.585  79.711    965
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 20.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.30), residues: 846
  helix:  0.02 (0.34), residues: 212
  sheet: -0.49 (0.35), residues: 235
  loop : -0.52 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.003   TRP D  38 
 HIS   0.004   0.001   HIS C 353 
 PHE   0.021   0.002   PHE D 228 
 TYR   0.029   0.002   TYR D  52 
 ARG   0.007   0.001   ARG C 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04023 (  301)
  hydrogen bonds       : angle       5.81983 (  828)
  SS BOND              : bond        0.00197 (    5)
  SS BOND              : angle       1.54949 (   10)
  covalent geometry    : bond        0.00389 ( 6975)
  covalent geometry    : angle       0.70738 ( 9498)
  Misc. bond           : bond        0.00007 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2943.57 seconds
wall clock time: 53 minutes 3.75 seconds (3183.75 seconds total)