Starting phenix.real_space_refine
on Sat May 10 22:33:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r0c_14221/05_2025/7r0c_14221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r0c_14221/05_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_14221/05_2025/7r0c_14221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r0c_14221/05_2025/7r0c_14221.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r0c_14221/05_2025/7r0c_14221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r0c_14221/05_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-5687/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: 4.52, per 1000 atoms: 0.66
  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: 1.95
  Conformation dependent library (CDL) restraints added in 926.6 milliseconds
  

  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: 0.71
  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: 1.88

  Time building geometry restraints manager: 2.17 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:             0.790
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.370
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.680
-------------------------------------------------------------------------------
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  : 0.817 
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: 0.1966
  time to fit residues: 34.0879
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  : 0.794 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.112657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.090862 restraints weight = 27341.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.093993 restraints weight = 17159.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.096129 restraints weight = 12272.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6981  Z= 0.138
  Angle     :  0.650   7.192   9508  Z= 0.332
  Chirality :  0.045   0.173   1086
  Planarity :  0.005   0.057   1191
  Dihedral  :  6.283  72.959    965
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  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: -0.65 (0.29), residues: 846
  helix: -0.01 (0.33), residues: 211
  sheet: -0.22 (0.34), residues: 244
  loop : -0.68 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  99 
 HIS   0.006   0.001   HIS A  75 
 PHE   0.023   0.002   PHE D 228 
 TYR   0.014   0.001   TYR A 128 
 ARG   0.003   0.001   ARG D 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  301)
  hydrogen bonds       : angle       5.89893 (  828)
  SS BOND              : bond        0.00436 (    5)
  SS BOND              : angle       0.99784 (   10)
  covalent geometry    : bond        0.00297 ( 6975)
  covalent geometry    : angle       0.64969 ( 9498)
  Misc. bond           : bond        0.00037 (    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
  134 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.724 
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: 0.9090 (ppp) cc_final: 0.8805 (ppp)
REVERT: A  272 MET cc_start: 0.8516 (ppp) cc_final: 0.8267 (ppp)
REVERT: A  288 PHE cc_start: 0.8959 (m-80) cc_final: 0.8467 (m-80)
REVERT: C   10 LYS cc_start: 0.7611 (pttt) cc_final: 0.7042 (pttt)
REVERT: C   75 PHE cc_start: 0.6460 (m-80) cc_final: 0.5686 (m-10)
REVERT: C  172 GLN cc_start: 0.8742 (mp-120) cc_final: 0.8083 (mp-120)
REVERT: C  315 LEU cc_start: 0.9210 (mm) cc_final: 0.9009 (mm)
REVERT: D   50 LEU cc_start: 0.8865 (mt) cc_final: 0.8664 (mt)
REVERT: D   74 PHE cc_start: 0.9094 (m-80) cc_final: 0.8487 (m-80)
REVERT: D   75 THR cc_start: 0.8621 (p) cc_final: 0.8313 (p)
REVERT: D  195 THR cc_start: 0.8806 (m) cc_final: 0.8579 (p)
REVERT: D  209 MET cc_start: 0.6937 (mpp) cc_final: 0.6382 (mpp)
REVERT: D  234 ASP cc_start: 0.8649 (p0) cc_final: 0.8333 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.2021
  time to fit residues: 35.6826
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  : 0.789 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 39 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 181 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 = 0.3930 r_free = 0.3930 target = 0.111994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.090067 restraints weight = 28054.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.093085 restraints weight = 17614.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.095133 restraints weight = 12631.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6981  Z= 0.141
  Angle     :  0.632   6.847   9508  Z= 0.324
  Chirality :  0.044   0.167   1086
  Planarity :  0.005   0.058   1191
  Dihedral  :  6.190  73.865    965
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  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: -0.54 (0.29), residues: 846
  helix:  0.20 (0.33), residues: 211
  sheet: -0.29 (0.34), residues: 255
  loop : -0.60 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A  99 
 HIS   0.005   0.001   HIS C 159 
 PHE   0.021   0.002   PHE D 228 
 TYR   0.025   0.001   TYR D  52 
 ARG   0.006   0.001   ARG D  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  301)
  hydrogen bonds       : angle       5.73740 (  828)
  SS BOND              : bond        0.00152 (    5)
  SS BOND              : angle       1.22283 (   10)
  covalent geometry    : bond        0.00305 ( 6975)
  covalent geometry    : angle       0.63150 ( 9498)
  Misc. bond           : bond        0.00007 (    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  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9108 (ppp) cc_final: 0.8796 (ppp)
REVERT: A  134 THR cc_start: 0.9048 (p) cc_final: 0.8798 (p)
REVERT: A  272 MET cc_start: 0.8513 (ppp) cc_final: 0.8293 (ppp)
REVERT: A  288 PHE cc_start: 0.8818 (m-80) cc_final: 0.8601 (m-80)
REVERT: C   29 ASP cc_start: 0.8133 (t0) cc_final: 0.7429 (t0)
REVERT: C  223 ASN cc_start: 0.8038 (m-40) cc_final: 0.7692 (p0)
REVERT: C  315 LEU cc_start: 0.9115 (mm) cc_final: 0.8882 (mm)
REVERT: D   48 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8577 (tmtt)
REVERT: D   49 LEU cc_start: 0.8563 (tp) cc_final: 0.8020 (tp)
REVERT: D   50 LEU cc_start: 0.8904 (mt) cc_final: 0.8159 (mt)
REVERT: D   74 PHE cc_start: 0.9063 (m-80) cc_final: 0.8806 (m-80)
REVERT: D  195 THR cc_start: 0.8804 (m) cc_final: 0.8536 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1730
  time to fit residues: 28.9983
Evaluate side-chains
  95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0070
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
C 122 ASN
** 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 = 0.3962 r_free = 0.3962 target = 0.114047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.091881 restraints weight = 27891.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.095108 restraints weight = 17061.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.097349 restraints weight = 12017.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6981  Z= 0.118
  Angle     :  0.619   6.568   9508  Z= 0.311
  Chirality :  0.044   0.169   1086
  Planarity :  0.005   0.056   1191
  Dihedral  :  6.030  74.807    965
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  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: -0.41 (0.29), residues: 846
  helix:  0.36 (0.34), residues: 211
  sheet: -0.18 (0.34), residues: 261
  loop : -0.58 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 284 
 HIS   0.004   0.001   HIS A  75 
 PHE   0.019   0.001   PHE D 228 
 TYR   0.015   0.001   TYR D  96 
 ARG   0.003   0.000   ARG C  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03578 (  301)
  hydrogen bonds       : angle       5.41636 (  828)
  SS BOND              : bond        0.00289 (    5)
  SS BOND              : angle       1.14428 (   10)
  covalent geometry    : bond        0.00258 ( 6975)
  covalent geometry    : angle       0.61822 ( 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
  129 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 PHE cc_start: 0.8807 (m-80) cc_final: 0.8543 (m-80)
REVERT: C   29 ASP cc_start: 0.8071 (t0) cc_final: 0.7616 (t0)
REVERT: C  172 GLN cc_start: 0.8723 (mp-120) cc_final: 0.8011 (mp-120)
REVERT: C  223 ASN cc_start: 0.8033 (m-40) cc_final: 0.7684 (p0)
REVERT: D   39 TYR cc_start: 0.7017 (m-10) cc_final: 0.6763 (m-10)
REVERT: D   49 LEU cc_start: 0.8378 (tp) cc_final: 0.8084 (tp)
REVERT: D   50 LEU cc_start: 0.8922 (mt) cc_final: 0.8711 (mt)
REVERT: D  195 THR cc_start: 0.8715 (m) cc_final: 0.8481 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1956
  time to fit residues: 33.5601
Evaluate side-chains
  95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 10 optimal weight:    0.1980
   chunk 63 optimal weight:    0.0020
   chunk 20 optimal weight:    0.6980
   overall best weight:    1.3792

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3929 r_free = 0.3929 target = 0.112152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.090130 restraints weight = 28385.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.093154 restraints weight = 17694.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.095202 restraints weight = 12658.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6981  Z= 0.141
  Angle     :  0.637   6.769   9508  Z= 0.323
  Chirality :  0.044   0.150   1086
  Planarity :  0.005   0.057   1191
  Dihedral  :  6.079  77.028    965
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  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: -0.42 (0.29), residues: 846
  helix:  0.35 (0.34), residues: 208
  sheet: -0.29 (0.34), residues: 258
  loop : -0.49 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP A  99 
 HIS   0.004   0.001   HIS C 159 
 PHE   0.018   0.001   PHE D 228 
 TYR   0.027   0.001   TYR D  52 
 ARG   0.004   0.000   ARG D 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  301)
  hydrogen bonds       : angle       5.41197 (  828)
  SS BOND              : bond        0.00109 (    5)
  SS BOND              : angle       1.32595 (   10)
  covalent geometry    : bond        0.00307 ( 6975)
  covalent geometry    : angle       0.63590 ( 9498)
  Misc. bond           : bond        0.00003 (    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
  127 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.737 
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: 0.9191 (ppp) cc_final: 0.8884 (ppp)
REVERT: A  272 MET cc_start: 0.8387 (ppp) cc_final: 0.8180 (ppp)
REVERT: A  288 PHE cc_start: 0.8857 (m-80) cc_final: 0.8478 (m-80)
REVERT: C   29 ASP cc_start: 0.8255 (t0) cc_final: 0.7802 (t0)
REVERT: C  172 GLN cc_start: 0.8637 (mp-120) cc_final: 0.7850 (mp-120)
REVERT: C  212 GLU cc_start: 0.8494 (mp0) cc_final: 0.8157 (mp0)
REVERT: C  223 ASN cc_start: 0.8089 (m-40) cc_final: 0.7782 (p0)
REVERT: D   57 LEU cc_start: 0.8693 (pp) cc_final: 0.8351 (pp)
REVERT: D  193 ARG cc_start: 0.8158 (ttt180) cc_final: 0.7891 (ttt180)
REVERT: D  195 THR cc_start: 0.8752 (m) cc_final: 0.8516 (p)
REVERT: D  209 MET cc_start: 0.7353 (mpp) cc_final: 0.6845 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1824
  time to fit residues: 30.8704
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  : 0.722 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 81 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.108059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.086092 restraints weight = 28620.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.089052 restraints weight = 18039.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.091094 restraints weight = 12906.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6981  Z= 0.202
  Angle     :  0.689   7.458   9508  Z= 0.356
  Chirality :  0.046   0.161   1086
  Planarity :  0.006   0.076   1191
  Dihedral  :  6.372  79.664    965
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 21.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.69 %
    Favored  : 96.17 %
  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: -0.42 (0.30), residues: 846
  helix:  0.41 (0.35), residues: 202
  sheet: -0.52 (0.34), residues: 255
  loop : -0.31 (0.34), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A 284 
 HIS   0.005   0.002   HIS C  30 
 PHE   0.023   0.002   PHE D  74 
 TYR   0.013   0.002   TYR A 280 
 ARG   0.009   0.001   ARG C 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04055 (  301)
  hydrogen bonds       : angle       5.70842 (  828)
  SS BOND              : bond        0.00461 (    5)
  SS BOND              : angle       1.31854 (   10)
  covalent geometry    : bond        0.00423 ( 6975)
  covalent geometry    : angle       0.68765 ( 9498)
  Misc. bond           : bond        0.00000 (    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
  120 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7515 (mmp) cc_final: 0.7247 (mmp)
REVERT: A  130 ILE cc_start: 0.9734 (mm) cc_final: 0.9528 (mm)
REVERT: A  134 THR cc_start: 0.9412 (p) cc_final: 0.9197 (p)
REVERT: A  288 PHE cc_start: 0.8859 (m-80) cc_final: 0.8624 (m-80)
REVERT: C   29 ASP cc_start: 0.8103 (t0) cc_final: 0.7663 (t0)
REVERT: C  172 GLN cc_start: 0.8449 (mp-120) cc_final: 0.7774 (mp-120)
REVERT: D   65 PHE cc_start: 0.7711 (m-80) cc_final: 0.7427 (m-80)
REVERT: D   74 PHE cc_start: 0.8945 (m-80) cc_final: 0.8483 (m-80)
REVERT: D  195 THR cc_start: 0.8777 (m) cc_final: 0.8545 (p)
REVERT: D  226 ARG cc_start: 0.8833 (ttp80) cc_final: 0.7982 (ttp80)
  outliers start: 1
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1928
  time to fit residues: 30.7690
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  : 0.794 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 67 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 58 optimal weight:    0.4980
   chunk 22 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3907 r_free = 0.3907 target = 0.110429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.088973 restraints weight = 28683.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.091747 restraints weight = 18253.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.093704 restraints weight = 13216.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6981  Z= 0.146
  Angle     :  0.652   6.874   9508  Z= 0.329
  Chirality :  0.045   0.148   1086
  Planarity :  0.005   0.060   1191
  Dihedral  :  6.190  78.154    965
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  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: -0.39 (0.30), residues: 846
  helix:  0.51 (0.35), residues: 202
  sheet: -0.27 (0.35), residues: 243
  loop : -0.53 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 284 
 HIS   0.004   0.001   HIS C 159 
 PHE   0.016   0.002   PHE D 228 
 TYR   0.028   0.002   TYR D  52 
 ARG   0.005   0.000   ARG C 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  301)
  hydrogen bonds       : angle       5.45037 (  828)
  SS BOND              : bond        0.00185 (    5)
  SS BOND              : angle       1.47280 (   10)
  covalent geometry    : bond        0.00316 ( 6975)
  covalent geometry    : angle       0.65017 ( 9498)
  Misc. bond           : bond        0.00000 (    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
  124 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7521 (mmp) cc_final: 0.7158 (mmp)
REVERT: A  133 MET cc_start: 0.9047 (ppp) cc_final: 0.8733 (ppp)
REVERT: A  212 MET cc_start: 0.8933 (ppp) cc_final: 0.8709 (ppp)
REVERT: A  272 MET cc_start: 0.8535 (ppp) cc_final: 0.8280 (ppp)
REVERT: A  288 PHE cc_start: 0.8914 (m-80) cc_final: 0.8698 (m-80)
REVERT: A  325 TYR cc_start: 0.9116 (t80) cc_final: 0.8781 (t80)
REVERT: C   29 ASP cc_start: 0.8135 (t0) cc_final: 0.7714 (t0)
REVERT: C  172 GLN cc_start: 0.8581 (mp-120) cc_final: 0.7823 (mp-120)
REVERT: D   39 TYR cc_start: 0.7103 (m-10) cc_final: 0.6661 (m-10)
REVERT: D   49 LEU cc_start: 0.8642 (tp) cc_final: 0.8333 (tp)
REVERT: D   50 LEU cc_start: 0.8650 (mm) cc_final: 0.7578 (mm)
REVERT: D   57 LEU cc_start: 0.8799 (pp) cc_final: 0.8525 (pp)
REVERT: D   65 PHE cc_start: 0.7555 (m-80) cc_final: 0.7340 (m-80)
REVERT: D   74 PHE cc_start: 0.9104 (m-80) cc_final: 0.8593 (m-80)
REVERT: D  169 LYS cc_start: 0.8977 (ptpp) cc_final: 0.8702 (ptpp)
REVERT: D  193 ARG cc_start: 0.8242 (ttt180) cc_final: 0.7987 (ttt180)
REVERT: D  195 THR cc_start: 0.8843 (m) cc_final: 0.8625 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2015
  time to fit residues: 32.6961
Evaluate side-chains
  95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 71 optimal weight:   20.0000
   chunk 82 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0970
   chunk 45 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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  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 = 0.3902 r_free = 0.3902 target = 0.110317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.088960 restraints weight = 28199.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.092002 restraints weight = 17674.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.094060 restraints weight = 12595.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.2667

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= 0.154
  Angle     :  0.665   6.894   9508  Z= 0.338
  Chirality :  0.045   0.147   1086
  Planarity :  0.005   0.059   1191
  Dihedral  :  6.268  78.362    965
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  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: -0.40 (0.29), residues: 846
  helix:  0.44 (0.35), residues: 203
  sheet: -0.28 (0.35), residues: 236
  loop : -0.50 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.003   TRP A  99 
 HIS   0.004   0.001   HIS C 159 
 PHE   0.015   0.002   PHE D  74 
 TYR   0.017   0.002   TYR A 280 
 ARG   0.008   0.001   ARG C  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  301)
  hydrogen bonds       : angle       5.48640 (  828)
  SS BOND              : bond        0.00402 (    5)
  SS BOND              : angle       1.19861 (   10)
  covalent geometry    : bond        0.00330 ( 6975)
  covalent geometry    : angle       0.66395 ( 9498)
  Misc. bond           : bond        0.00001 (    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
  115 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.9017 (ppp) cc_final: 0.8777 (ppp)
REVERT: A  272 MET cc_start: 0.8511 (ppp) cc_final: 0.8292 (ppp)
REVERT: A  280 TYR cc_start: 0.8961 (t80) cc_final: 0.8641 (t80)
REVERT: A  284 TRP cc_start: 0.8496 (m-10) cc_final: 0.7914 (m100)
REVERT: A  288 PHE cc_start: 0.8926 (m-80) cc_final: 0.7955 (m-80)
REVERT: A  325 TYR cc_start: 0.9175 (t80) cc_final: 0.8886 (t80)
REVERT: C   29 ASP cc_start: 0.8048 (t0) cc_final: 0.7625 (t0)
REVERT: C  166 LEU cc_start: 0.7890 (tt) cc_final: 0.7454 (tp)
REVERT: C  172 GLN cc_start: 0.8636 (mp-120) cc_final: 0.8002 (mp-120)
REVERT: D   39 TYR cc_start: 0.6812 (m-10) cc_final: 0.6589 (m-10)
REVERT: D   48 LYS cc_start: 0.8448 (tmtt) cc_final: 0.8216 (tptt)
REVERT: D   65 PHE cc_start: 0.7500 (m-80) cc_final: 0.7295 (m-80)
REVERT: D   74 PHE cc_start: 0.8964 (m-80) cc_final: 0.8520 (m-80)
REVERT: D   90 TYR cc_start: 0.7653 (m-10) cc_final: 0.7147 (m-80)
REVERT: D  169 LYS cc_start: 0.8881 (ptpp) cc_final: 0.8596 (ptpp)
REVERT: D  193 ARG cc_start: 0.8238 (ttt180) cc_final: 0.8004 (ttt180)
REVERT: D  195 THR cc_start: 0.8788 (m) cc_final: 0.8588 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1841
  time to fit residues: 28.3309
Evaluate side-chains
  99 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 67.1288 > 50:
  distance: 2 - 17:  22.045
  distance: 6 - 24:  33.404
  distance: 11 - 29:  19.975
  distance: 14 - 17:  23.383
  distance: 15 - 37:  31.416
  distance: 17 - 18:  16.793
  distance: 18 - 19:  10.752
  distance: 18 - 21:  19.670
  distance: 19 - 20:  10.316
  distance: 19 - 24:  13.295
  distance: 20 - 43:  24.560
  distance: 21 - 22:  25.177
  distance: 21 - 23:  23.345
  distance: 24 - 25:  27.428
  distance: 25 - 26:  32.372
  distance: 25 - 28:  32.676
  distance: 26 - 27:  51.723
  distance: 26 - 29:  56.792
  distance: 27 - 51:  24.910
  distance: 29 - 30:  57.077
  distance: 30 - 31:  23.323
  distance: 30 - 33:  28.415
  distance: 31 - 32:   9.009
  distance: 31 - 37:  23.682
  distance: 32 - 55:  47.866
  distance: 33 - 34:  11.449
  distance: 34 - 35:  22.356
  distance: 34 - 36:  20.974
  distance: 37 - 38:  25.249
  distance: 38 - 39:  32.594
  distance: 38 - 41:  17.553
  distance: 39 - 40:  34.233
  distance: 39 - 43:  38.423
  distance: 40 - 63:  17.786
  distance: 41 - 42:  45.427
  distance: 43 - 44:  49.000
  distance: 44 - 45:  24.156
  distance: 44 - 47:  53.330
  distance: 45 - 46:   9.649
  distance: 45 - 51:  15.830
  distance: 46 - 70:  20.407
  distance: 47 - 48:  18.370
  distance: 48 - 49:  22.846
  distance: 48 - 50:  16.472
  distance: 51 - 52:  16.661
  distance: 52 - 53:  26.851
  distance: 53 - 54:  18.933
  distance: 53 - 55:   5.327
  distance: 54 - 78:  43.379
  distance: 55 - 56:  34.439
  distance: 56 - 57:   8.592
  distance: 56 - 59:  10.224
  distance: 57 - 58:  28.172
  distance: 57 - 63:  29.879
  distance: 58 - 83:  29.136
  distance: 59 - 60:  50.749
  distance: 60 - 61:  56.890
  distance: 60 - 62:  55.044
  distance: 63 - 64:  22.206
  distance: 64 - 65:  32.596
  distance: 64 - 67:  26.460
  distance: 65 - 66:  31.583
  distance: 65 - 70:  24.437
  distance: 66 - 88:  21.607
  distance: 70 - 71:  17.380
  distance: 71 - 72:  25.544
  distance: 71 - 74:   9.698
  distance: 72 - 73:  11.266
  distance: 72 - 78:  39.546
  distance: 73 - 96:  29.335
  distance: 75 - 76:  26.034
  distance: 75 - 77:  31.891
  distance: 78 - 79:  37.945
  distance: 80 - 83:  34.759
  distance: 81 - 101:  31.245