Starting phenix.real_space_refine
on Tue Mar  3 16:18:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r0c_14221/03_2026/7r0c_14221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r0c_14221/03_2026/7r0c_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_14221/03_2026/7r0c_14221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r0c_14221/03_2026/7r0c_14221.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r0c_14221/03_2026/7r0c_14221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r0c_14221/03_2026/7r0c_14221.cif"
  }
  resolution = 4.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.035
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3, 'TPO:plan-1': 2}
          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: 1.57, per 1000 atoms: 0.23
  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: 0.70
  Conformation dependent library (CDL) restraints added in 255.2 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: 0.22
  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: 1.08

  Time building geometry restraints manager: 0.88 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:             0.660
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.970
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.110
-------------------------------------------------------------------------------
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 : 26.40
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.008   0.001   ARG D  64 
 TYR   0.020   0.002   TYR A 128 
 PHE   0.023   0.002   PHE D 228 
 TRP   0.042   0.003   TRP A  99 
 HIS   0.006   0.002   HIS C 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 6975)
  covalent geometry    : angle       0.90892 ( 9498)
  SS BOND              : bond        0.00161 (    5)
  SS BOND              : angle       1.12490 (   10)
  hydrogen bonds       : bond        0.15121 (  301)
  hydrogen bonds       : angle       6.94444 (  828)
  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  : 0.259 
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: 0.8336 (m-80)
REVERT: C   75 PHE cc_start: 0.6481 (m-80) cc_final: 0.5777 (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: 0.8828 (tmtt)
REVERT: D   49 LEU cc_start: 0.8528 (tp) cc_final: 0.8281 (tp)
REVERT: D   50 LEU cc_start: 0.8422 (mt) cc_final: 0.7654 (mt)
REVERT: D   74 PHE cc_start: 0.9063 (m-80) cc_final: 0.8474 (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: 0.6420 (mpp)
  outliers start: 1
  outliers final: 1
  residues processed: 131
  average time/residue: 0.0871
  time to fit residues: 15.1860
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  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 237 GLN
D   9 GLN
D 165 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.110167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.088401 restraints weight = 28287.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.091469 restraints weight = 17812.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.093606 restraints weight = 12730.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.095033 restraints weight = 9934.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.096042 restraints weight = 8296.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6981  Z= 0.179
  Angle     :  0.677   7.827   9508  Z= 0.349
  Chirality :  0.045   0.175   1086
  Planarity :  0.005   0.058   1191
  Dihedral  :  6.454  74.689    965
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 17.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.88 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.29), residues: 846
  helix: -0.06 (0.34), residues: 211
  sheet: -0.28 (0.34), residues: 244
  loop : -0.69 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 236 
 TYR   0.014   0.002   TYR A 128 
 PHE   0.024   0.002   PHE D 228 
 TRP   0.026   0.002   TRP A  99 
 HIS   0.006   0.002   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6975)
  covalent geometry    : angle       0.67627 ( 9498)
  SS BOND              : bond        0.00161 (    5)
  SS BOND              : angle       0.96432 (   10)
  hydrogen bonds       : bond        0.04136 (  301)
  hydrogen bonds       : angle       6.07802 (  828)
  Misc. bond           : bond        0.00008 (    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
  128 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.258 
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: 0.9094 (ppp) cc_final: 0.8821 (ppp)
REVERT: A  272 MET cc_start: 0.8488 (ppp) cc_final: 0.8261 (ppp)
REVERT: A  288 PHE cc_start: 0.8953 (m-80) cc_final: 0.8428 (m-80)
REVERT: C   10 LYS cc_start: 0.7749 (pttt) cc_final: 0.7183 (pmtt)
REVERT: C   75 PHE cc_start: 0.6577 (m-80) cc_final: 0.5777 (m-10)
REVERT: C  172 GLN cc_start: 0.8678 (mp-120) cc_final: 0.8006 (mp-120)
REVERT: C  223 ASN cc_start: 0.8090 (m-40) cc_final: 0.7734 (p0)
REVERT: C  233 ILE cc_start: 0.9020 (mm) cc_final: 0.8746 (mm)
REVERT: C  315 LEU cc_start: 0.9186 (mm) cc_final: 0.8983 (mm)
REVERT: D   74 PHE cc_start: 0.9025 (m-80) cc_final: 0.8621 (m-80)
REVERT: D  195 THR cc_start: 0.8725 (m) cc_final: 0.8520 (p)
REVERT: D  209 MET cc_start: 0.6927 (mpp) cc_final: 0.6360 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0813
  time to fit residues: 13.9475
Evaluate side-chains
  87 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 56 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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**
C 281 ASN
** 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 = 0.3856 r_free = 0.3856 target = 0.107929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.085812 restraints weight = 28455.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.088717 restraints weight = 18027.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.090775 restraints weight = 13004.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.092148 restraints weight = 10241.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.092993 restraints weight = 8625.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.1636

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= 0.194
  Angle     :  0.672   7.553   9508  Z= 0.348
  Chirality :  0.045   0.155   1086
  Planarity :  0.005   0.059   1191
  Dihedral  :  6.493  77.659    965
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 20.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.29), residues: 846
  helix:  0.10 (0.34), residues: 211
  sheet: -0.57 (0.34), residues: 256
  loop : -0.57 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 193 
 TYR   0.026   0.002   TYR D  52 
 PHE   0.025   0.002   PHE D 228 
 TRP   0.042   0.002   TRP A  99 
 HIS   0.005   0.002   HIS C 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6975)
  covalent geometry    : angle       0.67081 ( 9498)
  SS BOND              : bond        0.00282 (    5)
  SS BOND              : angle       1.34550 (   10)
  hydrogen bonds       : bond        0.04256 (  301)
  hydrogen bonds       : angle       6.00678 (  828)
  Misc. bond           : bond        0.00004 (    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
  121 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7417 (mmp) cc_final: 0.7099 (mmp)
REVERT: A  133 MET cc_start: 0.9016 (ppp) cc_final: 0.8757 (ppp)
REVERT: A  276 ILE cc_start: 0.9343 (pt) cc_final: 0.8828 (pt)
REVERT: A  288 PHE cc_start: 0.8835 (m-80) cc_final: 0.8432 (m-80)
REVERT: C  172 GLN cc_start: 0.8669 (mp-120) cc_final: 0.8187 (mp-120)
REVERT: C  223 ASN cc_start: 0.8140 (m-40) cc_final: 0.7868 (p0)
REVERT: D   48 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8565 (tmtt)
REVERT: D   49 LEU cc_start: 0.8574 (tp) cc_final: 0.8194 (tp)
REVERT: D   50 LEU cc_start: 0.8799 (mt) cc_final: 0.7991 (mm)
REVERT: D   65 PHE cc_start: 0.8274 (m-10) cc_final: 0.7926 (m-80)
REVERT: D   74 PHE cc_start: 0.8883 (m-80) cc_final: 0.8500 (m-80)
REVERT: D  195 THR cc_start: 0.8782 (m) cc_final: 0.8537 (p)
REVERT: D  209 MET cc_start: 0.7083 (mpp) cc_final: 0.6475 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0875
  time to fit residues: 14.2741
Evaluate side-chains
  87 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0770
   chunk 84 optimal weight:    0.4980
   chunk 83 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0570
   chunk 15 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
C 122 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 = 0.3966 r_free = 0.3966 target = 0.114444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.092463 restraints weight = 28882.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.095751 restraints weight = 17664.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.097991 restraints weight = 12426.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.099478 restraints weight = 9583.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.100601 restraints weight = 7924.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6981  Z= 0.119
  Angle     :  0.632   8.512   9508  Z= 0.317
  Chirality :  0.045   0.164   1086
  Planarity :  0.004   0.057   1191
  Dihedral  :  6.156  77.585    965
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.29), residues: 846
  helix:  0.30 (0.34), residues: 210
  sheet: -0.40 (0.33), residues: 263
  loop : -0.56 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  62 
 TYR   0.010   0.001   TYR C 238 
 PHE   0.020   0.001   PHE D 228 
 TRP   0.031   0.002   TRP D  38 
 HIS   0.005   0.001   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6975)
  covalent geometry    : angle       0.63179 ( 9498)
  SS BOND              : bond        0.00118 (    5)
  SS BOND              : angle       0.74004 (   10)
  hydrogen bonds       : bond        0.03657 (  301)
  hydrogen bonds       : angle       5.49446 (  828)
  Misc. bond           : bond        0.00001 (    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
  136 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.220 
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: 0.9094 (ppp) cc_final: 0.8828 (ppp)
REVERT: A  134 THR cc_start: 0.9266 (p) cc_final: 0.9055 (p)
REVERT: A  288 PHE cc_start: 0.8915 (m-80) cc_final: 0.8625 (m-80)
REVERT: C   29 ASP cc_start: 0.8193 (t0) cc_final: 0.7675 (t0)
REVERT: C  172 GLN cc_start: 0.8695 (mp-120) cc_final: 0.8163 (mm-40)
REVERT: C  315 LEU cc_start: 0.9205 (mm) cc_final: 0.8994 (mm)
REVERT: D   39 TYR cc_start: 0.6994 (m-10) cc_final: 0.6749 (m-10)
REVERT: D   49 LEU cc_start: 0.8508 (tp) cc_final: 0.8279 (tp)
REVERT: D   50 LEU cc_start: 0.8878 (mt) cc_final: 0.8153 (mt)
REVERT: D   57 LEU cc_start: 0.8795 (pp) cc_final: 0.8553 (pp)
REVERT: D   65 PHE cc_start: 0.8207 (m-10) cc_final: 0.7994 (m-80)
REVERT: D   74 PHE cc_start: 0.8917 (m-80) cc_final: 0.8596 (m-80)
REVERT: D   75 THR cc_start: 0.8480 (p) cc_final: 0.8190 (p)
REVERT: D  195 THR cc_start: 0.8667 (m) cc_final: 0.8414 (p)
REVERT: D  209 MET cc_start: 0.6920 (mpp) cc_final: 0.6418 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1062
  time to fit residues: 18.4275
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  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.2980
   chunk 0 optimal weight:   20.0000
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0020
   chunk 38 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.8190

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.113343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.090822 restraints weight = 28332.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.094094 restraints weight = 17258.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.096248 restraints weight = 12105.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.097747 restraints weight = 9402.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.098728 restraints weight = 7819.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6981  Z= 0.125
  Angle     :  0.636   6.636   9508  Z= 0.320
  Chirality :  0.045   0.175   1086
  Planarity :  0.005   0.057   1191
  Dihedral  :  6.107  78.882    965
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.01 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.29), residues: 846
  helix:  0.36 (0.34), residues: 211
  sheet: -0.35 (0.33), residues: 265
  loop : -0.52 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 213 
 TYR   0.025   0.001   TYR D  52 
 PHE   0.016   0.001   PHE D 228 
 TRP   0.059   0.003   TRP A  99 
 HIS   0.013   0.002   HIS A  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6975)
  covalent geometry    : angle       0.63417 ( 9498)
  SS BOND              : bond        0.00614 (    5)
  SS BOND              : angle       1.45978 (   10)
  hydrogen bonds       : bond        0.03612 (  301)
  hydrogen bonds       : angle       5.36768 (  828)
  Misc. bond           : bond        0.00000 (    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
  133 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.258 
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: 0.9725 (mm) cc_final: 0.9525 (mm)
REVERT: A  133 MET cc_start: 0.9185 (ppp) cc_final: 0.8926 (ppp)
REVERT: A  288 PHE cc_start: 0.8811 (m-80) cc_final: 0.8508 (m-80)
REVERT: C   29 ASP cc_start: 0.8130 (t0) cc_final: 0.7705 (t0)
REVERT: C  172 GLN cc_start: 0.8649 (mp-120) cc_final: 0.7885 (mp-120)
REVERT: C  223 ASN cc_start: 0.8047 (m-40) cc_final: 0.7765 (p0)
REVERT: C  315 LEU cc_start: 0.9133 (mm) cc_final: 0.8898 (mm)
REVERT: D   39 TYR cc_start: 0.7064 (m-10) cc_final: 0.6858 (m-10)
REVERT: D   65 PHE cc_start: 0.8071 (m-10) cc_final: 0.7857 (m-80)
REVERT: D   74 PHE cc_start: 0.8904 (m-80) cc_final: 0.8658 (m-80)
REVERT: D  106 LYS cc_start: 0.8875 (tptp) cc_final: 0.8647 (tptt)
REVERT: D  193 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7863 (ttt180)
REVERT: D  195 THR cc_start: 0.8590 (m) cc_final: 0.8324 (p)
REVERT: D  209 MET cc_start: 0.7130 (mpp) cc_final: 0.6639 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0847
  time to fit residues: 15.1133
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  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 83 optimal weight:    0.5980
   chunk 74 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0980
   chunk 35 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0270
   chunk 80 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.4438

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.115315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.093247 restraints weight = 27373.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.096437 restraints weight = 17003.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.098578 restraints weight = 12115.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.100058 restraints weight = 9479.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.101067 restraints weight = 7903.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.2722

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= 0.116
  Angle     :  0.633   6.695   9508  Z= 0.316
  Chirality :  0.045   0.162   1086
  Planarity :  0.005   0.076   1191
  Dihedral  :  5.967  79.106    965
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.30), residues: 846
  helix:  0.64 (0.36), residues: 202
  sheet: -0.11 (0.34), residues: 255
  loop : -0.49 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 236 
 TYR   0.015   0.001   TYR A 325 
 PHE   0.016   0.001   PHE D 228 
 TRP   0.035   0.003   TRP A  99 
 HIS   0.004   0.001   HIS D 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6975)
  covalent geometry    : angle       0.63191 ( 9498)
  SS BOND              : bond        0.00234 (    5)
  SS BOND              : angle       1.44361 (   10)
  hydrogen bonds       : bond        0.03491 (  301)
  hydrogen bonds       : angle       5.16081 (  828)
  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
  128 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.283 
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: 0.7612 (mmp) cc_final: 0.7386 (mmp)
REVERT: A  130 ILE cc_start: 0.9658 (mm) cc_final: 0.9458 (mm)
REVERT: A  133 MET cc_start: 0.9168 (ppp) cc_final: 0.8912 (ppp)
REVERT: A  280 TYR cc_start: 0.8871 (t80) cc_final: 0.8486 (t80)
REVERT: A  284 TRP cc_start: 0.7981 (m-10) cc_final: 0.7458 (m100)
REVERT: A  288 PHE cc_start: 0.8872 (m-80) cc_final: 0.8031 (m-80)
REVERT: C   29 ASP cc_start: 0.8070 (t0) cc_final: 0.7684 (t0)
REVERT: C  172 GLN cc_start: 0.8755 (mp-120) cc_final: 0.7965 (mp-120)
REVERT: C  223 ASN cc_start: 0.8020 (m-40) cc_final: 0.7737 (p0)
REVERT: C  315 LEU cc_start: 0.9086 (mm) cc_final: 0.8841 (mm)
REVERT: D   73 ASP cc_start: 0.8865 (m-30) cc_final: 0.8345 (m-30)
REVERT: D   74 PHE cc_start: 0.9170 (m-80) cc_final: 0.8471 (m-80)
REVERT: D  193 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7686 (ttt-90)
REVERT: D  195 THR cc_start: 0.8665 (m) cc_final: 0.8325 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0770
  time to fit residues: 13.0700
Evaluate side-chains
  101 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 59 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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 159 HIS ** 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 = 0.3946 r_free = 0.3946 target = 0.113333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.091120 restraints weight = 27502.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.094262 restraints weight = 17283.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.096385 restraints weight = 12329.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.097699 restraints weight = 9617.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.098810 restraints weight = 8142.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6981  Z= 0.124
  Angle     :  0.625   6.800   9508  Z= 0.315
  Chirality :  0.044   0.145   1086
  Planarity :  0.005   0.090   1191
  Dihedral  :  5.966  79.237    965
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.30), residues: 846
  helix:  0.73 (0.36), residues: 202
  sheet: -0.08 (0.35), residues: 240
  loop : -0.54 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 236 
 TYR   0.024   0.002   TYR A 325 
 PHE   0.018   0.002   PHE D 228 
 TRP   0.027   0.002   TRP A 284 
 HIS   0.006   0.001   HIS C 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6975)
  covalent geometry    : angle       0.62364 ( 9498)
  SS BOND              : bond        0.00232 (    5)
  SS BOND              : angle       1.44280 (   10)
  hydrogen bonds       : bond        0.03476 (  301)
  hydrogen bonds       : angle       5.12603 (  828)
  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
  128 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7611 (mmp) cc_final: 0.7285 (mmp)
REVERT: A  134 THR cc_start: 0.9350 (m) cc_final: 0.9037 (m)
REVERT: A  272 MET cc_start: 0.8488 (ppp) cc_final: 0.8282 (ppp)
REVERT: A  288 PHE cc_start: 0.8893 (m-80) cc_final: 0.8490 (m-80)
REVERT: C   29 ASP cc_start: 0.8215 (t0) cc_final: 0.7823 (t0)
REVERT: C  172 GLN cc_start: 0.8737 (mp-120) cc_final: 0.8037 (mp-120)
REVERT: C  223 ASN cc_start: 0.8063 (m-40) cc_final: 0.7813 (p0)
REVERT: D   50 LEU cc_start: 0.8978 (mp) cc_final: 0.8573 (mp)
REVERT: D   65 PHE cc_start: 0.7519 (m-80) cc_final: 0.7302 (m-80)
REVERT: D   73 ASP cc_start: 0.8902 (m-30) cc_final: 0.8525 (m-30)
REVERT: D   74 PHE cc_start: 0.9181 (m-80) cc_final: 0.8450 (m-80)
REVERT: D  193 ARG cc_start: 0.8134 (ttt180) cc_final: 0.7884 (ttt180)
REVERT: D  195 THR cc_start: 0.8756 (m) cc_final: 0.8545 (p)
REVERT: D  209 MET cc_start: 0.7108 (mpp) cc_final: 0.6483 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0799
  time to fit residues: 13.8993
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  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 27 optimal weight:    9.9990
   chunk 58 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 299 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.113601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.091161 restraints weight = 27619.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.094398 restraints weight = 17160.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.096586 restraints weight = 12154.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.098045 restraints weight = 9460.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.099141 restraints weight = 7883.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.2855

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= 0.128
  Angle     :  0.639   6.940   9508  Z= 0.320
  Chirality :  0.044   0.143   1086
  Planarity :  0.005   0.059   1191
  Dihedral  :  5.976  79.234    965
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.29), residues: 846
  helix:  0.58 (0.35), residues: 203
  sheet: -0.05 (0.34), residues: 248
  loop : -0.51 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 213 
 TYR   0.012   0.001   TYR A 325 
 PHE   0.023   0.002   PHE A 307 
 TRP   0.068   0.003   TRP A  99 
 HIS   0.004   0.001   HIS C 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6975)
  covalent geometry    : angle       0.63697 ( 9498)
  SS BOND              : bond        0.00177 (    5)
  SS BOND              : angle       1.60008 (   10)
  hydrogen bonds       : bond        0.03504 (  301)
  hydrogen bonds       : angle       5.11345 (  828)
  Misc. bond           : bond        0.00000 (    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
  128 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.8916 (ppp) cc_final: 0.8647 (ppp)
REVERT: A  134 THR cc_start: 0.9428 (m) cc_final: 0.9097 (m)
REVERT: A  166 PHE cc_start: 0.7592 (t80) cc_final: 0.7383 (t80)
REVERT: A  280 TYR cc_start: 0.8994 (t80) cc_final: 0.8617 (t80)
REVERT: A  284 TRP cc_start: 0.8179 (m-10) cc_final: 0.7600 (m100)
REVERT: A  288 PHE cc_start: 0.8865 (m-80) cc_final: 0.7838 (m-80)
REVERT: A  325 TYR cc_start: 0.9267 (t80) cc_final: 0.9027 (t80)
REVERT: C   29 ASP cc_start: 0.7965 (t0) cc_final: 0.7562 (t0)
REVERT: C  172 GLN cc_start: 0.8645 (mp-120) cc_final: 0.7966 (mp-120)
REVERT: C  223 ASN cc_start: 0.8041 (m-40) cc_final: 0.7836 (p0)
REVERT: D   48 LYS cc_start: 0.8392 (tmtt) cc_final: 0.8187 (tptt)
REVERT: D   65 PHE cc_start: 0.7436 (m-80) cc_final: 0.7208 (m-80)
REVERT: D   73 ASP cc_start: 0.8813 (m-30) cc_final: 0.8371 (m-30)
REVERT: D   74 PHE cc_start: 0.8957 (m-80) cc_final: 0.8094 (m-80)
REVERT: D   75 THR cc_start: 0.8470 (p) cc_final: 0.8203 (p)
REVERT: D  193 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7725 (ttt-90)
REVERT: D  195 THR cc_start: 0.8664 (m) cc_final: 0.8458 (p)
REVERT: D  209 MET cc_start: 0.6951 (mpp) cc_final: 0.6308 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0767
  time to fit residues: 13.4175
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  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 159 HIS ** 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 = 0.3913 r_free = 0.3913 target = 0.110899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.088762 restraints weight = 28893.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.091845 restraints weight = 17984.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.093973 restraints weight = 12792.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.095421 restraints weight = 9952.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.096428 restraints weight = 8313.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6981  Z= 0.168
  Angle     :  0.667   7.032   9508  Z= 0.338
  Chirality :  0.045   0.141   1086
  Planarity :  0.005   0.059   1191
  Dihedral  :  6.151  80.142    965
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.30), residues: 846
  helix:  0.46 (0.35), residues: 202
  sheet: -0.11 (0.35), residues: 239
  loop : -0.49 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 213 
 TYR   0.023   0.002   TYR D  52 
 PHE   0.022   0.002   PHE D 228 
 TRP   0.057   0.003   TRP D  38 
 HIS   0.005   0.001   HIS C 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6975)
  covalent geometry    : angle       0.66498 ( 9498)
  SS BOND              : bond        0.00160 (    5)
  SS BOND              : angle       1.62169 (   10)
  hydrogen bonds       : bond        0.03800 (  301)
  hydrogen bonds       : angle       5.34342 (  828)
  Misc. bond           : bond        0.00000 (    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
  129 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.8925 (ppp) cc_final: 0.8679 (ppp)
REVERT: A  134 THR cc_start: 0.9490 (m) cc_final: 0.9147 (m)
REVERT: A  288 PHE cc_start: 0.8871 (m-80) cc_final: 0.8568 (m-80)
REVERT: A  325 TYR cc_start: 0.9312 (t80) cc_final: 0.9019 (t80)
REVERT: C   29 ASP cc_start: 0.7989 (t0) cc_final: 0.7540 (t0)
REVERT: C  172 GLN cc_start: 0.8602 (mp-120) cc_final: 0.7885 (mp-120)
REVERT: D   48 LYS cc_start: 0.8550 (tmtt) cc_final: 0.8261 (tptt)
REVERT: D   65 PHE cc_start: 0.7420 (m-80) cc_final: 0.7180 (m-80)
REVERT: D   73 ASP cc_start: 0.8900 (m-30) cc_final: 0.8461 (m-30)
REVERT: D   74 PHE cc_start: 0.9133 (m-80) cc_final: 0.8441 (m-80)
REVERT: D  193 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7821 (ttt180)
REVERT: D  195 THR cc_start: 0.8719 (m) cc_final: 0.8464 (p)
REVERT: D  202 LYS cc_start: 0.9191 (tppt) cc_final: 0.8812 (tppt)
REVERT: D  209 MET cc_start: 0.6988 (mpp) cc_final: 0.6255 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0875
  time to fit residues: 15.1807
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  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 14 optimal weight:   20.0000
   chunk 78 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0000
   chunk 13 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   overall best weight:    4.7992

-------------------------------------------------------------------------------
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**
B   4 GLN
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 HIS ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.103095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.081528 restraints weight = 29848.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.084333 restraints weight = 18881.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.086284 restraints weight = 13587.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.087591 restraints weight = 10717.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.088586 restraints weight = 9034.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   6981  Z= 0.351
  Angle     :  0.889   9.983   9508  Z= 0.462
  Chirality :  0.052   0.187   1086
  Planarity :  0.007   0.062   1191
  Dihedral  :  7.131  81.719    965
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 31.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.29), residues: 846
  helix: -0.16 (0.35), residues: 202
  sheet: -0.69 (0.35), residues: 227
  loop : -0.71 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 236 
 TYR   0.026   0.003   TYR D 181 
 PHE   0.035   0.004   PHE C  27 
 TRP   0.075   0.005   TRP D  38 
 HIS   0.010   0.003   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00722 ( 6975)
  covalent geometry    : angle       0.88650 ( 9498)
  SS BOND              : bond        0.00415 (    5)
  SS BOND              : angle       2.11417 (   10)
  hydrogen bonds       : bond        0.05231 (  301)
  hydrogen bonds       : angle       6.47945 (  828)
  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
  110 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7312 (mmp) cc_final: 0.7026 (mmp)
REVERT: A  133 MET cc_start: 0.8880 (ppp) cc_final: 0.8633 (ppp)
REVERT: A  134 THR cc_start: 0.9571 (m) cc_final: 0.9183 (m)
REVERT: A  272 MET cc_start: 0.8498 (ppp) cc_final: 0.8244 (ppp)
REVERT: A  288 PHE cc_start: 0.8989 (m-80) cc_final: 0.8579 (m-80)
REVERT: A  325 TYR cc_start: 0.9399 (t80) cc_final: 0.9118 (t80)
REVERT: D   65 PHE cc_start: 0.7548 (m-80) cc_final: 0.7245 (m-80)
REVERT: D   73 ASP cc_start: 0.9007 (m-30) cc_final: 0.8763 (m-30)
REVERT: D  195 THR cc_start: 0.8816 (m) cc_final: 0.8554 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0812
  time to fit residues: 12.1407
Evaluate side-chains
  83 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 56 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0970
   chunk 7 optimal weight:    6.9990
   overall best weight:    2.5984

-------------------------------------------------------------------------------
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 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 = 0.3847 r_free = 0.3847 target = 0.106535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.085549 restraints weight = 28948.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.088396 restraints weight = 18302.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.090358 restraints weight = 13152.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.091589 restraints weight = 10335.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.092627 restraints weight = 8734.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6981  Z= 0.214
  Angle     :  0.754   9.764   9508  Z= 0.384
  Chirality :  0.048   0.164   1086
  Planarity :  0.006   0.058   1191
  Dihedral  :  6.868  80.793    965
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 25.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.30), residues: 846
  helix: -0.10 (0.35), residues: 202
  sheet: -0.70 (0.35), residues: 231
  loop : -0.68 (0.33), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 213 
 TYR   0.029   0.002   TYR D  52 
 PHE   0.023   0.002   PHE D 228 
 TRP   0.063   0.003   TRP D  38 
 HIS   0.005   0.002   HIS C  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 6975)
  covalent geometry    : angle       0.75333 ( 9498)
  SS BOND              : bond        0.00164 (    5)
  SS BOND              : angle       1.49453 (   10)
  hydrogen bonds       : bond        0.04335 (  301)
  hydrogen bonds       : angle       6.11723 (  828)
  Misc. bond           : bond        0.00006 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1308.25 seconds
wall clock time: 23 minutes 22.43 seconds (1402.43 seconds total)