Starting phenix.real_space_refine
on Fri Mar 14 02:59:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v8i_31802/03_2025/7v8i_31802_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v8i_31802/03_2025/7v8i_31802.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v8i_31802/03_2025/7v8i_31802.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v8i_31802/03_2025/7v8i_31802.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v8i_31802/03_2025/7v8i_31802_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v8i_31802/03_2025/7v8i_31802_neut.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.077
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      47      5.16       5
     C    5956      2.51       5
     N    1651      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9388
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 2841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 2841
          Classifications: {'peptide': 396}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 21, 'TRANS': 374}
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 108
    Chain: "D"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1751
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 2978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 2978
          Classifications: {'peptide': 407}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 14, 'TRANS': 392}
          Unresolved non-hydrogen bonds: 171
          Unresolved non-hydrogen angles: 207
          Unresolved non-hydrogen dihedrals: 150
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 101
    Chain: "F"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1754
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.24, per 1000 atoms: 0.66
  Number of scatterers: 9388
  At special positions: 0
  Unit cell: (95, 86, 159, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      47     16.00
     P       6     15.00
     Mg      2     11.99
     O    1726      8.00
     N    1651      7.00
     C    5956      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2308

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 9 sheets defined
      48.8% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'C' and resid 7 through 16
    Processing helix  chain 'C' and resid 22 through 28
    Processing helix  chain 'C' and resid 28 through 59
      removed outlier: 3.764A  pdb=" N   ILE C  34 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'C' and resid 148 through 155
    Processing helix  chain 'C' and resid 195 through 198
      removed outlier: 3.549A  pdb=" N   GLY C 198 " --> pdb=" O   GLU C 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 195 through 198'
    Processing helix  chain 'C' and resid 205 through 212
    Processing helix  chain 'C' and resid 233 through 237
      removed outlier: 3.824A  pdb=" N   SER C 236 " --> pdb=" O   ASP C 233 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLN C 237 " --> pdb=" O   SER C 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 233 through 237'
    Processing helix  chain 'C' and resid 254 through 293
      removed outlier: 3.816A  pdb=" N   GLN C 258 " --> pdb=" O   GLY C 254 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   SER C 285 " --> pdb=" O   ASN C 281 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU C 286 " --> pdb=" O   ILE C 282 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   MET C 291 " --> pdb=" O   GLY C 287 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS C 293 " --> pdb=" O   MET C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 303
    Processing helix  chain 'C' and resid 306 through 335
    Processing helix  chain 'C' and resid 340 through 344
    Processing helix  chain 'C' and resid 361 through 379
    Processing helix  chain 'C' and resid 381 through 390
    Processing helix  chain 'D' and resid 48 through 56
    Processing helix  chain 'D' and resid 77 through 88
    Processing helix  chain 'D' and resid 103 through 115
      Proline residue:  D 111  - end of helix
    Processing helix  chain 'D' and resid 118 through 134
      removed outlier: 3.744A  pdb=" N   SER D 124 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 146
    Processing helix  chain 'D' and resid 147 through 161
    Processing helix  chain 'D' and resid 177 through 195
    Processing helix  chain 'D' and resid 205 through 211
    Processing helix  chain 'E' and resid 11 through 17
      removed outlier: 4.169A  pdb=" N   ARG E  15 " --> pdb=" O   LEU E  11 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 60
      removed outlier: 3.601A  pdb=" N   LEU E  60 " --> pdb=" O   ASN E  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 87
      removed outlier: 4.254A  pdb=" N   ALA E  81 " --> pdb=" O   ASN E  77 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LYS E  87 " --> pdb=" O   ASP E  83 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 127
    Processing helix  chain 'E' and resid 128 through 133
      removed outlier: 3.657A  pdb=" N   VAL E 133 " --> pdb=" O   LEU E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 137 through 142
    Processing helix  chain 'E' and resid 151 through 159
      removed outlier: 5.161A  pdb=" N   ALA E 157 " --> pdb=" O   GLY E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 197 through 201
      removed outlier: 3.536A  pdb=" N   HIS E 201 " --> pdb=" O   GLN E 198 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 215
    Processing helix  chain 'E' and resid 233 through 243
    Processing helix  chain 'E' and resid 258 through 294
      removed outlier: 4.044A  pdb=" N   LEU E 278 " --> pdb=" O   LEU E 274 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET E 293 " --> pdb=" O   SER E 289 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 296 through 305
    Processing helix  chain 'E' and resid 313 through 344
      removed outlier: 3.879A  pdb=" N   GLN E 344 " --> pdb=" O   VAL E 340 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 348 through 353
      removed outlier: 4.552A  pdb=" N   ILE E 352 " --> pdb=" O   ILE E 348 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 354 through 356
      No H-bonds generated for 'chain 'E' and resid 354 through 356'
    Processing helix  chain 'E' and resid 376 through 405
      Proline residue:  E 398  - end of helix
      removed outlier: 3.593A  pdb=" N   ILE E 405 " --> pdb=" O   ARG E 401 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 406 through 410
    Processing helix  chain 'F' and resid 48 through 56
    Processing helix  chain 'F' and resid 77 through 88
    Processing helix  chain 'F' and resid 103 through 115
      Proline residue:  F 111  - end of helix
    Processing helix  chain 'F' and resid 118 through 134
    Processing helix  chain 'F' and resid 142 through 146
    Processing helix  chain 'F' and resid 147 through 162
      removed outlier: 4.798A  pdb=" N   ASN F 162 " --> pdb=" O   ARG F 158 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 194
    Processing helix  chain 'F' and resid 205 through 211
    Processing sheet with id=AA1, first strand: chain 'C' and resid 176 through 185
      removed outlier: 11.767A  pdb=" N   GLY C 176 " --> pdb=" O   SER C 170 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   SER C 170 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
      removed outlier: 9.671A  pdb=" N   ILE C 178 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   SER C 168 " --> pdb=" O   ILE C 178 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER C 180 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
      removed outlier: 9.748A  pdb=" N   ASP C 100 " --> pdb=" O   PRO C 167 " (cutoff:3.500A)
      removed outlier: 11.076A  pdb=" N   ALA C 169 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 15.544A  pdb=" N   THR C  98 " --> pdb=" O   ALA C 169 " (cutoff:3.500A)
      removed outlier: 22.573A  pdb=" N   GLN C 171 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
      removed outlier: 27.579A  pdb=" N   ILE C  96 " --> pdb=" O   GLN C 171 " (cutoff:3.500A)
      removed outlier: 35.076A  pdb=" N   THR C 173 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 39.560A  pdb=" N   ALA C  94 " --> pdb=" O   THR C 173 " (cutoff:3.500A)
      removed outlier: 8.380A  pdb=" N   MET C 201 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL C 113 " --> pdb=" O   MET C 201 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   VAL C 203 " --> pdb=" O   VAL C 113 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   LEU C 115 " --> pdb=" O   VAL C 203 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 176 through 185
      removed outlier: 11.767A  pdb=" N   GLY C 176 " --> pdb=" O   SER C 170 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   SER C 170 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
      removed outlier: 9.671A  pdb=" N   ILE C 178 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   SER C 168 " --> pdb=" O   ILE C 178 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER C 180 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
      removed outlier: 9.748A  pdb=" N   ASP C 100 " --> pdb=" O   PRO C 167 " (cutoff:3.500A)
      removed outlier: 11.076A  pdb=" N   ALA C 169 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 15.544A  pdb=" N   THR C  98 " --> pdb=" O   ALA C 169 " (cutoff:3.500A)
      removed outlier: 22.573A  pdb=" N   GLN C 171 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
      removed outlier: 27.579A  pdb=" N   ILE C  96 " --> pdb=" O   GLN C 171 " (cutoff:3.500A)
      removed outlier: 35.076A  pdb=" N   THR C 173 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 39.560A  pdb=" N   ALA C  94 " --> pdb=" O   THR C 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 129 through 130
      removed outlier: 4.188A  pdb=" N   VAL C 130 " --> pdb=" O   THR C 189 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   THR C 189 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 25 through 32
      removed outlier: 7.029A  pdb=" N   HIS D  26 " --> pdb=" O   CYS D  12 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   CYS D  12 " --> pdb=" O   HIS D  26 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   VAL D  28 " --> pdb=" O   ASN D  10 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASN D  10 " --> pdb=" O   VAL D  28 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LEU D  11 " --> pdb=" O   SER D  63 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER D  63 " --> pdb=" O   LEU D  11 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 92
      removed outlier: 6.439A  pdb=" N   VAL D 167 " --> pdb=" O   LEU D 200 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   VAL D 202 " --> pdb=" O   VAL D 167 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA D 169 " --> pdb=" O   VAL D 202 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   GLN D 215 " --> pdb=" O   GLU D 226 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   GLU D 226 " --> pdb=" O   GLN D 215 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   GLU D 217 " --> pdb=" O   THR D 224 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 109 through 117
    Processing sheet with id=AA7, first strand: chain 'E' and resid 165 through 169
    Processing sheet with id=AA8, first strand: chain 'F' and resid 22 through 32
      removed outlier: 6.513A  pdb=" N   ASP F  23 " --> pdb=" O   TYR F  15 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   TYR F  15 " --> pdb=" O   ASP F  23 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   LEU F  11 " --> pdb=" O   ASN F  27 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   SER F  29 " --> pdb=" O   ASP F   9 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ASP F   9 " --> pdb=" O   SER F  29 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   SER F  31 " --> pdb=" O   GLN F   7 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   GLN F   7 " --> pdb=" O   SER F  31 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU F  11 " --> pdb=" O   SER F  63 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   SER F  63 " --> pdb=" O   LEU F  11 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 89 through 92
      removed outlier: 6.179A  pdb=" N   VAL F 167 " --> pdb=" O   LEU F 200 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   VAL F 202 " --> pdb=" O   VAL F 167 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ALA F 169 " --> pdb=" O   VAL F 202 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   GLN F 215 " --> pdb=" O   GLU F 226 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU F 226 " --> pdb=" O   GLN F 215 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   GLU F 217 " --> pdb=" O   THR F 224 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1458 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: 3.49

  Time building geometry restraints manager: 3.02 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1901
        1.33 -     1.45: 2032
        1.45 -     1.57: 5510
        1.57 -     1.69: 9
        1.69 -     1.82: 90
  Bond restraints: 9542
  Sorted by residual:
  bond pdb=" O3A ANP F 302 "
       pdb=" PB  ANP F 302 "
    ideal  model  delta    sigma   weight residual
    1.700  1.554  0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" O3A ANP D 302 "
       pdb=" PB  ANP D 302 "
    ideal  model  delta    sigma   weight residual
    1.700  1.585  0.115 2.00e-02 2.50e+03 3.31e+01
  bond pdb=" N3B ANP F 302 "
       pdb=" PG  ANP F 302 "
    ideal  model  delta    sigma   weight residual
    1.795  1.688  0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" C4  ANP D 302 "
       pdb=" C5  ANP D 302 "
    ideal  model  delta    sigma   weight residual
    1.387  1.469 -0.082 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" O5' ANP F 302 "
       pdb=" PA  ANP F 302 "
    ideal  model  delta    sigma   weight residual
    1.655  1.578  0.077 2.00e-02 2.50e+03 1.49e+01
  ... (remaining 9537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.49: 12864
        3.49 -     6.99: 93
        6.99 -    10.48: 20
       10.48 -    13.98: 3
       13.98 -    17.47: 2
  Bond angle restraints: 12982
  Sorted by residual:
  angle pdb=" N   ARG E 306 "
        pdb=" CA  ARG E 306 "
        pdb=" C   ARG E 306 "
      ideal   model   delta    sigma   weight residual
     110.41  119.15   -8.74 1.23e+00 6.61e-01 5.05e+01
  angle pdb=" N   GLY F  18 "
        pdb=" CA  GLY F  18 "
        pdb=" C   GLY F  18 "
      ideal   model   delta    sigma   weight residual
     111.36  119.66   -8.30 1.17e+00 7.31e-01 5.03e+01
  angle pdb=" N   VAL C 349 "
        pdb=" CA  VAL C 349 "
        pdb=" C   VAL C 349 "
      ideal   model   delta    sigma   weight residual
     113.10  106.98    6.12 9.70e-01 1.06e+00 3.98e+01
  angle pdb=" PB  ANP F 302 "
        pdb=" N3B ANP F 302 "
        pdb=" PG  ANP F 302 "
      ideal   model   delta    sigma   weight residual
     126.95  109.48   17.47 3.00e+00 1.11e-01 3.39e+01
  angle pdb=" PB  ANP D 302 "
        pdb=" N3B ANP D 302 "
        pdb=" PG  ANP D 302 "
      ideal   model   delta    sigma   weight residual
     126.95  110.77   16.18 3.00e+00 1.11e-01 2.91e+01
  ... (remaining 12977 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.39: 5608
       35.39 -    70.79: 144
       70.79 -   106.18: 18
      106.18 -   141.57: 0
      141.57 -   176.96: 2
  Dihedral angle restraints: 5772
    sinusoidal: 2186
      harmonic: 3586
  Sorted by residual:
  dihedral pdb=" O1A ANP D 302 "
           pdb=" O3A ANP D 302 "
           pdb=" PA  ANP D 302 "
           pdb=" PB  ANP D 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -93.85  176.96     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O1A ANP F 302 "
           pdb=" O3A ANP F 302 "
           pdb=" PA  ANP F 302 "
           pdb=" PB  ANP F 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -72.13  155.24     1      3.00e+01 1.11e-03 2.04e+01
  dihedral pdb=" CA  MET D  37 "
           pdb=" C   MET D  37 "
           pdb=" N   MET D  38 "
           pdb=" CA  MET D  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.86  -19.14     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1306
       0.065 -    0.131: 223
       0.131 -    0.196: 9
       0.196 -    0.262: 5
       0.262 -    0.327: 4
  Chirality restraints: 1547
  Sorted by residual:
  chirality pdb=" CA  PRO E  74 "
            pdb=" N   PRO E  74 "
            pdb=" C   PRO E  74 "
            pdb=" CB  PRO E  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.33 2.00e-01 2.50e+01 2.68e+00
  chirality pdb=" CA  ARG E 306 "
            pdb=" N   ARG E 306 "
            pdb=" C   ARG E 306 "
            pdb=" CB  ARG E 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.33 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  ILE E 280 "
            pdb=" CA  ILE E 280 "
            pdb=" CG1 ILE E 280 "
            pdb=" CG2 ILE E 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 1544 not shown)

  Planarity restraints: 1664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E  73 "    0.075 5.00e-02 4.00e+02   1.11e-01 1.98e+01
        pdb=" N   PRO E  74 "   -0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO E  74 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO E  74 "    0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E  95 "   -0.039 5.00e-02 4.00e+02   5.94e-02 5.65e+00
        pdb=" N   PRO E  96 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO E  96 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E  96 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 391 "    0.033 5.00e-02 4.00e+02   4.94e-02 3.90e+00
        pdb=" N   PRO C 392 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO C 392 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 392 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1661 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 74
        2.59 -     3.16: 7945
        3.16 -     3.74: 14415
        3.74 -     4.32: 18971
        4.32 -     4.90: 30974
  Nonbonded interactions: 72379
  Sorted by model distance:
  nonbonded pdb="MG    MG F 301 "
            pdb=" O3G ANP F 302 "
     model   vdw
     2.007 2.170
  nonbonded pdb="MG    MG D 301 "
            pdb=" O3G ANP D 302 "
     model   vdw
     2.021 2.170
  nonbonded pdb="MG    MG D 301 "
            pdb=" O2B ANP D 302 "
     model   vdw
     2.059 2.170
  nonbonded pdb="MG    MG F 301 "
            pdb=" O2B ANP F 302 "
     model   vdw
     2.079 2.170
  nonbonded pdb=" O1B ANP F 302 "
            pdb=" O3G ANP F 302 "
     model   vdw
     2.081 3.040
  ... (remaining 72374 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
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = (chain 'F' and (resid 2 through 22 or (resid 23 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 24 through 230 or resid 301 through 302))
}

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=1.00 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:             1.270
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.130
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6019
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   0.146   9542  Z= 0.330
  Angle     :  0.869  17.473  12982  Z= 0.458
  Chirality :  0.050   0.327   1547
  Planarity :  0.005   0.111   1664
  Dihedral  : 15.814 176.965   3464
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.91 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  0.42 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.24), residues: 1253
  helix:  0.29 (0.22), residues: 589
  sheet: -0.19 (0.42), residues: 160
  loop : -1.51 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 246 
 HIS   0.002   0.001   HIS D  96 
 PHE   0.014   0.001   PHE E  13 
 TYR   0.009   0.001   TYR C 128 
 ARG   0.007   0.000   ARG D 138 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 197
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  344 MET cc_start: 0.1542 (tpp) cc_final: 0.1117 (tpt)
REVERT: E   68 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6435 (tp)
REVERT: E   69 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6024 (mt-10)
REVERT: E   72 ASP cc_start: 0.4498 (OUTLIER) cc_final: 0.4091 (m-30)
REVERT: F   46 SER cc_start: 0.7564 (OUTLIER) cc_final: 0.7071 (t)
REVERT: F  147 SER cc_start: 0.8906 (p) cc_final: 0.8039 (p)
REVERT: F  182 ASP cc_start: 0.6877 (m-30) cc_final: 0.6601 (m-30)
REVERT: F  210 LYS cc_start: 0.7896 (tttp) cc_final: 0.7601 (tppt)
  outliers start: 13
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2286
  time to fit residues: 66.6627
Evaluate side-chains
  159 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 155
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   69 GLU
Chi-restraints excluded: chain E residue   72 ASP
Chi-restraints excluded: chain F residue   46 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0070
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  76 ASN
C 181 GLN
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 309 GLN
E 122 GLN
** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 286 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.208540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.164006 restraints weight = 13131.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.162905 restraints weight = 8446.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.164657 restraints weight = 7154.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   9542  Z= 0.203
  Angle     :  0.638   7.585  12982  Z= 0.313
  Chirality :  0.045   0.251   1547
  Planarity :  0.005   0.116   1664
  Dihedral  : 11.787 172.895   1408
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.91 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.09 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.24), residues: 1253
  helix:  0.45 (0.22), residues: 597
  sheet: -0.19 (0.40), residues: 170
  loop : -1.56 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 246 
 HIS   0.002   0.000   HIS D  96 
 PHE   0.021   0.001   PHE C  51 
 TYR   0.008   0.001   TYR E 260 
 ARG   0.003   0.000   ARG C 252 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  201 MET cc_start: 0.6933 (tpp) cc_final: 0.6707 (tpp)
REVERT: C  262 MET cc_start: 0.7910 (ptm) cc_final: 0.7603 (ptp)
REVERT: D  110 MET cc_start: 0.8106 (tpp) cc_final: 0.7570 (tpp)
REVERT: E   68 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6224 (tp)
REVERT: E   69 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7092 (mp0)
REVERT: F  182 ASP cc_start: 0.6957 (m-30) cc_final: 0.6589 (m-30)
REVERT: F  212 MET cc_start: 0.6585 (ttm) cc_final: 0.6355 (ttm)
  outliers start: 18
  outliers final: 9
  residues processed: 177
  average time/residue: 0.2112
  time to fit residues: 53.3888
Evaluate side-chains
  158 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   69 GLU
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain F residue   89 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 115 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 94 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
C 161 GLN
C 181 GLN
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   7 GLN
E 122 GLN
** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.206529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.163568 restraints weight = 13181.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.162495 restraints weight = 12396.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.166105 restraints weight = 8471.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   9542  Z= 0.223
  Angle     :  0.626  11.626  12982  Z= 0.305
  Chirality :  0.044   0.230   1547
  Planarity :  0.005   0.107   1664
  Dihedral  : 11.381 172.683   1405
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.15 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.81 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.24), residues: 1253
  helix:  0.48 (0.22), residues: 601
  sheet: -0.12 (0.41), residues: 160
  loop : -1.51 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  75 
 HIS   0.002   0.001   HIS D  96 
 PHE   0.010   0.001   PHE E 319 
 TYR   0.011   0.001   TYR C 199 
 ARG   0.010   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
REVERT: C  262 MET cc_start: 0.7838 (ptm) cc_final: 0.6462 (ptp)
REVERT: D  106 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7046 (mp0)
REVERT: E   68 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6238 (tp)
REVERT: F   27 ASN cc_start: 0.7046 (t0) cc_final: 0.6812 (t0)
REVERT: F  182 ASP cc_start: 0.6856 (m-30) cc_final: 0.6589 (m-30)
  outliers start: 25
  outliers final: 17
  residues processed: 170
  average time/residue: 0.2348
  time to fit residues: 56.0458
Evaluate side-chains
  161 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  228 MET
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain F residue  218 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 120 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   chunk 101 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
C 218 ASN
C 294 GLN
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 137 HIS
E 201 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.204256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.160881 restraints weight = 13102.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.160083 restraints weight = 11178.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.162399 restraints weight = 7840.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   9542  Z= 0.251
  Angle     :  0.640  13.755  12982  Z= 0.311
  Chirality :  0.045   0.233   1547
  Planarity :  0.005   0.106   1664
  Dihedral  : 11.112 174.422   1402
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.23 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.17 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.24), residues: 1253
  helix:  0.35 (0.21), residues: 607
  sheet: -0.10 (0.40), residues: 166
  loop : -1.52 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 246 
 HIS   0.003   0.001   HIS D  96 
 PHE   0.013   0.001   PHE E 319 
 TYR   0.018   0.001   TYR E 258 
 ARG   0.010   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 0.986 
Fit side-chains
REVERT: C  262 MET cc_start: 0.7897 (ptm) cc_final: 0.7264 (ptp)
REVERT: D  106 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6988 (mp0)
REVERT: E   68 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6363 (tp)
REVERT: F   27 ASN cc_start: 0.7045 (t0) cc_final: 0.6812 (t0)
REVERT: F  182 ASP cc_start: 0.6878 (m-30) cc_final: 0.6620 (m-30)
  outliers start: 32
  outliers final: 23
  residues processed: 172
  average time/residue: 0.2100
  time to fit residues: 50.3713
Evaluate side-chains
  170 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  279 VAL
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  101 ASP
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain F residue  218 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0970
   chunk 67 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.205647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.160666 restraints weight = 12980.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.160049 restraints weight = 8857.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.162665 restraints weight = 7038.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   9542  Z= 0.195
  Angle     :  0.605  10.760  12982  Z= 0.294
  Chirality :  0.043   0.196   1547
  Planarity :  0.004   0.103   1664
  Dihedral  : 10.669 175.388   1402
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.07 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 17.26 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.24), residues: 1253
  helix:  0.57 (0.22), residues: 594
  sheet: -0.03 (0.41), residues: 160
  loop : -1.48 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  75 
 HIS   0.002   0.000   HIS D  96 
 PHE   0.010   0.001   PHE E 319 
 TYR   0.015   0.001   TYR C 199 
 ARG   0.007   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 0.994 
Fit side-chains
REVERT: C   25 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5345 (m-80)
REVERT: C  195 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7382 (mt-10)
REVERT: C  245 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7235 (mtmm)
REVERT: C  262 MET cc_start: 0.7946 (ptm) cc_final: 0.7610 (ptt)
REVERT: D   54 LEU cc_start: 0.8560 (tp) cc_final: 0.8243 (tp)
REVERT: D  106 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6966 (mp0)
REVERT: D  110 MET cc_start: 0.8104 (tpp) cc_final: 0.7475 (tpp)
REVERT: E  228 MET cc_start: 0.3395 (OUTLIER) cc_final: 0.2809 (mmt)
REVERT: F   27 ASN cc_start: 0.7103 (t0) cc_final: 0.6837 (t0)
REVERT: F  182 ASP cc_start: 0.6813 (m-30) cc_final: 0.6588 (m-30)
  outliers start: 28
  outliers final: 19
  residues processed: 170
  average time/residue: 0.2258
  time to fit residues: 53.1409
Evaluate side-chains
  167 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   39 MET
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  245 LYS
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  228 MET
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  161 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 73 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   chunk 68 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0370
   chunk 20 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9980
   chunk 102 optimal weight:    0.1980
   overall best weight:    0.2756

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

Flipped N/Q/H residues before XYZ refinement:
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.208505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.167000 restraints weight = 13208.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.164560 restraints weight = 9316.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.164737 restraints weight = 7054.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   9542  Z= 0.166
  Angle     :  0.590   8.554  12982  Z= 0.288
  Chirality :  0.042   0.192   1547
  Planarity :  0.004   0.100   1664
  Dihedral  : 10.236 177.039   1402
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.51 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.41 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.24), residues: 1253
  helix:  0.86 (0.22), residues: 585
  sheet: -0.01 (0.42), residues: 160
  loop : -1.50 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 246 
 HIS   0.003   0.000   HIS D  53 
 PHE   0.010   0.001   PHE E 319 
 TYR   0.014   0.001   TYR F  15 
 ARG   0.007   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.5291 (m-80)
REVERT: C  201 MET cc_start: 0.6852 (tpp) cc_final: 0.6562 (tpp)
REVERT: C  245 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7687 (mtmm)
REVERT: C  262 MET cc_start: 0.7985 (ptm) cc_final: 0.7497 (ptt)
REVERT: D   54 LEU cc_start: 0.8468 (tp) cc_final: 0.8119 (tp)
REVERT: D  106 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6826 (mp0)
REVERT: D  110 MET cc_start: 0.8051 (tpp) cc_final: 0.7833 (mmm)
REVERT: E   55 LEU cc_start: 0.8499 (tt) cc_final: 0.8256 (tt)
  outliers start: 26
  outliers final: 14
  residues processed: 169
  average time/residue: 0.2333
  time to fit residues: 54.6517
Evaluate side-chains
  162 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  245 LYS
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   66 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 77 optimal weight:    0.0040
   chunk 101 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 86 optimal weight:    9.9990
   chunk 16 optimal weight:   40.0000
   chunk 87 optimal weight:    4.9990
   chunk 113 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    1.4996

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

Flipped N/Q/H residues before XYZ refinement:
C 247 GLN
** C 303 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 = 0.4488 r_free = 0.4488 target = 0.204110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.160405 restraints weight = 13098.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.160302 restraints weight = 10851.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.162476 restraints weight = 7214.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9542  Z= 0.266
  Angle     :  0.636   7.852  12982  Z= 0.309
  Chirality :  0.044   0.235   1547
  Planarity :  0.005   0.098   1664
  Dihedral  : 10.218 177.014   1402
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.31 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.61 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.24), residues: 1253
  helix:  0.63 (0.22), residues: 593
  sheet: -0.09 (0.41), residues: 160
  loop : -1.50 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  75 
 HIS   0.002   0.001   HIS D  96 
 PHE   0.030   0.002   PHE E 203 
 TYR   0.016   0.001   TYR C 199 
 ARG   0.008   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5241 (m-80)
REVERT: C  245 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7262 (mtmm)
REVERT: C  262 MET cc_start: 0.7815 (ptm) cc_final: 0.7501 (ptt)
REVERT: C  263 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8058 (tp30)
REVERT: D   54 LEU cc_start: 0.8617 (tp) cc_final: 0.8216 (tp)
REVERT: D  106 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6962 (mp0)
REVERT: D  110 MET cc_start: 0.8189 (tpp) cc_final: 0.7918 (mmm)
REVERT: D  212 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7088 (mpt)
  outliers start: 25
  outliers final: 18
  residues processed: 161
  average time/residue: 0.2090
  time to fit residues: 47.0526
Evaluate side-chains
  160 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  245 LYS
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain F residue    8 CYS
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  101 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 116 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 79 optimal weight:   30.0000
   chunk 96 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** C 303 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 = 0.4463 r_free = 0.4463 target = 0.201576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.159503 restraints weight = 13335.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.156278 restraints weight = 10113.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.157181 restraints weight = 8230.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   9542  Z= 0.282
  Angle     :  0.659   8.660  12982  Z= 0.322
  Chirality :  0.045   0.258   1547
  Planarity :  0.005   0.095   1664
  Dihedral  : 10.342 179.370   1402
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.79 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.29 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.24), residues: 1253
  helix:  0.45 (0.22), residues: 593
  sheet: -0.16 (0.41), residues: 160
  loop : -1.52 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  75 
 HIS   0.002   0.001   HIS D  96 
 PHE   0.024   0.002   PHE E 203 
 TYR   0.021   0.002   TYR F  15 
 ARG   0.003   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5331 (m-80)
REVERT: C  245 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.6794 (mtmm)
REVERT: C  262 MET cc_start: 0.7905 (ptm) cc_final: 0.7660 (ptt)
REVERT: D   54 LEU cc_start: 0.8758 (tp) cc_final: 0.8436 (tp)
REVERT: D  106 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7147 (mp0)
REVERT: D  212 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7289 (mpt)
REVERT: E  296 LYS cc_start: 0.7962 (tmtt) cc_final: 0.7200 (ttmt)
  outliers start: 33
  outliers final: 23
  residues processed: 166
  average time/residue: 0.2200
  time to fit residues: 50.5227
Evaluate side-chains
  168 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  245 LYS
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  316 VAL
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  284 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain F residue    8 CYS
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  101 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 85 optimal weight:    9.9990
   chunk 105 optimal weight:    0.3980
   chunk 67 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 98 optimal weight:    0.0020
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
** C 303 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 = 0.4501 r_free = 0.4501 target = 0.205604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.161351 restraints weight = 13086.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.160246 restraints weight = 9199.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.161346 restraints weight = 7568.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   9542  Z= 0.186
  Angle     :  0.617   8.904  12982  Z= 0.301
  Chirality :  0.043   0.205   1547
  Planarity :  0.004   0.092   1664
  Dihedral  : 10.150 176.703   1402
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.31 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.65 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.24), residues: 1253
  helix:  0.74 (0.22), residues: 584
  sheet: -0.14 (0.42), residues: 160
  loop : -1.45 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  75 
 HIS   0.003   0.000   HIS D  53 
 PHE   0.018   0.001   PHE F  68 
 TYR   0.018   0.001   TYR C 199 
 ARG   0.006   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5276 (m-80)
REVERT: C  195 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7704 (mt-10)
REVERT: D   54 LEU cc_start: 0.8663 (tp) cc_final: 0.8343 (tp)
REVERT: D  110 MET cc_start: 0.8222 (tpp) cc_final: 0.7536 (tpp)
REVERT: D  212 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7224 (mpt)
REVERT: E   55 LEU cc_start: 0.8511 (tt) cc_final: 0.8144 (tt)
REVERT: E  296 LYS cc_start: 0.7742 (tmtt) cc_final: 0.7047 (ttmt)
  outliers start: 24
  outliers final: 18
  residues processed: 169
  average time/residue: 0.2111
  time to fit residues: 50.2311
Evaluate side-chains
  166 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain F residue    8 CYS
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   66 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 118 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 171 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.204849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.162330 restraints weight = 13195.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.160741 restraints weight = 9214.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.161443 restraints weight = 6983.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9542  Z= 0.207
  Angle     :  0.628  11.127  12982  Z= 0.305
  Chirality :  0.044   0.209   1547
  Planarity :  0.004   0.090   1664
  Dihedral  : 10.122 176.206   1402
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.63 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 22.38 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.24), residues: 1253
  helix:  0.74 (0.22), residues: 583
  sheet: -0.12 (0.42), residues: 160
  loop : -1.39 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  75 
 HIS   0.002   0.000   HIS D 204 
 PHE   0.018   0.001   PHE F  68 
 TYR   0.012   0.001   TYR E 258 
 ARG   0.006   0.000   ARG C 261 

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   25 PHE cc_start: 0.6242 (OUTLIER) cc_final: 0.5310 (m-80)
REVERT: C  263 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8029 (tp30)
REVERT: C  282 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7186 (mt)
REVERT: D   54 LEU cc_start: 0.8628 (tp) cc_final: 0.8246 (tp)
REVERT: D  212 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7241 (mpt)
REVERT: E   55 LEU cc_start: 0.8580 (tt) cc_final: 0.8225 (tt)
REVERT: E  296 LYS cc_start: 0.7806 (tmtt) cc_final: 0.7067 (ttmt)
  outliers start: 25
  outliers final: 20
  residues processed: 173
  average time/residue: 0.2212
  time to fit residues: 54.1838
Evaluate side-chains
  170 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  316 VAL
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  366 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  212 MET
Chi-restraints excluded: chain E residue   22 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain F residue    8 CYS
Chi-restraints excluded: chain F residue   28 VAL
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   66 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 92 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 19 optimal weight:    0.4980
   chunk 10 optimal weight:    0.2980
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0670
   chunk 60 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.4520

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

Flipped N/Q/H residues before XYZ refinement:
** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 171 GLN
** F 152 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 = 0.4511 r_free = 0.4511 target = 0.206557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.162432 restraints weight = 13145.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.161554 restraints weight = 9370.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.163218 restraints weight = 7587.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   9542  Z= 0.183
  Angle     :  0.623  10.241  12982  Z= 0.303
  Chirality :  0.043   0.190   1547
  Planarity :  0.004   0.088   1664
  Dihedral  : 10.079 177.378   1402
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.47 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.38 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.24), residues: 1253
  helix:  0.85 (0.22), residues: 581
  sheet: -0.11 (0.42), residues: 160
  loop : -1.37 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  75 
 HIS   0.002   0.000   HIS D  53 
 PHE   0.017   0.001   PHE F  68 
 TYR   0.017   0.001   TYR C 199 
 ARG   0.005   0.000   ARG C 261 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2960.82 seconds
wall clock time: 52 minutes 32.33 seconds (3152.33 seconds total)