Starting phenix.real_space_refine
on Sat Jun  7 06:43:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hqm_34950/06_2025/8hqm_34950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hqm_34950/06_2025/8hqm_34950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hqm_34950/06_2025/8hqm_34950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hqm_34950/06_2025/8hqm_34950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hqm_34950/06_2025/8hqm_34950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hqm_34950/06_2025/8hqm_34950.cif"
  }
  resolution = 2.95
  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=   0.005 sd=   0.040
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    5484      2.51       5
     N    1461      2.21       5
     O    1609      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8618
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2245
          Classifications: {'peptide': 296}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 291}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "C"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "H"
      Number of atoms: 1768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1768
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "R"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2440
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 6, 'TRANS': 300}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1719
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'140': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.63, per 1000 atoms: 0.54
  Number of scatterers: 8618
  At special positions: 0
  Unit cell: (104, 119.6, 130, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    1609      8.00
     N    1461      7.00
     C    5484      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 115 " - pdb=" SG  CYS R 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.97
  Conformation dependent library (CDL) restraints added in 894.1 milliseconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 15 sheets defined
      37.3% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.48
  Creating SS restraints...
    Processing helix  chain 'C' and resid 10 through 21
      removed outlier: 4.487A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU C  15 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN C  18 " --> pdb=" O   LYS C  14 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU C  19 " --> pdb=" O   LEU C  15 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS C  20 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.579A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA C  43 " --> pdb=" O   ALA C  39 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   HIS C  44 " --> pdb=" O   TYR C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'R' and resid 38 through 72
      Proline residue:  R  58  - end of helix
      removed outlier: 3.976A  pdb=" N   LEU R  72 " --> pdb=" O   LEU R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 87
    Processing helix  chain 'R' and resid 94 through 102
      removed outlier: 3.557A  pdb=" N   TRP R  98 " --> pdb=" O   THR R  94 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 145
    Processing helix  chain 'R' and resid 146 through 154
      removed outlier: 3.914A  pdb=" N   ARG R 151 " --> pdb=" O   ALA R 147 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   GLY R 152 " --> pdb=" O   LEU R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 180
      Proline residue:  R 176  - end of helix
    Processing helix  chain 'R' and resid 194 through 208
    Processing helix  chain 'R' and resid 208 through 228
    Processing helix  chain 'R' and resid 233 through 272
      Proline residue:  R 257  - end of helix
    Processing helix  chain 'R' and resid 279 through 312
      Proline residue:  R 305  - end of helix
    Processing helix  chain 'R' and resid 312 through 331
      removed outlier: 3.701A  pdb=" N   ARG R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 334 through 346
      removed outlier: 4.211A  pdb=" N   GLU R 346 " --> pdb=" O   ARG R 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.752A  pdb=" N   ASP A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.647A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 287 through 291
      removed outlier: 3.557A  pdb=" N   TYR A 290 " --> pdb=" O   TYR A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.623A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50
      removed outlier: 3.508A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.626A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.060A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.501A  pdb=" N   THR B 159 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 191
      removed outlier: 3.820A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 234
      removed outlier: 4.091A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLY B 244 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA B 242 " --> pdb=" O   CYS B 233 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.755A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU B 308 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.994A  pdb=" N   SER H  21 " --> pdb=" O   SER H   7 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG H  18 " --> pdb=" O   MET H  83 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   MET H  83 " --> pdb=" O   ARG H  18 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  81 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU H  79 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.567A  pdb=" N   TYR H  59 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG H  98 " --> pdb=" O   PHE H 110 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.567A  pdb=" N   TYR H  59 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   TYR H  94 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 129 through 130
    Processing sheet with id=AB4, first strand: chain 'H' and resid 134 through 136
      removed outlier: 3.874A  pdb=" N   GLY H 213 " --> pdb=" O   LEU H 233 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE H 177 " --> pdb=" O   TRP H 164 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   LEU H 166 " --> pdb=" O   LEU H 175 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   LEU H 175 " --> pdb=" O   LEU H 166 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 143 through 145
      removed outlier: 3.557A  pdb=" N   ILE H 145 " --> pdb=" O   LEU H 202 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER H 192 " --> pdb=" O   THR H 203 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 185 through 191
      removed outlier: 5.990A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)

    414 hydrogen bonds defined for protein.
    1188 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: 3.18

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1394
        1.31 -     1.44: 2438
        1.44 -     1.57: 4869
        1.57 -     1.69: 0
        1.69 -     1.82: 89
  Bond restraints: 8790
  Sorted by residual:
  bond pdb=" N   140 R 401 "
       pdb=" C3  140 R 401 "
    ideal  model  delta    sigma   weight residual
    1.337  1.450 -0.113 2.00e-02 2.50e+03 3.20e+01
  bond pdb=" N   LYS A 314 "
       pdb=" CA  LYS A 314 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.10e-02 8.26e+03 8.21e+00
  bond pdb=" N   LEU R 282 "
       pdb=" CA  LEU R 282 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.22e+00
  bond pdb=" N   PHE R 141 "
       pdb=" CA  PHE R 141 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.029 1.20e-02 6.94e+03 6.02e+00
  bond pdb=" N   LEU B 286 "
       pdb=" CA  LEU B 286 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.028 1.22e-02 6.72e+03 5.33e+00
  ... (remaining 8785 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 11536
        2.24 -     4.48: 295
        4.48 -     6.72: 46
        6.72 -     8.96: 16
        8.96 -    11.20: 4
  Bond angle restraints: 11897
  Sorted by residual:
  angle pdb=" C   GLU R  88 "
        pdb=" N   LEU R  89 "
        pdb=" CA  LEU R  89 "
      ideal   model   delta    sigma   weight residual
     121.54  130.10   -8.56 1.91e+00 2.74e-01 2.01e+01
  angle pdb=" N   VAL R  57 "
        pdb=" CA  VAL R  57 "
        pdb=" C   VAL R  57 "
      ideal   model   delta    sigma   weight residual
     108.88  117.77   -8.89 2.16e+00 2.14e-01 1.70e+01
  angle pdb=" C   TYR H 178 "
        pdb=" N   ARG H 179 "
        pdb=" CA  ARG H 179 "
      ideal   model   delta    sigma   weight residual
     122.46  127.80   -5.34 1.41e+00 5.03e-01 1.43e+01
  angle pdb=" CB  MET R 192 "
        pdb=" CG  MET R 192 "
        pdb=" SD  MET R 192 "
      ideal   model   delta    sigma   weight residual
     112.70  123.90  -11.20 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" C   CYS H 217 "
        pdb=" N   MET H 218 "
        pdb=" CA  MET H 218 "
      ideal   model   delta    sigma   weight residual
     121.54  128.43   -6.89 1.91e+00 2.74e-01 1.30e+01
  ... (remaining 11892 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 4539
       17.59 -    35.17: 512
       35.17 -    52.76: 129
       52.76 -    70.35: 18
       70.35 -    87.93: 8
  Dihedral angle restraints: 5206
    sinusoidal: 2004
      harmonic: 3202
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    6.39   86.61     1      1.00e+01 1.00e-02 9.03e+01
  dihedral pdb=" CB  CYS R 115 "
           pdb=" SG  CYS R 115 "
           pdb=" SG  CYS R 186 "
           pdb=" CB  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.58  -48.58     1      1.00e+01 1.00e-02 3.25e+01
  dihedral pdb=" CA  ASP B 205 "
           pdb=" C   ASP B 205 "
           pdb=" N   ALA B 206 "
           pdb=" CA  ALA B 206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.68  -22.32     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 5203 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 989
       0.052 -    0.103: 283
       0.103 -    0.155: 77
       0.155 -    0.207: 6
       0.207 -    0.258: 3
  Chirality restraints: 1358
  Sorted by residual:
  chirality pdb=" CB  ILE R 245 "
            pdb=" CA  ILE R 245 "
            pdb=" CG1 ILE R 245 "
            pdb=" CG2 ILE R 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CB  ILE R 136 "
            pdb=" CA  ILE R 136 "
            pdb=" CG1 ILE R 136 "
            pdb=" CG2 ILE R 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CG  LEU H   4 "
            pdb=" CB  LEU H   4 "
            pdb=" CD1 LEU H   4 "
            pdb=" CD2 LEU H   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1355 not shown)

  Planarity restraints: 1495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 314 "   -0.011 2.00e-02 2.50e+03   2.19e-02 4.78e+00
        pdb=" C   LYS A 314 "    0.038 2.00e-02 2.50e+03
        pdb=" O   LYS A 314 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP A 315 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU H 225 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   LEU H 225 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   LEU H 225 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR H 226 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 252 "   -0.010 2.00e-02 2.50e+03   2.05e-02 4.19e+00
        pdb=" C   LEU R 252 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU R 252 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL R 253 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1492 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1663
        2.77 -     3.30: 8474
        3.30 -     3.84: 15030
        3.84 -     4.37: 16831
        4.37 -     4.90: 28471
  Nonbonded interactions: 70469
  Sorted by model distance:
  nonbonded pdb=" O   ALA B  56 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER A 228 "
            pdb=" O   LYS A 270 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   VAL R 142 "
            pdb=" OG  SER R 150 "
     model   vdw
     2.276 3.040
  ... (remaining 70464 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.400
  Find NCS groups from input model:        0.150
  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:14.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
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   0.113   8793  Z= 0.246
  Angle     :  0.899  11.196  11903  Z= 0.476
  Chirality :  0.052   0.258   1358
  Planarity :  0.006   0.044   1495
  Dihedral  : 16.059  87.934   3133
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 20.71 %
    Favored  : 78.86 %
  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: -1.84 (0.24), residues: 1084
  helix: -0.55 (0.25), residues: 383
  sheet: -1.26 (0.31), residues: 265
  loop : -1.65 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 111 
 HIS   0.006   0.002   HIS R 242 
 PHE   0.022   0.003   PHE A 189 
 TYR   0.021   0.002   TYR R  49 
 ARG   0.006   0.001   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18839 (  401)
  hydrogen bonds       : angle       7.99979 ( 1188)
  SS BOND              : bond        0.00408 (    3)
  SS BOND              : angle       1.52453 (    6)
  covalent geometry    : bond        0.00507 ( 8790)
  covalent geometry    : angle       0.89861 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 48
  average time/residue: 1.6575
  time to fit residues: 84.4301
Evaluate side-chains
  42 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 55 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 84 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
B 293 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  18 GLN
R  70 GLN
A 244 HIS
A 346 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2309 r_free = 0.2309 target = 0.029151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2116 r_free = 0.2116 target = 0.024930 restraints weight = 88351.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.2100 rms_B_bonded: 2.99
r_work: 0.2036 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9220
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8793  Z= 0.201
  Angle     :  0.596   7.008  11903  Z= 0.316
  Chirality :  0.041   0.149   1358
  Planarity :  0.004   0.043   1495
  Dihedral  :  5.989  57.444   1215
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 21.35 %
    Favored  : 76.93 %
  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: -1.16 (0.25), residues: 1084
  helix:  0.31 (0.26), residues: 396
  sheet: -1.13 (0.31), residues: 269
  loop : -1.44 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.011   0.001   PHE H 227 
 TYR   0.014   0.001   TYR R  49 
 ARG   0.004   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04554 (  401)
  hydrogen bonds       : angle       5.43488 ( 1188)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       0.87848 (    6)
  covalent geometry    : bond        0.00437 ( 8790)
  covalent geometry    : angle       0.59581 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.973 
Fit side-chains
REVERT: C   21 MET cc_start: 0.8644 (ppp) cc_final: 0.8402 (ppp)
REVERT: H  111 TRP cc_start: 0.9690 (OUTLIER) cc_final: 0.9273 (m100)
  outliers start: 16
  outliers final: 2
  residues processed: 56
  average time/residue: 1.3078
  time to fit residues: 78.4477
Evaluate side-chains
  42 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue  212 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 102 optimal weight:    9.9990
   chunk 104 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    5.7588

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** 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 = 0.2283 r_free = 0.2283 target = 0.028441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2093 r_free = 0.2093 target = 0.024241 restraints weight = 89972.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.2078 rms_B_bonded: 3.08
r_work: 0.2020 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work: 0.2020 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9221
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   8793  Z= 0.211
  Angle     :  0.570   7.324  11903  Z= 0.301
  Chirality :  0.041   0.145   1358
  Planarity :  0.004   0.042   1495
  Dihedral  :  5.553  50.070   1213
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.53 %
    Favored  : 75.11 %
  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: -0.96 (0.25), residues: 1084
  helix:  0.62 (0.26), residues: 393
  sheet: -1.15 (0.31), residues: 269
  loop : -1.38 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 211 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.011   0.001   PHE B 253 
 TYR   0.013   0.001   TYR R  49 
 ARG   0.004   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04486 (  401)
  hydrogen bonds       : angle       5.15685 ( 1188)
  SS BOND              : bond        0.00360 (    3)
  SS BOND              : angle       0.83920 (    6)
  covalent geometry    : bond        0.00460 ( 8790)
  covalent geometry    : angle       0.56998 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 40
  time to evaluate  : 1.024 
Fit side-chains
  outliers start: 22
  outliers final: 8
  residues processed: 61
  average time/residue: 1.7319
  time to fit residues: 113.6727
Evaluate side-chains
  48 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 105 optimal weight:    0.0770
   chunk 47 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    4.8146

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2292 r_free = 0.2292 target = 0.028591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2099 r_free = 0.2099 target = 0.024386 restraints weight = 89870.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.2084 rms_B_bonded: 3.04
r_work: 0.2029 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work: 0.2029 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9217
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   8793  Z= 0.182
  Angle     :  0.555   7.623  11903  Z= 0.290
  Chirality :  0.040   0.141   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.364  44.097   1213
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.00 %
    Favored  : 74.79 %
  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: -0.86 (0.25), residues: 1084
  helix:  0.75 (0.26), residues: 393
  sheet: -1.06 (0.31), residues: 264
  loop : -1.41 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.011   0.001   PHE B 253 
 TYR   0.012   0.001   TYR R  49 
 ARG   0.003   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04107 (  401)
  hydrogen bonds       : angle       4.96936 ( 1188)
  SS BOND              : bond        0.00317 (    3)
  SS BOND              : angle       0.71567 (    6)
  covalent geometry    : bond        0.00396 ( 8790)
  covalent geometry    : angle       0.55483 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 43
  time to evaluate  : 0.961 
Fit side-chains
REVERT: H   93 MET cc_start: 0.9629 (OUTLIER) cc_final: 0.9369 (tpp)
REVERT: H  111 TRP cc_start: 0.9673 (OUTLIER) cc_final: 0.9210 (m100)
REVERT: H  128 MET cc_start: 0.9413 (mtp) cc_final: 0.9003 (mtm)
  outliers start: 30
  outliers final: 10
  residues processed: 71
  average time/residue: 1.1445
  time to fit residues: 87.7962
Evaluate side-chains
  53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain H residue   93 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  132 THR
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 47 optimal weight:    0.3980
   chunk 89 optimal weight:    0.5980
   chunk 64 optimal weight:    8.9990
   chunk 101 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** 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 = 0.2314 r_free = 0.2314 target = 0.029070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2126 r_free = 0.2126 target = 0.024854 restraints weight = 87687.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.2112 rms_B_bonded: 3.07
r_work: 0.2054 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9203
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8793  Z= 0.134
  Angle     :  0.537   7.373  11903  Z= 0.280
  Chirality :  0.040   0.144   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.138  42.180   1213
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.67 %
    Favored  : 74.79 %
  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: -0.77 (0.25), residues: 1084
  helix:  0.86 (0.26), residues: 397
  sheet: -1.02 (0.31), residues: 264
  loop : -1.41 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.002   0.000   HIS R 323 
 PHE   0.011   0.001   PHE B 253 
 TYR   0.013   0.001   TYR R  49 
 ARG   0.003   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  401)
  hydrogen bonds       : angle       4.75500 ( 1188)
  SS BOND              : bond        0.00236 (    3)
  SS BOND              : angle       0.71568 (    6)
  covalent geometry    : bond        0.00291 ( 8790)
  covalent geometry    : angle       0.53722 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 41
  time to evaluate  : 1.026 
Fit side-chains
REVERT: H   93 MET cc_start: 0.9627 (OUTLIER) cc_final: 0.9376 (tpp)
REVERT: H  111 TRP cc_start: 0.9681 (OUTLIER) cc_final: 0.9219 (m100)
REVERT: H  218 MET cc_start: 0.9173 (ttp) cc_final: 0.8946 (ttm)
REVERT: R  331 MET cc_start: 0.9184 (mpp) cc_final: 0.8913 (mpp)
  outliers start: 33
  outliers final: 11
  residues processed: 71
  average time/residue: 1.0709
  time to fit residues: 82.4042
Evaluate side-chains
  54 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain H residue   93 MET
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  132 THR
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 81 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** 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 = 0.2294 r_free = 0.2294 target = 0.028470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2101 r_free = 0.2101 target = 0.024260 restraints weight = 88729.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.2085 rms_B_bonded: 3.05
r_work: 0.2029 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9218
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8793  Z= 0.204
  Angle     :  0.559   8.335  11903  Z= 0.291
  Chirality :  0.041   0.141   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.193  44.484   1213
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 22.75 %
    Favored  : 74.25 %
  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 (0.25), residues: 1084
  helix:  0.91 (0.26), residues: 393
  sheet: -1.08 (0.31), residues: 270
  loop : -1.38 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 211 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.013   0.001   PHE H  80 
 TYR   0.012   0.001   TYR R  49 
 ARG   0.003   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04120 (  401)
  hydrogen bonds       : angle       4.87598 ( 1188)
  SS BOND              : bond        0.00379 (    3)
  SS BOND              : angle       0.73174 (    6)
  covalent geometry    : bond        0.00445 ( 8790)
  covalent geometry    : angle       0.55869 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 41
  time to evaluate  : 1.043 
Fit side-chains
REVERT: H  111 TRP cc_start: 0.9683 (OUTLIER) cc_final: 0.9194 (m100)
REVERT: H  218 MET cc_start: 0.9290 (ttp) cc_final: 0.9064 (ttm)
REVERT: R  221 ARG cc_start: 0.9854 (OUTLIER) cc_final: 0.9610 (mmp80)
  outliers start: 28
  outliers final: 13
  residues processed: 66
  average time/residue: 1.1873
  time to fit residues: 84.5285
Evaluate side-chains
  56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain H residue   80 PHE
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  132 THR
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 20 optimal weight:   20.0000
   chunk 81 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 68 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 75 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** 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 = 0.2295 r_free = 0.2295 target = 0.028486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2102 r_free = 0.2102 target = 0.024282 restraints weight = 89320.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.2086 rms_B_bonded: 3.05
r_work: 0.2031 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9217
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8793  Z= 0.193
  Angle     :  0.562   9.222  11903  Z= 0.291
  Chirality :  0.040   0.141   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.178  45.801   1213
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.71 %
    Favored  : 73.61 %
  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: -0.75 (0.25), residues: 1084
  helix:  0.92 (0.26), residues: 393
  sheet: -1.07 (0.31), residues: 270
  loop : -1.39 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 211 
 HIS   0.003   0.000   HIS H  35 
 PHE   0.013   0.001   PHE H  80 
 TYR   0.012   0.001   TYR R  49 
 ARG   0.003   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  401)
  hydrogen bonds       : angle       4.84879 ( 1188)
  SS BOND              : bond        0.00352 (    3)
  SS BOND              : angle       0.70169 (    6)
  covalent geometry    : bond        0.00423 ( 8790)
  covalent geometry    : angle       0.56151 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 41
  time to evaluate  : 0.954 
Fit side-chains
REVERT: H  111 TRP cc_start: 0.9682 (OUTLIER) cc_final: 0.9199 (m100)
REVERT: H  218 MET cc_start: 0.9282 (ttp) cc_final: 0.9054 (ttm)
REVERT: R  221 ARG cc_start: 0.9850 (OUTLIER) cc_final: 0.9608 (mmp80)
REVERT: R  331 MET cc_start: 0.9156 (mpp) cc_final: 0.8904 (mpp)
  outliers start: 25
  outliers final: 12
  residues processed: 64
  average time/residue: 1.1873
  time to fit residues: 81.8892
Evaluate side-chains
  55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain H residue   80 PHE
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  132 THR
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 88 optimal weight:    8.9990
   chunk 60 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 99 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** 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 = 0.2295 r_free = 0.2295 target = 0.028464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2101 r_free = 0.2101 target = 0.024238 restraints weight = 90428.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.2086 rms_B_bonded: 3.06
r_work: 0.2034 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9218
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8793  Z= 0.193
  Angle     :  0.561   9.821  11903  Z= 0.291
  Chirality :  0.040   0.139   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.177  46.829   1213
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 24.14 %
    Favored  : 73.71 %
  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 (0.25), residues: 1084
  helix:  0.93 (0.26), residues: 393
  sheet: -1.08 (0.31), residues: 270
  loop : -1.41 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.013   0.001   PHE H  80 
 TYR   0.012   0.001   TYR R  49 
 ARG   0.003   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04055 (  401)
  hydrogen bonds       : angle       4.84771 ( 1188)
  SS BOND              : bond        0.00345 (    3)
  SS BOND              : angle       0.66724 (    6)
  covalent geometry    : bond        0.00424 ( 8790)
  covalent geometry    : angle       0.56090 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 41
  time to evaluate  : 0.918 
Fit side-chains
REVERT: B   95 LEU cc_start: 0.9783 (OUTLIER) cc_final: 0.9496 (mt)
REVERT: H  111 TRP cc_start: 0.9685 (OUTLIER) cc_final: 0.9194 (m100)
REVERT: H  128 MET cc_start: 0.9419 (mtp) cc_final: 0.9080 (mtm)
REVERT: H  218 MET cc_start: 0.9294 (ttp) cc_final: 0.9028 (ttm)
REVERT: R  221 ARG cc_start: 0.9850 (OUTLIER) cc_final: 0.9600 (mmp80)
  outliers start: 20
  outliers final: 12
  residues processed: 60
  average time/residue: 1.3451
  time to fit residues: 86.5062
Evaluate side-chains
  56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain H residue   80 PHE
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  132 THR
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 69 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** 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 = 0.2290 r_free = 0.2290 target = 0.028305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2095 r_free = 0.2095 target = 0.024103 restraints weight = 90569.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2079 rms_B_bonded: 3.04
r_work: 0.2026 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9221
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   8793  Z= 0.211
  Angle     :  0.569  10.612  11903  Z= 0.295
  Chirality :  0.040   0.140   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.206  48.338   1213
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 23.71 %
    Favored  : 73.82 %
  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: -0.79 (0.25), residues: 1084
  helix:  0.93 (0.26), residues: 393
  sheet: -1.08 (0.31), residues: 268
  loop : -1.45 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.014   0.001   PHE H  80 
 TYR   0.013   0.001   TYR R  49 
 ARG   0.003   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04126 (  401)
  hydrogen bonds       : angle       4.89510 ( 1188)
  SS BOND              : bond        0.00365 (    3)
  SS BOND              : angle       0.69755 (    6)
  covalent geometry    : bond        0.00462 ( 8790)
  covalent geometry    : angle       0.56857 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 41
  time to evaluate  : 0.930 
Fit side-chains
REVERT: B   95 LEU cc_start: 0.9785 (OUTLIER) cc_final: 0.9495 (mp)
REVERT: H  111 TRP cc_start: 0.9687 (OUTLIER) cc_final: 0.9196 (m100)
REVERT: H  128 MET cc_start: 0.9433 (mtp) cc_final: 0.9115 (mtm)
REVERT: H  218 MET cc_start: 0.9296 (ttp) cc_final: 0.9025 (ttm)
REVERT: R  221 ARG cc_start: 0.9850 (OUTLIER) cc_final: 0.9601 (mmp80)
REVERT: R  331 MET cc_start: 0.9130 (mpp) cc_final: 0.8877 (mpp)
  outliers start: 23
  outliers final: 12
  residues processed: 63
  average time/residue: 1.1973
  time to fit residues: 81.2230
Evaluate side-chains
  56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain H residue   80 PHE
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  132 THR
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 71 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 57 optimal weight:    0.0270
   chunk 26 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 49 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   overall best weight:    4.8046

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** 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 = 0.2297 r_free = 0.2297 target = 0.028495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2103 r_free = 0.2103 target = 0.024284 restraints weight = 89595.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.2088 rms_B_bonded: 3.04
r_work: 0.2034 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9216
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8793  Z= 0.182
  Angle     :  0.569  11.190  11903  Z= 0.292
  Chirality :  0.041   0.165   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.170  48.667   1213
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 24.57 %
    Favored  : 73.82 %
  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: -0.77 (0.25), residues: 1084
  helix:  0.95 (0.26), residues: 393
  sheet: -1.03 (0.31), residues: 263
  loop : -1.48 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.000   HIS H  35 
 PHE   0.013   0.001   PHE H  80 
 TYR   0.012   0.001   TYR R  49 
 ARG   0.003   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03990 (  401)
  hydrogen bonds       : angle       4.83513 ( 1188)
  SS BOND              : bond        0.00312 (    3)
  SS BOND              : angle       0.67770 (    6)
  covalent geometry    : bond        0.00401 ( 8790)
  covalent geometry    : angle       0.56915 (11897)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 1.014 
Fit side-chains
REVERT: B   95 LEU cc_start: 0.9783 (OUTLIER) cc_final: 0.9502 (mt)
REVERT: H  111 TRP cc_start: 0.9685 (OUTLIER) cc_final: 0.9190 (m100)
REVERT: H  128 MET cc_start: 0.9424 (mtp) cc_final: 0.9161 (mtm)
REVERT: R  221 ARG cc_start: 0.9847 (OUTLIER) cc_final: 0.9511 (mmp80)
REVERT: R  331 MET cc_start: 0.9141 (mpp) cc_final: 0.8884 (mpp)
  outliers start: 15
  outliers final: 12
  residues processed: 55
  average time/residue: 1.3539
  time to fit residues: 79.7571
Evaluate side-chains
  56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain H residue   80 PHE
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  132 THR
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  186 CYS
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0270
   chunk 21 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 35 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:   20.0000
   chunk 83 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    2.6046

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** 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 = 0.2326 r_free = 0.2326 target = 0.029223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2136 r_free = 0.2136 target = 0.025013 restraints weight = 88316.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.2121 rms_B_bonded: 3.04
r_work: 0.2068 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9200
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8793  Z= 0.126
  Angle     :  0.557  12.474  11903  Z= 0.282
  Chirality :  0.040   0.137   1358
  Planarity :  0.003   0.043   1495
  Dihedral  :  5.026  46.819   1213
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 24.46 %
    Favored  : 73.82 %
  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: -0.67 (0.25), residues: 1084
  helix:  1.04 (0.27), residues: 394
  sheet: -0.92 (0.32), residues: 257
  loop : -1.48 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 108 
 HIS   0.002   0.000   HIS H  35 
 PHE   0.012   0.001   PHE H  80 
 TYR   0.012   0.001   TYR R  49 
 ARG   0.003   0.000   ARG R 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  401)
  hydrogen bonds       : angle       4.62066 ( 1188)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       0.85859 (    6)
  covalent geometry    : bond        0.00275 ( 8790)
  covalent geometry    : angle       0.55687 (11897)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5086.69 seconds
wall clock time: 89 minutes 12.51 seconds (5352.51 seconds total)