Starting phenix.real_space_refine
on Fri Aug 22 23:22:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hqm_34950/08_2025/8hqm_34950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hqm_34950/08_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_34950/08_2025/8hqm_34950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hqm_34950/08_2025/8hqm_34950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hqm_34950/08_2025/8hqm_34950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hqm_34950/08_2025/8hqm_34950.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP: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: 2.24, per 1000 atoms: 0.26
  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: 0.71
  Conformation dependent library (CDL) restraints added in 435.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.33
  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: 1.38

  Time building geometry restraints manager: 0.96 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:             0.340
  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:          0.120
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.640
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:7.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.780
-------------------------------------------------------------------------------
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 : 10.22
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.001   ARG B  68 
 TYR   0.021   0.002   TYR R  49 
 PHE   0.022   0.003   PHE A 189 
 TRP   0.014   0.002   TRP H 111 
 HIS   0.006   0.002   HIS R 242 

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

*********************** 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  : 0.346 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 48
  average time/residue: 0.8201
  time to fit residues: 41.5093
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  : 0.350 
-------------------------------------------------------------------------------
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 49 optimal weight:    9.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.2281 r_free = 0.2281 target = 0.028583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2091 r_free = 0.2091 target = 0.024375 restraints weight = 89424.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.2075 rms_B_bonded: 3.07
r_work: 0.2015 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work: 0.2015 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9217
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   8793  Z= 0.231
  Angle     :  0.605   7.151  11903  Z= 0.321
  Chirality :  0.042   0.149   1358
  Planarity :  0.004   0.043   1495
  Dihedral  :  6.029  58.037   1215
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.25), residues: 1084
  helix:  0.29 (0.26), residues: 396
  sheet: -1.15 (0.31), residues: 269
  loop : -1.44 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 314 
 TYR   0.013   0.001   TYR H 178 
 PHE   0.012   0.001   PHE R 141 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 8790)
  covalent geometry    : angle       0.60490 (11897)
  SS BOND              : bond        0.00417 (    3)
  SS BOND              : angle       0.90461 (    6)
  hydrogen bonds       : bond        0.04847 (  401)
  hydrogen bonds       : angle       5.49876 ( 1188)

*********************** 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  : 0.332 
Fit side-chains
REVERT: C   21 MET cc_start: 0.8677 (ppp) cc_final: 0.8374 (ppp)
REVERT: H  111 TRP cc_start: 0.9667 (OUTLIER) cc_final: 0.9200 (m100)
  outliers start: 16
  outliers final: 2
  residues processed: 56
  average time/residue: 0.5970
  time to fit residues: 35.6220
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  : 0.321 
-------------------------------------------------------------------------------
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 63 optimal weight:   20.0000
   chunk 90 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0270
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 92 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    3.4046

-------------------------------------------------------------------------------
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 = 0.2308 r_free = 0.2308 target = 0.029125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2119 r_free = 0.2119 target = 0.024903 restraints weight = 88409.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.2106 rms_B_bonded: 3.09
r_work: 0.2048 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9204
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   8793  Z= 0.142
  Angle     :  0.549   7.314  11903  Z= 0.288
  Chirality :  0.040   0.145   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.437  49.049   1213
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.00 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.25), residues: 1084
  helix:  0.63 (0.26), residues: 397
  sheet: -1.02 (0.31), residues: 266
  loop : -1.42 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 342 
 TYR   0.012   0.001   TYR H 178 
 PHE   0.011   0.001   PHE H 227 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8790)
  covalent geometry    : angle       0.54934 (11897)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       0.68166 (    6)
  hydrogen bonds       : bond        0.04096 (  401)
  hydrogen bonds       : angle       4.98804 ( 1188)

*********************** 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
  63 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 41
  time to evaluate  : 0.340 
Fit side-chains
REVERT: H  128 MET cc_start: 0.9434 (mtp) cc_final: 0.9114 (mtm)
  outliers start: 22
  outliers final: 6
  residues processed: 61
  average time/residue: 0.5547
  time to fit residues: 36.1328
Evaluate side-chains
  46 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  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 102 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 36 optimal weight:   20.0000
   chunk 23 optimal weight:   20.0000
   chunk 4 optimal weight:    7.9990
   chunk 99 optimal weight:    0.0570
   chunk 65 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 71 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    4.8106

-------------------------------------------------------------------------------
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**
R  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2295 r_free = 0.2295 target = 0.028650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2104 r_free = 0.2104 target = 0.024457 restraints weight = 89870.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.2090 rms_B_bonded: 3.05
r_work: 0.2032 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9214
moved from start:          0.1711

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= 0.183
  Angle     :  0.551   7.372  11903  Z= 0.289
  Chirality :  0.040   0.140   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.318  43.382   1213
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 22.32 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.25), residues: 1084
  helix:  0.80 (0.26), residues: 397
  sheet: -1.01 (0.31), residues: 264
  loop : -1.39 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 219 
 TYR   0.012   0.001   TYR H 178 
 PHE   0.011   0.001   PHE B 253 
 TRP   0.008   0.001   TRP B 211 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8790)
  covalent geometry    : angle       0.55111 (11897)
  SS BOND              : bond        0.00345 (    3)
  SS BOND              : angle       0.70905 (    6)
  hydrogen bonds       : bond        0.04114 (  401)
  hydrogen bonds       : angle       4.92472 ( 1188)

*********************** 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
  68 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 40
  time to evaluate  : 0.356 
Fit side-chains
REVERT: H   93 MET cc_start: 0.9628 (OUTLIER) cc_final: 0.9324 (tpp)
REVERT: H  111 TRP cc_start: 0.9681 (OUTLIER) cc_final: 0.9223 (m100)
REVERT: H  128 MET cc_start: 0.9392 (mtp) cc_final: 0.9095 (mtm)
  outliers start: 28
  outliers final: 10
  residues processed: 66
  average time/residue: 0.5493
  time to fit residues: 39.0038
Evaluate side-chains
  52 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
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  186 CYS
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 100 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 93 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 56 optimal weight:   20.0000
   chunk 106 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0010
   chunk 24 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    4.1994

-------------------------------------------------------------------------------
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 = 0.2301 r_free = 0.2301 target = 0.028729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2110 r_free = 0.2110 target = 0.024547 restraints weight = 89388.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.2096 rms_B_bonded: 3.04
r_work: 0.2040 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work: 0.2040 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9211
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8793  Z= 0.165
  Angle     :  0.545   7.721  11903  Z= 0.284
  Chirality :  0.040   0.138   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.208  42.247   1213
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 23.18 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.25), residues: 1084
  helix:  0.87 (0.26), residues: 394
  sheet: -1.05 (0.31), residues: 270
  loop : -1.33 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 342 
 TYR   0.012   0.001   TYR R  49 
 PHE   0.011   0.001   PHE B 253 
 TRP   0.008   0.001   TRP B 211 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8790)
  covalent geometry    : angle       0.54465 (11897)
  SS BOND              : bond        0.00297 (    3)
  SS BOND              : angle       0.70646 (    6)
  hydrogen bonds       : bond        0.03970 (  401)
  hydrogen bonds       : angle       4.84792 ( 1188)

*********************** 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
  69 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 42
  time to evaluate  : 0.387 
Fit side-chains
REVERT: H   93 MET cc_start: 0.9621 (OUTLIER) cc_final: 0.9338 (tpp)
REVERT: H  111 TRP cc_start: 0.9679 (OUTLIER) cc_final: 0.9223 (m100)
REVERT: H  218 MET cc_start: 0.9264 (ttp) cc_final: 0.9008 (ttm)
  outliers start: 27
  outliers final: 10
  residues processed: 65
  average time/residue: 0.5160
  time to fit residues: 36.1266
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  : 0.231 
-------------------------------------------------------------------------------
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  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 10 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 100 optimal weight:    2.9990
   overall best weight:    3.9588

-------------------------------------------------------------------------------
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 = 0.2307 r_free = 0.2307 target = 0.028818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2119 r_free = 0.2119 target = 0.024607 restraints weight = 88497.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.2105 rms_B_bonded: 3.07
r_work: 0.2045 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work: 0.2045 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9209
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8793  Z= 0.158
  Angle     :  0.544   8.110  11903  Z= 0.282
  Chirality :  0.040   0.141   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.124  42.786   1213
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 22.64 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.25), residues: 1084
  helix:  0.91 (0.26), residues: 394
  sheet: -1.01 (0.31), residues: 264
  loop : -1.37 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 342 
 TYR   0.013   0.001   TYR R  49 
 PHE   0.011   0.001   PHE B 253 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8790)
  covalent geometry    : angle       0.54382 (11897)
  SS BOND              : bond        0.00281 (    3)
  SS BOND              : angle       0.65147 (    6)
  hydrogen bonds       : bond        0.03891 (  401)
  hydrogen bonds       : angle       4.77428 ( 1188)

*********************** 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
  68 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 41
  time to evaluate  : 0.262 
Fit side-chains
REVERT: H  111 TRP cc_start: 0.9684 (OUTLIER) cc_final: 0.9187 (m100)
REVERT: H  218 MET cc_start: 0.9236 (ttp) cc_final: 0.8957 (ttm)
REVERT: R  221 ARG cc_start: 0.9848 (OUTLIER) cc_final: 0.9518 (mmp80)
REVERT: R  331 MET cc_start: 0.9182 (mpp) cc_final: 0.8926 (mpp)
  outliers start: 27
  outliers final: 12
  residues processed: 66
  average time/residue: 0.5623
  time to fit residues: 39.6122
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  : 0.302 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 105 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 92 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   overall best weight:    3.4588

-------------------------------------------------------------------------------
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 = 0.2316 r_free = 0.2316 target = 0.029013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2126 r_free = 0.2126 target = 0.024792 restraints weight = 89536.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2112 rms_B_bonded: 3.08
r_work: 0.2055 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9205
moved from start:          0.1969

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= 0.144
  Angle     :  0.541   9.284  11903  Z= 0.280
  Chirality :  0.040   0.135   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.050  42.948   1213
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 23.28 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.25), residues: 1084
  helix:  0.97 (0.26), residues: 394
  sheet: -0.99 (0.31), residues: 264
  loop : -1.36 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 342 
 TYR   0.012   0.001   TYR R  49 
 PHE   0.011   0.001   PHE B 253 
 TRP   0.008   0.001   TRP B 211 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8790)
  covalent geometry    : angle       0.54106 (11897)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       0.60744 (    6)
  hydrogen bonds       : bond        0.03795 (  401)
  hydrogen bonds       : angle       4.68626 ( 1188)

*********************** 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
  65 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 42
  time to evaluate  : 0.356 
Fit side-chains
REVERT: H  111 TRP cc_start: 0.9694 (OUTLIER) cc_final: 0.9191 (m100)
  outliers start: 23
  outliers final: 12
  residues processed: 64
  average time/residue: 0.6186
  time to fit residues: 42.3532
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  : 0.359 
-------------------------------------------------------------------------------
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  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 70 optimal weight:   10.0000
   chunk 99 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.4980
   chunk 35 optimal weight:   10.0000
   overall best weight:    3.6786

-------------------------------------------------------------------------------
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 = 0.2317 r_free = 0.2317 target = 0.029006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2126 r_free = 0.2126 target = 0.024801 restraints weight = 88213.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.2111 rms_B_bonded: 3.03
r_work: 0.2056 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9205
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8793  Z= 0.149
  Angle     :  0.549  10.004  11903  Z= 0.282
  Chirality :  0.040   0.134   1358
  Planarity :  0.003   0.042   1495
  Dihedral  :  5.028  43.246   1213
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.93 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.25), residues: 1084
  helix:  1.00 (0.26), residues: 394
  sheet: -0.98 (0.31), residues: 264
  loop : -1.35 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 342 
 TYR   0.012   0.001   TYR R  49 
 PHE   0.010   0.001   PHE B 253 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8790)
  covalent geometry    : angle       0.54938 (11897)
  SS BOND              : bond        0.00268 (    3)
  SS BOND              : angle       0.73003 (    6)
  hydrogen bonds       : bond        0.03808 (  401)
  hydrogen bonds       : angle       4.66509 ( 1188)

*********************** 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
  59 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.366 
Fit side-chains
REVERT: H  111 TRP cc_start: 0.9695 (OUTLIER) cc_final: 0.9197 (m100)
REVERT: R  331 MET cc_start: 0.9152 (mpp) cc_final: 0.8900 (mpp)
  outliers start: 18
  outliers final: 11
  residues processed: 58
  average time/residue: 0.6355
  time to fit residues: 39.3916
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  : 0.348 
-------------------------------------------------------------------------------
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 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  282 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 37 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.2312 r_free = 0.2312 target = 0.028912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2121 r_free = 0.2121 target = 0.024703 restraints weight = 88789.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.2107 rms_B_bonded: 3.05
r_work: 0.2051 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9208
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   8793  Z= 0.163
  Angle     :  0.552  10.673  11903  Z= 0.284
  Chirality :  0.040   0.135   1358
  Planarity :  0.003   0.043   1495
  Dihedral  :  5.045  43.984   1213
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 23.93 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.25), residues: 1084
  helix:  1.01 (0.26), residues: 394
  sheet: -0.99 (0.31), residues: 264
  loop : -1.36 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 342 
 TYR   0.012   0.001   TYR R  49 
 PHE   0.010   0.001   PHE B 253 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8790)
  covalent geometry    : angle       0.55229 (11897)
  SS BOND              : bond        0.00282 (    3)
  SS BOND              : angle       0.72723 (    6)
  hydrogen bonds       : bond        0.03866 (  401)
  hydrogen bonds       : angle       4.69684 ( 1188)

*********************** 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
  60 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.354 
Fit side-chains
REVERT: H  111 TRP cc_start: 0.9698 (OUTLIER) cc_final: 0.9200 (m100)
REVERT: R  331 MET cc_start: 0.9158 (mpp) cc_final: 0.8898 (mpp)
  outliers start: 19
  outliers final: 11
  residues processed: 60
  average time/residue: 0.6291
  time to fit residues: 40.4879
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  : 0.399 
-------------------------------------------------------------------------------
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 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  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 88 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:   20.0000
   chunk 34 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.9386

-------------------------------------------------------------------------------
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 = 0.2329 r_free = 0.2329 target = 0.029293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2140 r_free = 0.2140 target = 0.025071 restraints weight = 87280.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.2126 rms_B_bonded: 3.06
r_work: 0.2069 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work: 0.2069 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9198
moved from start:          0.2077

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= 0.130
  Angle     :  0.551  11.050  11903  Z= 0.281
  Chirality :  0.040   0.186   1358
  Planarity :  0.003   0.043   1495
  Dihedral  :  4.973  43.237   1213
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 24.57 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.25), residues: 1084
  helix:  1.06 (0.26), residues: 394
  sheet: -0.90 (0.32), residues: 259
  loop : -1.39 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 342 
 TYR   0.012   0.001   TYR R  49 
 PHE   0.010   0.001   PHE B 253 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8790)
  covalent geometry    : angle       0.55105 (11897)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       0.78961 (    6)
  hydrogen bonds       : bond        0.03676 (  401)
  hydrogen bonds       : angle       4.58789 ( 1188)

********************** 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
  55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.339 
Fit side-chains
REVERT: B  337 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8722 (ptmm)
REVERT: H  111 TRP cc_start: 0.9703 (OUTLIER) cc_final: 0.9199 (m100)
REVERT: R  331 MET cc_start: 0.9151 (mpp) cc_final: 0.8894 (mpp)
  outliers start: 14
  outliers final: 11
  residues processed: 55
  average time/residue: 0.6523
  time to fit residues: 38.2796
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  : 0.384 
-------------------------------------------------------------------------------
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 B residue  337 LYS
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  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   overall best weight:    3.1986

-------------------------------------------------------------------------------
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 = 0.2328 r_free = 0.2328 target = 0.029250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2137 r_free = 0.2137 target = 0.025051 restraints weight = 88059.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.2123 rms_B_bonded: 3.01
r_work: 0.2066 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9198
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8793  Z= 0.137
  Angle     :  0.554  12.325  11903  Z= 0.281
  Chirality :  0.040   0.139   1358
  Planarity :  0.003   0.043   1495
  Dihedral  :  4.966  43.148   1213
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 24.68 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.25), residues: 1084
  helix:  1.08 (0.26), residues: 394
  sheet: -0.90 (0.32), residues: 259
  loop : -1.38 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 342 
 TYR   0.012   0.001   TYR R  49 
 PHE   0.010   0.001   PHE B 253 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8790)
  covalent geometry    : angle       0.55386 (11897)
  SS BOND              : bond        0.00269 (    3)
  SS BOND              : angle       0.82033 (    6)
  hydrogen bonds       : bond        0.03704 (  401)
  hydrogen bonds       : angle       4.58022 ( 1188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2334.54 seconds
wall clock time: 40 minutes 56.16 seconds (2456.16 seconds total)