Starting phenix.real_space_refine
on Tue Mar 11 18:26:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ged_29966/03_2025/8ged_29966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ged_29966/03_2025/8ged_29966.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ged_29966/03_2025/8ged_29966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ged_29966/03_2025/8ged_29966.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ged_29966/03_2025/8ged_29966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ged_29966/03_2025/8ged_29966.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.028
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      37      5.16       5
     C    4179      2.51       5
     N    1142      2.21       5
     O    1147      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6505
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1885
          Classifications: {'peptide': 281}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 127}
          Link IDs: {'PTRANS': 6, 'TRANS': 274}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 444
          Unresolved non-hydrogen angles: 544
          Unresolved non-hydrogen dihedrals: 352
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 271
    Chain: "B"
      Number of atoms: 2332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2332
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Unresolved non-hydrogen bonds: 236
          Unresolved non-hydrogen angles: 293
          Unresolved non-hydrogen dihedrals: 181
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 6, 'ASP:plan': 17, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 182
    Chain: "G"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 301
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "R"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1972
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 93}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 292
          Unresolved non-hydrogen angles: 369
          Unresolved non-hydrogen dihedrals: 227
          Unresolved non-hydrogen chiralities: 42
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 115
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.45, per 1000 atoms: 0.68
  Number of scatterers: 6505
  At special positions: 0
  Unit cell: (71.02, 97.52, 126.14, 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      37     16.00
     O    1147      8.00
     N    1142      7.00
     C    4179      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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: 1.57
  Conformation dependent library (CDL) restraints added in 957.8 milliseconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1794

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      50.4% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.651A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 89 through 113
    Processing helix  chain 'A' and resid 164 through 168
      removed outlier: 4.069A  pdb=" N   ASN A 167 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 238
    Processing helix  chain 'A' and resid 251 through 254
      removed outlier: 4.385A  pdb=" N   ASN A 254 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 251 through 254'
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.446A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.993A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.217A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 8 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.745A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.900A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 96
      removed outlier: 4.345A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.191A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 164
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.597A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.907A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.600A  pdb=" N   VAL R 222 " --> pdb=" O   VAL R 218 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.906A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.970A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.508A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 6.841A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.161A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.346A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.780A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.516A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.735A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.579A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.870A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1161 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: 1.82

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2140
        1.34 -     1.46: 1724
        1.46 -     1.58: 2732
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 6644
  Sorted by residual:
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.580 -0.057 2.00e-02 2.50e+03 8.00e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.453 -0.056 2.00e-02 2.50e+03 7.75e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.570 -0.050 2.00e-02 2.50e+03 6.14e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.442 -0.048 2.00e-02 2.50e+03 5.68e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.492 -0.041 2.00e-02 2.50e+03 4.26e+00
  ... (remaining 6639 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 9018
        1.74 -     3.49: 78
        3.49 -     5.23: 15
        5.23 -     6.98: 2
        6.98 -     8.72: 1
  Bond angle restraints: 9114
  Sorted by residual:
  angle pdb=" CA  LEU A  46 "
        pdb=" CB  LEU A  46 "
        pdb=" CG  LEU A  46 "
      ideal   model   delta    sigma   weight residual
     116.30  125.02   -8.72 3.50e+00 8.16e-02 6.21e+00
  angle pdb=" N   CYS B 233 "
        pdb=" CA  CYS B 233 "
        pdb=" C   CYS B 233 "
      ideal   model   delta    sigma   weight residual
     108.46  111.90   -3.44 1.51e+00 4.39e-01 5.19e+00
  angle pdb=" CB  LEU A  46 "
        pdb=" CG  LEU A  46 "
        pdb=" CD2 LEU A  46 "
      ideal   model   delta    sigma   weight residual
     110.70  104.13    6.57 3.00e+00 1.11e-01 4.79e+00
  angle pdb=" N   ASP B 258 "
        pdb=" CA  ASP B 258 "
        pdb=" C   ASP B 258 "
      ideal   model   delta    sigma   weight residual
     113.56  110.67    2.89 1.39e+00 5.18e-01 4.32e+00
  angle pdb=" N   GLY B 244 "
        pdb=" CA  GLY B 244 "
        pdb=" C   GLY B 244 "
      ideal   model   delta    sigma   weight residual
     113.02  110.05    2.97 1.59e+00 3.96e-01 3.50e+00
  ... (remaining 9109 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.10: 3438
       14.10 -    28.20: 260
       28.20 -    42.30: 92
       42.30 -    56.40: 15
       56.40 -    70.50: 5
  Dihedral angle restraints: 3810
    sinusoidal: 1049
      harmonic: 2761
  Sorted by residual:
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.22   16.78     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ARG B  68 "
           pdb=" C   ARG B  68 "
           pdb=" N   LEU B  69 "
           pdb=" CA  LEU B  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.89  -16.11     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  THR B  65 "
           pdb=" C   THR B  65 "
           pdb=" N   ASP B  66 "
           pdb=" CA  ASP B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.10   15.90     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 3807 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 798
       0.037 -    0.075: 224
       0.075 -    0.112: 64
       0.112 -    0.150: 11
       0.150 -    0.187: 2
  Chirality restraints: 1099
  Sorted by residual:
  chirality pdb=" CG  LEU A  46 "
            pdb=" CB  LEU A  46 "
            pdb=" CD1 LEU A  46 "
            pdb=" CD2 LEU A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.19 2.00e-01 2.50e+01 8.74e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.56   -0.16 2.00e-01 2.50e+01 6.22e-01
  chirality pdb=" CA  ILE A 288 "
            pdb=" N   ILE A 288 "
            pdb=" C   ILE A 288 "
            pdb=" CB  ILE A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 1096 not shown)

  Planarity restraints: 1163
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 277 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.67e+00
        pdb=" C   ILE R 277 "    0.022 2.00e-02 2.50e+03
        pdb=" O   ILE R 277 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ILE R 278 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO B 236 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 233 "   -0.005 2.00e-02 2.50e+03   1.04e-02 1.09e+00
        pdb=" C   LYS A 233 "    0.018 2.00e-02 2.50e+03
        pdb=" O   LYS A 233 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   TRP A 234 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1160 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1395
        2.78 -     3.31: 6296
        3.31 -     3.84: 10884
        3.84 -     4.37: 11330
        4.37 -     4.90: 20841
  Nonbonded interactions: 50746
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   GLY B 224 "
            pdb=" NH1 ARG B 251 "
     model   vdw
     2.332 3.120
  nonbonded pdb=" OG1 THR B 249 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" OG  SER B 201 "
            pdb=" NE1 TRP B 211 "
     model   vdw
     2.364 3.120
  ... (remaining 50741 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  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:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.840
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
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      :  0.003   0.057   6644  Z= 0.151
  Angle     :  0.475   8.721   9114  Z= 0.252
  Chirality :  0.039   0.187   1099
  Planarity :  0.003   0.031   1163
  Dihedral  : 12.401  70.496   2010
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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:  1.82 (0.28), residues: 928
  helix:  2.97 (0.25), residues: 415
  sheet: -0.04 (0.42), residues: 147
  loop : -0.34 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 277 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.008   0.001   PHE R 133 
 TYR   0.006   0.001   TYR B 105 
 ARG   0.006   0.000   ARG G  27 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1440
  time to fit residues: 22.3041
Evaluate side-chains
  81 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0370
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0020
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.3866

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
R 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.153441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.133300 restraints weight = 9828.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.136827 restraints weight = 5118.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.139167 restraints weight = 3288.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6644  Z= 0.159
  Angle     :  0.468   6.395   9114  Z= 0.253
  Chirality :  0.040   0.161   1099
  Planarity :  0.003   0.031   1163
  Dihedral  :  4.042  17.240   1013
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.62 %
    Favored  : 85.60 %
  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:  2.09 (0.28), residues: 928
  helix:  3.01 (0.25), residues: 421
  sheet:  0.29 (0.41), residues: 151
  loop : -0.11 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 193 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.005   0.000   ARG G  27 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 ASN cc_start: 0.8589 (t0) cc_final: 0.8339 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1331
  time to fit residues: 19.5109
Evaluate side-chains
  92 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue  111 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0000
   chunk 88 optimal weight:    0.9990
   chunk 73 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.150958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.130506 restraints weight = 9997.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.134047 restraints weight = 5247.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.136102 restraints weight = 3378.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6644  Z= 0.175
  Angle     :  0.461   6.148   9114  Z= 0.247
  Chirality :  0.040   0.176   1099
  Planarity :  0.003   0.031   1163
  Dihedral  :  3.904  16.089   1013
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.60 %
    Favored  : 82.45 %
  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:  2.08 (0.28), residues: 928
  helix:  2.87 (0.25), residues: 429
  sheet:  0.31 (0.41), residues: 154
  loop : -0.02 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.012   0.001   PHE R 193 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.004   0.000   ARG G  27 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8147 (mmt) cc_final: 0.7637 (mmt)
REVERT: B   75 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7489 (mm110)
REVERT: B  237 ASN cc_start: 0.8560 (t0) cc_final: 0.8325 (t0)
REVERT: B  340 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7369 (m-40)
  outliers start: 15
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1330
  time to fit residues: 19.5289
Evaluate side-chains
  97 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 225 HIS
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.148866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.127809 restraints weight = 10025.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.131260 restraints weight = 5364.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.133597 restraints weight = 3514.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6644  Z= 0.240
  Angle     :  0.483   5.796   9114  Z= 0.261
  Chirality :  0.041   0.149   1099
  Planarity :  0.003   0.029   1163
  Dihedral  :  4.087  19.557   1013
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.79 %
    Favored  : 82.05 %
  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:  1.98 (0.29), residues: 928
  helix:  2.79 (0.25), residues: 430
  sheet:  0.10 (0.40), residues: 159
  loop :  0.01 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.011   0.001   PHE R 193 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.003   0.000   ARG G  27 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7601 (mm110)
REVERT: B  237 ASN cc_start: 0.8549 (t0) cc_final: 0.8328 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1274
  time to fit residues: 18.7569
Evaluate side-chains
  93 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0870
   chunk 86 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 70 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
B 142 HIS
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.149736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.128821 restraints weight = 9864.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.132320 restraints weight = 5287.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.134659 restraints weight = 3429.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6644  Z= 0.178
  Angle     :  0.450   6.624   9114  Z= 0.243
  Chirality :  0.040   0.145   1099
  Planarity :  0.003   0.029   1163
  Dihedral  :  4.028  21.237   1013
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 16.17 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.29), residues: 928
  helix:  2.80 (0.25), residues: 430
  sheet: -0.10 (0.39), residues: 166
  loop :  0.09 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 313 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.003   0.000   ARG G  27 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 17
  residues processed: 101
  average time/residue: 0.1139
  time to fit residues: 17.8469
Evaluate side-chains
  98 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0270
   chunk 72 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.7242

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.149247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.128220 restraints weight = 9853.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.131625 restraints weight = 5305.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.133958 restraints weight = 3488.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6644  Z= 0.199
  Angle     :  0.461   5.822   9114  Z= 0.248
  Chirality :  0.040   0.144   1099
  Planarity :  0.003   0.029   1163
  Dihedral  :  4.026  20.680   1013
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.17 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.89 (0.29), residues: 928
  helix:  2.77 (0.25), residues: 430
  sheet: -0.20 (0.39), residues: 166
  loop :  0.04 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 313 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.004   0.000   ARG B  49 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8065 (mmt) cc_final: 0.7647 (mmt)
  outliers start: 21
  outliers final: 17
  residues processed: 99
  average time/residue: 0.1289
  time to fit residues: 20.0555
Evaluate side-chains
  94 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 92 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.139863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.118591 restraints weight = 10851.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.121815 restraints weight = 6070.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.123998 restraints weight = 4059.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6644  Z= 0.310
  Angle     :  0.522   7.240   9114  Z= 0.279
  Chirality :  0.042   0.141   1099
  Planarity :  0.003   0.029   1163
  Dihedral  :  4.294  19.484   1013
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.77 %
    Favored  : 79.09 %
  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:  1.65 (0.28), residues: 928
  helix:  2.63 (0.25), residues: 430
  sheet: -0.52 (0.38), residues: 167
  loop : -0.04 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 235 
 TYR   0.022   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B  68 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8193 (mmt) cc_final: 0.7763 (mmt)
  outliers start: 21
  outliers final: 19
  residues processed: 89
  average time/residue: 0.1199
  time to fit residues: 17.2185
Evaluate side-chains
  91 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  114 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0020
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.139992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.119124 restraints weight = 10492.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.122382 restraints weight = 5763.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.124612 restraints weight = 3825.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6644  Z= 0.194
  Angle     :  0.472   7.415   9114  Z= 0.252
  Chirality :  0.040   0.146   1099
  Planarity :  0.003   0.029   1163
  Dihedral  :  4.187  19.693   1013
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 17.55 %
    Favored  : 78.30 %
  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:  1.64 (0.29), residues: 928
  helix:  2.63 (0.25), residues: 436
  sheet: -0.51 (0.39), residues: 167
  loop : -0.11 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B  49 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: B  155 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7929 (t0)
REVERT: R  107 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7019 (mm-30)
REVERT: R  174 TYR cc_start: 0.8252 (p90) cc_final: 0.7882 (p90)
  outliers start: 21
  outliers final: 18
  residues processed: 92
  average time/residue: 0.1144
  time to fit residues: 16.4678
Evaluate side-chains
  91 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 87 optimal weight:    0.0040
   chunk 60 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.141061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.120293 restraints weight = 10545.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.123616 restraints weight = 5777.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.125847 restraints weight = 3815.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6644  Z= 0.175
  Angle     :  0.460   6.975   9114  Z= 0.247
  Chirality :  0.040   0.145   1099
  Planarity :  0.003   0.029   1163
  Dihedral  :  4.156  25.693   1013
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.95 %
    Favored  : 78.30 %
  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:  1.69 (0.28), residues: 928
  helix:  2.66 (0.25), residues: 436
  sheet: -0.42 (0.39), residues: 165
  loop : -0.12 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.002   0.000   ARG G  27 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: B  155 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7910 (t0)
  outliers start: 19
  outliers final: 17
  residues processed: 89
  average time/residue: 0.1176
  time to fit residues: 16.6203
Evaluate side-chains
  90 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 7 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.139870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.118350 restraints weight = 11048.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.121589 restraints weight = 6163.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.123795 restraints weight = 4137.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6644  Z= 0.298
  Angle     :  0.523   6.430   9114  Z= 0.278
  Chirality :  0.042   0.140   1099
  Planarity :  0.003   0.029   1163
  Dihedral  :  4.356  22.160   1013
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 18.74 %
    Favored  : 77.51 %
  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:  1.46 (0.28), residues: 928
  helix:  2.49 (0.25), residues: 436
  sheet: -0.59 (0.39), residues: 167
  loop : -0.23 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R  99 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.022   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B  68 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: B  155 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7900 (t0)
  outliers start: 19
  outliers final: 17
  residues processed: 88
  average time/residue: 0.1183
  time to fit residues: 16.5926
Evaluate side-chains
  88 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 7 optimal weight:    7.9990
   chunk 90 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.139440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.118366 restraints weight = 10800.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.121605 restraints weight = 5886.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.123899 restraints weight = 3924.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6644  Z= 0.208
  Angle     :  0.470   6.762   9114  Z= 0.251
  Chirality :  0.040   0.143   1099
  Planarity :  0.003   0.029   1163
  Dihedral  :  4.204  18.681   1013
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.74 %
    Favored  : 77.91 %
  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:  1.55 (0.29), residues: 928
  helix:  2.59 (0.25), residues: 436
  sheet: -0.58 (0.39), residues: 167
  loop : -0.19 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 313 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B  49 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2347.89 seconds
wall clock time: 41 minutes 10.77 seconds (2470.77 seconds total)