Starting phenix.real_space_refine
on Thu Jul 31 01:47:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ebf_31053/07_2025/7ebf_31053.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ebf_31053/07_2025/7ebf_31053.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ebf_31053/07_2025/7ebf_31053.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ebf_31053/07_2025/7ebf_31053.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ebf_31053/07_2025/7ebf_31053.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ebf_31053/07_2025/7ebf_31053.cif"
  }
  resolution = 2.63
  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=   0.000 sd=   0.004
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      32      5.16       5
     C    8340      2.51       5
     N    2276      2.21       5
     O    2404      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13052
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3263
          Classifications: {'peptide': 410}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 396}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 14
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 6.93, per 1000 atoms: 0.53
  Number of scatterers: 13052
  At special positions: 0
  Unit cell: (96.291, 147.317, 92.999, 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      32     16.00
     O    2404      8.00
     N    2276      7.00
     C    8340      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3088

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 12 sheets defined
      55.9% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 26
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 39 through 47
    Processing helix  chain 'A' and resid 54 through 74
      removed outlier: 3.901A  pdb=" N   GLN A  58 " --> pdb=" O   HIS A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 151
    Processing helix  chain 'A' and resid 156 through 160
    Processing helix  chain 'A' and resid 180 through 193
    Processing helix  chain 'A' and resid 220 through 239
    Processing helix  chain 'A' and resid 261 through 266
      removed outlier: 3.583A  pdb=" N   HIS A 265 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   TYR A 266 " --> pdb=" O   HIS A 262 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 261 through 266'
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 292 through 307
      removed outlier: 4.311A  pdb=" N   ALA A 298 " --> pdb=" O   ASN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 321
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'A' and resid 346 through 358
    Processing helix  chain 'A' and resid 380 through 393
      removed outlier: 3.996A  pdb=" N   CYS A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 407 through 422
    Processing helix  chain 'A' and resid 445 through 457
    Processing helix  chain 'B' and resid 9 through 26
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 39 through 47
    Processing helix  chain 'B' and resid 54 through 74
      removed outlier: 3.901A  pdb=" N   GLN B  58 " --> pdb=" O   HIS B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 151
    Processing helix  chain 'B' and resid 156 through 160
    Processing helix  chain 'B' and resid 180 through 193
    Processing helix  chain 'B' and resid 220 through 239
    Processing helix  chain 'B' and resid 261 through 266
      removed outlier: 3.583A  pdb=" N   HIS B 265 " --> pdb=" O   ASP B 261 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   TYR B 266 " --> pdb=" O   HIS B 262 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 261 through 266'
    Processing helix  chain 'B' and resid 278 through 286
    Processing helix  chain 'B' and resid 292 through 307
      removed outlier: 4.310A  pdb=" N   ALA B 298 " --> pdb=" O   ASN B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 321
    Processing helix  chain 'B' and resid 329 through 339
    Processing helix  chain 'B' and resid 346 through 358
    Processing helix  chain 'B' and resid 380 through 393
      removed outlier: 3.995A  pdb=" N   CYS B 384 " --> pdb=" O   GLY B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 396
      No H-bonds generated for 'chain 'B' and resid 394 through 396'
    Processing helix  chain 'B' and resid 407 through 422
    Processing helix  chain 'B' and resid 445 through 457
    Processing helix  chain 'C' and resid 9 through 26
    Processing helix  chain 'C' and resid 28 through 32
    Processing helix  chain 'C' and resid 39 through 47
    Processing helix  chain 'C' and resid 54 through 74
      removed outlier: 3.902A  pdb=" N   GLN C  58 " --> pdb=" O   HIS C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 151
    Processing helix  chain 'C' and resid 156 through 160
    Processing helix  chain 'C' and resid 180 through 193
    Processing helix  chain 'C' and resid 220 through 239
    Processing helix  chain 'C' and resid 261 through 266
      removed outlier: 3.584A  pdb=" N   HIS C 265 " --> pdb=" O   ASP C 261 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   TYR C 266 " --> pdb=" O   HIS C 262 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 261 through 266'
    Processing helix  chain 'C' and resid 278 through 286
    Processing helix  chain 'C' and resid 292 through 307
      removed outlier: 4.309A  pdb=" N   ALA C 298 " --> pdb=" O   ASN C 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 321
    Processing helix  chain 'C' and resid 329 through 339
    Processing helix  chain 'C' and resid 346 through 358
    Processing helix  chain 'C' and resid 380 through 393
      removed outlier: 3.995A  pdb=" N   CYS C 384 " --> pdb=" O   GLY C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 394 through 396
      No H-bonds generated for 'chain 'C' and resid 394 through 396'
    Processing helix  chain 'C' and resid 407 through 422
    Processing helix  chain 'C' and resid 445 through 457
    Processing helix  chain 'D' and resid 9 through 26
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 39 through 47
    Processing helix  chain 'D' and resid 54 through 74
      removed outlier: 3.902A  pdb=" N   GLN D  58 " --> pdb=" O   HIS D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 151
    Processing helix  chain 'D' and resid 156 through 160
    Processing helix  chain 'D' and resid 180 through 193
    Processing helix  chain 'D' and resid 220 through 239
    Processing helix  chain 'D' and resid 261 through 266
      removed outlier: 3.583A  pdb=" N   HIS D 265 " --> pdb=" O   ASP D 261 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   TYR D 266 " --> pdb=" O   HIS D 262 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 261 through 266'
    Processing helix  chain 'D' and resid 278 through 286
    Processing helix  chain 'D' and resid 292 through 307
      removed outlier: 4.310A  pdb=" N   ALA D 298 " --> pdb=" O   ASN D 294 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 321
    Processing helix  chain 'D' and resid 329 through 339
    Processing helix  chain 'D' and resid 346 through 358
    Processing helix  chain 'D' and resid 380 through 393
      removed outlier: 3.995A  pdb=" N   CYS D 384 " --> pdb=" O   GLY D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 396
      No H-bonds generated for 'chain 'D' and resid 394 through 396'
    Processing helix  chain 'D' and resid 407 through 422
    Processing helix  chain 'D' and resid 445 through 457
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78
      removed outlier: 5.820A  pdb=" N   SER A  77 " --> pdb=" O   GLN A 461 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU A 427 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   GLN A 461 " --> pdb=" O   LEU A 427 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   TYR A 429 " --> pdb=" O   GLN A 461 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ILE A 399 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   ASN A 430 " --> pdb=" O   ILE A 399 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   MET A 401 " --> pdb=" O   ASN A 430 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ALA A 244 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   TRP A 400 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ALA A 246 " --> pdb=" O   TRP A 400 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   GLU A 402 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   THR A 248 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ILE A 198 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   ARG A 247 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE A 200 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 218
      removed outlier: 5.551A  pdb=" N   LYS A 216 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271
    Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 78
      removed outlier: 5.819A  pdb=" N   SER B  77 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   LEU B 427 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   GLN B 461 " --> pdb=" O   LEU B 427 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   TYR B 429 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ILE B 399 " --> pdb=" O   ALA B 428 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   ASN B 430 " --> pdb=" O   ILE B 399 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   MET B 401 " --> pdb=" O   ASN B 430 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ALA B 244 " --> pdb=" O   LEU B 398 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   TRP B 400 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ALA B 246 " --> pdb=" O   TRP B 400 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   GLU B 402 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   THR B 248 " --> pdb=" O   GLU B 402 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ILE B 198 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   ARG B 247 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE B 200 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 216 through 218
      removed outlier: 5.551A  pdb=" N   LYS B 216 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 270 through 271
    Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78
      removed outlier: 5.820A  pdb=" N   SER C  77 " --> pdb=" O   GLN C 461 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU C 427 " --> pdb=" O   VAL C 459 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   GLN C 461 " --> pdb=" O   LEU C 427 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   TYR C 429 " --> pdb=" O   GLN C 461 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ILE C 399 " --> pdb=" O   ALA C 428 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   ASN C 430 " --> pdb=" O   ILE C 399 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   MET C 401 " --> pdb=" O   ASN C 430 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ALA C 244 " --> pdb=" O   LEU C 398 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   TRP C 400 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ALA C 246 " --> pdb=" O   TRP C 400 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   GLU C 402 " --> pdb=" O   ALA C 246 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   THR C 248 " --> pdb=" O   GLU C 402 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ILE C 198 " --> pdb=" O   VAL C 245 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   ARG C 247 " --> pdb=" O   ILE C 198 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ILE C 200 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 216 through 218
      removed outlier: 5.552A  pdb=" N   LYS C 216 " --> pdb=" O   ALA C 253 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 270 through 271
    Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 78
      removed outlier: 5.819A  pdb=" N   SER D  77 " --> pdb=" O   GLN D 461 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU D 427 " --> pdb=" O   VAL D 459 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   GLN D 461 " --> pdb=" O   LEU D 427 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   TYR D 429 " --> pdb=" O   GLN D 461 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ILE D 399 " --> pdb=" O   ALA D 428 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ASN D 430 " --> pdb=" O   ILE D 399 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   MET D 401 " --> pdb=" O   ASN D 430 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ALA D 244 " --> pdb=" O   LEU D 398 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   TRP D 400 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ALA D 246 " --> pdb=" O   TRP D 400 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   GLU D 402 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   THR D 248 " --> pdb=" O   GLU D 402 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ILE D 198 " --> pdb=" O   VAL D 245 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   ARG D 247 " --> pdb=" O   ILE D 198 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ILE D 200 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 216 through 218
      removed outlier: 5.551A  pdb=" N   LYS D 216 " --> pdb=" O   ALA D 253 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 270 through 271

    665 hydrogen bonds defined for protein.
    1935 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.93

  Time building geometry restraints manager: 3.12 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: 4237
        1.34 -     1.46: 3029
        1.46 -     1.58: 5998
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 13320
  Sorted by residual:
  bond pdb=" C   GLU C  28 "
       pdb=" N   PRO C  29 "
    ideal  model  delta    sigma   weight residual
    1.336  1.347 -0.011 1.08e-02 8.57e+03 1.11e+00
  bond pdb=" C   GLU A  28 "
       pdb=" N   PRO A  29 "
    ideal  model  delta    sigma   weight residual
    1.336  1.347 -0.011 1.08e-02 8.57e+03 1.04e+00
  bond pdb=" CA  VAL A 127 "
       pdb=" CB  VAL A 127 "
    ideal  model  delta    sigma   weight residual
    1.534  1.541 -0.006 6.80e-03 2.16e+04 8.73e-01
  bond pdb=" CA  VAL D 127 "
       pdb=" CB  VAL D 127 "
    ideal  model  delta    sigma   weight residual
    1.534  1.540 -0.006 6.80e-03 2.16e+04 7.36e-01
  bond pdb=" CA  VAL C 127 "
       pdb=" CB  VAL C 127 "
    ideal  model  delta    sigma   weight residual
    1.534  1.540 -0.006 6.80e-03 2.16e+04 7.25e-01
  ... (remaining 13315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 17708
        1.40 -     2.81: 197
        2.81 -     4.21: 27
        4.21 -     5.61: 8
        5.61 -     7.01: 4
  Bond angle restraints: 17944
  Sorted by residual:
  angle pdb=" CA  LEU B 331 "
        pdb=" CB  LEU B 331 "
        pdb=" CG  LEU B 331 "
      ideal   model   delta    sigma   weight residual
     116.30  123.31   -7.01 3.50e+00 8.16e-02 4.01e+00
  angle pdb=" CA  LEU A 331 "
        pdb=" CB  LEU A 331 "
        pdb=" CG  LEU A 331 "
      ideal   model   delta    sigma   weight residual
     116.30  123.30   -7.00 3.50e+00 8.16e-02 4.00e+00
  angle pdb=" CA  LEU C 331 "
        pdb=" CB  LEU C 331 "
        pdb=" CG  LEU C 331 "
      ideal   model   delta    sigma   weight residual
     116.30  123.29   -6.99 3.50e+00 8.16e-02 3.99e+00
  angle pdb=" CA  LEU D 331 "
        pdb=" CB  LEU D 331 "
        pdb=" CG  LEU D 331 "
      ideal   model   delta    sigma   weight residual
     116.30  123.24   -6.94 3.50e+00 8.16e-02 3.93e+00
  angle pdb=" C   ALA D 297 "
        pdb=" N   ALA D 298 "
        pdb=" CA  ALA D 298 "
      ideal   model   delta    sigma   weight residual
     120.29  122.62   -2.33 1.42e+00 4.96e-01 2.69e+00
  ... (remaining 17939 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 7562
       17.62 -    35.25: 338
       35.25 -    52.87: 56
       52.87 -    70.49: 16
       70.49 -    88.11: 12
  Dihedral angle restraints: 7984
    sinusoidal: 3228
      harmonic: 4756
  Sorted by residual:
  dihedral pdb=" CA  GLU D 285 "
           pdb=" CB  GLU D 285 "
           pdb=" CG  GLU D 285 "
           pdb=" CD  GLU D 285 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.42   57.58     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CA  GLU A 285 "
           pdb=" CB  GLU A 285 "
           pdb=" CG  GLU A 285 "
           pdb=" CD  GLU A 285 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.44   57.56     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CA  GLU C 285 "
           pdb=" CB  GLU C 285 "
           pdb=" CG  GLU C 285 "
           pdb=" CD  GLU C 285 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.45   57.55     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 7981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1126
       0.025 -    0.050: 514
       0.050 -    0.075: 181
       0.075 -    0.101: 78
       0.101 -    0.126: 49
  Chirality restraints: 1948
  Sorted by residual:
  chirality pdb=" CA  VAL A 219 "
            pdb=" N   VAL A 219 "
            pdb=" C   VAL A 219 "
            pdb=" CB  VAL A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.96e-01
  chirality pdb=" CA  VAL D 219 "
            pdb=" N   VAL D 219 "
            pdb=" C   VAL D 219 "
            pdb=" CB  VAL D 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  ILE C 170 "
            pdb=" N   ILE C 170 "
            pdb=" C   ILE C 170 "
            pdb=" CB  ILE C 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 1945 not shown)

  Planarity restraints: 2276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  28 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.36e+00
        pdb=" N   PRO B  29 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B  29 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  29 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  28 "   -0.019 5.00e-02 4.00e+02   2.89e-02 1.33e+00
        pdb=" N   PRO C  29 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C  29 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  29 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D  28 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO D  29 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO D  29 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D  29 "    0.016 5.00e-02 4.00e+02
  ... (remaining 2273 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 3639
        2.82 -     3.34: 12524
        3.34 -     3.86: 23176
        3.86 -     4.38: 26458
        4.38 -     4.90: 44140
  Nonbonded interactions: 109937
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 204 "
            pdb=" OG1 THR C 207 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ALA B 204 "
            pdb=" OG1 THR B 207 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ALA D 204 "
            pdb=" OG1 THR D 207 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   ALA A 204 "
            pdb=" OG1 THR A 207 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OE2 GLU A 201 "
            pdb=" NH2 ARG A 247 "
     model   vdw
     2.322 3.120
  ... (remaining 109932 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

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:             3.300
  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:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.140
  Process input model:                     29.440
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
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      :  0.002   0.035  13320  Z= 0.092
  Angle     :  0.417   7.013  17944  Z= 0.223
  Chirality :  0.037   0.126   1948
  Planarity :  0.003   0.029   2276
  Dihedral  : 11.012  88.114   4896
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  4.52 %
    Favored  : 93.37 %
  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:  1.61 (0.21), residues: 1576
  helix:  1.91 (0.18), residues: 840
  sheet:  1.53 (0.39), residues: 164
  loop : -0.30 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  31 
 HIS   0.003   0.001   HIS D 199 
 PHE   0.007   0.001   PHE B 462 
 TYR   0.005   0.001   TYR C 378 
 ARG   0.002   0.000   ARG A 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14215 (  665)
  hydrogen bonds       : angle       4.39589 ( 1935)
  covalent geometry    : bond        0.00187 (13320)
  covalent geometry    : angle       0.41660 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 244
  time to evaluate  : 2.452 
Fit side-chains
REVERT: A  129 ASN cc_start: 0.7386 (m-40) cc_final: 0.7186 (m-40)
REVERT: A  213 MET cc_start: 0.2623 (ttt) cc_final: 0.2310 (ptp)
REVERT: A  285 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5444 (mp0)
REVERT: A  336 THR cc_start: 0.7130 (m) cc_final: 0.6926 (t)
REVERT: A  358 THR cc_start: 0.7519 (m) cc_final: 0.7293 (t)
REVERT: B  285 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5494 (mp0)
REVERT: B  358 THR cc_start: 0.7642 (m) cc_final: 0.7398 (t)
REVERT: C  213 MET cc_start: 0.2610 (ttt) cc_final: 0.2316 (ptp)
REVERT: C  285 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5557 (mp0)
REVERT: C  336 THR cc_start: 0.7055 (m) cc_final: 0.6828 (t)
REVERT: C  358 THR cc_start: 0.7635 (m) cc_final: 0.7431 (t)
REVERT: D  129 ASN cc_start: 0.7392 (m-40) cc_final: 0.7178 (m-40)
REVERT: D  213 MET cc_start: 0.3053 (ttt) cc_final: 0.2407 (ptt)
REVERT: D  285 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5229 (mp0)
REVERT: D  336 THR cc_start: 0.7049 (m) cc_final: 0.6814 (t)
REVERT: D  358 THR cc_start: 0.7622 (m) cc_final: 0.7418 (t)
  outliers start: 28
  outliers final: 4
  residues processed: 252
  average time/residue: 1.6225
  time to fit residues: 438.4634
Evaluate side-chains
  149 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 138 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 148 optimal weight:    7.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
A 461 GLN
B 461 GLN
C 340 ASN
C 461 GLN
D 340 ASN
D 461 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.182420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.147709 restraints weight = 15393.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 1.75
r_work: 0.3639 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13320  Z= 0.125
  Angle     :  0.470   7.372  17944  Z= 0.246
  Chirality :  0.040   0.147   1948
  Planarity :  0.004   0.030   2276
  Dihedral  :  5.344  59.631   1768
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 11.45 %
    Favored  : 84.49 %
  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:  1.38 (0.20), residues: 1576
  helix:  1.81 (0.18), residues: 860
  sheet:  1.42 (0.37), residues: 160
  loop : -0.66 (0.23), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  31 
 HIS   0.004   0.001   HIS C 347 
 PHE   0.008   0.001   PHE D 335 
 TYR   0.011   0.001   TYR A 162 
 ARG   0.003   0.001   ARG A 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  665)
  hydrogen bonds       : angle       3.94245 ( 1935)
  covalent geometry    : bond        0.00276 (13320)
  covalent geometry    : angle       0.47008 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 157
  time to evaluate  : 1.511 
Fit side-chains
REVERT: A  132 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7756 (tt0)
REVERT: A  213 MET cc_start: 0.3300 (ttt) cc_final: 0.2418 (ptp)
REVERT: A  285 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5454 (mp0)
REVERT: A  336 THR cc_start: 0.7342 (m) cc_final: 0.7092 (t)
REVERT: A  358 THR cc_start: 0.7807 (m) cc_final: 0.7344 (t)
REVERT: B  285 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5442 (mp0)
REVERT: B  358 THR cc_start: 0.7821 (m) cc_final: 0.7447 (t)
REVERT: B  372 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7449 (ttm-80)
REVERT: C  132 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7679 (tt0)
REVERT: C  213 MET cc_start: 0.3133 (ttt) cc_final: 0.2286 (ptp)
REVERT: C  285 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5389 (mp0)
REVERT: C  336 THR cc_start: 0.7237 (m) cc_final: 0.6968 (t)
REVERT: C  358 THR cc_start: 0.7819 (m) cc_final: 0.7375 (t)
REVERT: C  372 ARG cc_start: 0.7621 (tpp80) cc_final: 0.7406 (ttm-80)
REVERT: D  132 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7746 (tt0)
REVERT: D  213 MET cc_start: 0.3456 (ttt) cc_final: 0.2418 (ptt)
REVERT: D  285 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5256 (mp0)
REVERT: D  302 GLU cc_start: 0.5352 (OUTLIER) cc_final: 0.4350 (tt0)
REVERT: D  336 THR cc_start: 0.7297 (m) cc_final: 0.7043 (t)
REVERT: D  358 THR cc_start: 0.7825 (m) cc_final: 0.7382 (t)
  outliers start: 54
  outliers final: 14
  residues processed: 183
  average time/residue: 1.5000
  time to fit residues: 295.3518
Evaluate side-chains
  161 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  402 GLU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue  132 GLU
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  410 GLN
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 146 optimal weight:    9.9990
   chunk 134 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 141 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 105 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
C 133 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.178150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.142936 restraints weight = 15756.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.78
r_work: 0.3583 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13320  Z= 0.227
  Angle     :  0.591   8.345  17944  Z= 0.311
  Chirality :  0.043   0.154   1948
  Planarity :  0.004   0.034   2276
  Dihedral  :  5.821  57.374   1768
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 12.20 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.20), residues: 1576
  helix:  1.17 (0.17), residues: 868
  sheet:  0.89 (0.37), residues: 164
  loop : -0.74 (0.24), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 400 
 HIS   0.006   0.001   HIS C 347 
 PHE   0.016   0.002   PHE D  80 
 TYR   0.014   0.002   TYR B 408 
 ARG   0.005   0.001   ARG C  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05017 (  665)
  hydrogen bonds       : angle       4.45110 ( 1935)
  covalent geometry    : bond        0.00521 (13320)
  covalent geometry    : angle       0.59072 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 137
  time to evaluate  : 1.692 
Fit side-chains
REVERT: A  132 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7689 (tt0)
REVERT: A  213 MET cc_start: 0.3378 (ttt) cc_final: 0.2613 (ptp)
REVERT: A  285 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5821 (mp0)
REVERT: A  333 LYS cc_start: 0.7264 (tmmt) cc_final: 0.6973 (tmmt)
REVERT: A  358 THR cc_start: 0.7877 (m) cc_final: 0.7354 (t)
REVERT: B  132 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7679 (tt0)
REVERT: B  285 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5881 (mp0)
REVERT: B  358 THR cc_start: 0.7911 (m) cc_final: 0.7472 (t)
REVERT: C  132 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7636 (tt0)
REVERT: C  213 MET cc_start: 0.3394 (ttt) cc_final: 0.2600 (ptp)
REVERT: C  285 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5854 (mp0)
REVERT: C  358 THR cc_start: 0.7895 (m) cc_final: 0.7404 (t)
REVERT: D  132 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7667 (tt0)
REVERT: D  213 MET cc_start: 0.3333 (ttt) cc_final: 0.2513 (ptp)
REVERT: D  285 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5715 (mp0)
REVERT: D  302 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.4541 (tt0)
REVERT: D  358 THR cc_start: 0.7919 (m) cc_final: 0.7447 (t)
REVERT: D  372 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7328 (mtm-85)
  outliers start: 55
  outliers final: 28
  residues processed: 170
  average time/residue: 1.4671
  time to fit residues: 268.9644
Evaluate side-chains
  157 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 1.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LYS
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  338 LYS
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   91 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  143 ARG
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  338 LYS
Chi-restraints excluded: chain C residue  402 GLU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue   69 LYS
Chi-restraints excluded: chain D residue   91 MET
Chi-restraints excluded: chain D residue  132 GLU
Chi-restraints excluded: chain D residue  143 ARG
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  410 GLN
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 133 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 163 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 121 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 131 optimal weight:    0.7980
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.180417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.145657 restraints weight = 15622.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 1.77
r_work: 0.3622 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13320  Z= 0.118
  Angle     :  0.465   7.193  17944  Z= 0.245
  Chirality :  0.040   0.141   1948
  Planarity :  0.004   0.035   2276
  Dihedral  :  5.484  57.449   1768
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.01 %
    Favored  : 82.53 %
  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:  1.08 (0.20), residues: 1576
  helix:  1.46 (0.18), residues: 868
  sheet:  1.38 (0.38), residues: 152
  loop : -0.62 (0.24), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 135 
 HIS   0.004   0.001   HIS C 347 
 PHE   0.013   0.001   PHE A 238 
 TYR   0.008   0.001   TYR B 162 
 ARG   0.002   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  665)
  hydrogen bonds       : angle       4.08362 ( 1935)
  covalent geometry    : bond        0.00262 (13320)
  covalent geometry    : angle       0.46517 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 135
  time to evaluate  : 1.455 
Fit side-chains
REVERT: A  213 MET cc_start: 0.3269 (ttt) cc_final: 0.2338 (ptt)
REVERT: A  285 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5864 (mp0)
REVERT: A  333 LYS cc_start: 0.7172 (tmmt) cc_final: 0.6895 (tmmt)
REVERT: A  358 THR cc_start: 0.7860 (m) cc_final: 0.7353 (t)
REVERT: B  285 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5841 (mp0)
REVERT: B  358 THR cc_start: 0.7833 (m) cc_final: 0.7387 (t)
REVERT: B  410 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6864 (tt0)
REVERT: C  213 MET cc_start: 0.3307 (ttt) cc_final: 0.2372 (ptt)
REVERT: C  285 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5751 (mp0)
REVERT: C  358 THR cc_start: 0.7845 (m) cc_final: 0.7360 (t)
REVERT: D  213 MET cc_start: 0.3292 (ttt) cc_final: 0.2320 (ptt)
REVERT: D  285 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5625 (mp0)
REVERT: D  302 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.4441 (tt0)
REVERT: D  358 THR cc_start: 0.7860 (m) cc_final: 0.7403 (t)
REVERT: D  372 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7327 (mtm-85)
  outliers start: 46
  outliers final: 19
  residues processed: 157
  average time/residue: 1.3022
  time to fit residues: 222.7910
Evaluate side-chains
  149 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   69 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   91 MET
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue   69 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  305 LYS
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 154 optimal weight:    0.0060
   chunk 54 optimal weight:    0.4980
   chunk 34 optimal weight:    2.9990
   chunk 159 optimal weight:    1.9990
   chunk 145 optimal weight:    0.9980
   chunk 123 optimal weight:    9.9990
   chunk 118 optimal weight:    4.9990
   chunk 142 optimal weight:    0.3980
   chunk 110 optimal weight:    5.9990
   chunk 161 optimal weight:    3.9990
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
B 410 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.181830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.147121 restraints weight = 15621.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 1.77
r_work: 0.3641 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  13320  Z= 0.101
  Angle     :  0.441   6.891  17944  Z= 0.232
  Chirality :  0.039   0.136   1948
  Planarity :  0.003   0.035   2276
  Dihedral  :  5.305  57.894   1768
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.61 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.21), residues: 1576
  helix:  1.58 (0.18), residues: 868
  sheet:  1.49 (0.39), residues: 152
  loop : -0.61 (0.24), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 400 
 HIS   0.004   0.001   HIS D 224 
 PHE   0.015   0.001   PHE D 238 
 TYR   0.007   0.001   TYR B 162 
 ARG   0.002   0.000   ARG D 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03581 (  665)
  hydrogen bonds       : angle       3.90805 ( 1935)
  covalent geometry    : bond        0.00220 (13320)
  covalent geometry    : angle       0.44051 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 144
  time to evaluate  : 1.590 
Fit side-chains
REVERT: A  213 MET cc_start: 0.3286 (ttt) cc_final: 0.2349 (ptt)
REVERT: A  285 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5751 (mp0)
REVERT: A  336 THR cc_start: 0.7660 (m) cc_final: 0.7448 (t)
REVERT: A  358 THR cc_start: 0.7845 (m) cc_final: 0.7309 (t)
REVERT: B  285 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5756 (mp0)
REVERT: B  336 THR cc_start: 0.7564 (m) cc_final: 0.7342 (t)
REVERT: B  358 THR cc_start: 0.7833 (m) cc_final: 0.7374 (t)
REVERT: C  213 MET cc_start: 0.3194 (ttt) cc_final: 0.2308 (ptt)
REVERT: C  285 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5722 (mp0)
REVERT: C  336 THR cc_start: 0.7657 (m) cc_final: 0.7415 (t)
REVERT: C  358 THR cc_start: 0.7825 (m) cc_final: 0.7310 (t)
REVERT: D  213 MET cc_start: 0.3275 (ttt) cc_final: 0.2322 (ptt)
REVERT: D  285 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5520 (mp0)
REVERT: D  302 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4432 (tt0)
REVERT: D  336 THR cc_start: 0.7680 (m) cc_final: 0.7439 (t)
REVERT: D  358 THR cc_start: 0.7841 (m) cc_final: 0.7340 (t)
  outliers start: 46
  outliers final: 15
  residues processed: 165
  average time/residue: 1.1719
  time to fit residues: 212.9964
Evaluate side-chains
  142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 1.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   69 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 121 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 89 optimal weight:    7.9990
   chunk 138 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.178978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.143748 restraints weight = 15805.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.79
r_work: 0.3595 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  13320  Z= 0.183
  Angle     :  0.531   7.611  17944  Z= 0.279
  Chirality :  0.042   0.141   1948
  Planarity :  0.004   0.036   2276
  Dihedral  :  5.564  55.530   1768
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 14.31 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.21), residues: 1576
  helix:  1.33 (0.18), residues: 864
  sheet:  0.92 (0.38), residues: 164
  loop : -0.80 (0.24), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 400 
 HIS   0.004   0.001   HIS C 347 
 PHE   0.016   0.002   PHE C  80 
 TYR   0.011   0.002   TYR B 408 
 ARG   0.004   0.001   ARG D 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04496 (  665)
  hydrogen bonds       : angle       4.28717 ( 1935)
  covalent geometry    : bond        0.00418 (13320)
  covalent geometry    : angle       0.53075 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 129
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A  167 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7871 (mmm160)
REVERT: A  213 MET cc_start: 0.3273 (ttt) cc_final: 0.2315 (ptt)
REVERT: A  285 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.5853 (mp0)
REVERT: A  358 THR cc_start: 0.7891 (m) cc_final: 0.7358 (t)
REVERT: B  132 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7705 (tt0)
REVERT: B  285 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.5879 (mp0)
REVERT: B  358 THR cc_start: 0.7870 (m) cc_final: 0.7397 (t)
REVERT: C  167 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7898 (mmm160)
REVERT: C  213 MET cc_start: 0.3208 (ttt) cc_final: 0.2265 (ptt)
REVERT: C  285 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.5839 (mp0)
REVERT: C  334 LYS cc_start: 0.6552 (ptpp) cc_final: 0.6318 (ptpp)
REVERT: C  358 THR cc_start: 0.7884 (m) cc_final: 0.7368 (t)
REVERT: D  213 MET cc_start: 0.3333 (ttt) cc_final: 0.2352 (ptt)
REVERT: D  285 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5602 (mp0)
REVERT: D  302 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.4487 (tt0)
REVERT: D  358 THR cc_start: 0.7899 (m) cc_final: 0.7403 (t)
REVERT: D  410 GLN cc_start: 0.7440 (pt0) cc_final: 0.6970 (tt0)
  outliers start: 62
  outliers final: 24
  residues processed: 167
  average time/residue: 1.3495
  time to fit residues: 245.0423
Evaluate side-chains
  153 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   69 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   91 MET
Chi-restraints excluded: chain C residue  167 ARG
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue   69 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   91 MET
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  287 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 125 optimal weight:   10.0000
   chunk 132 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 122 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 123 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.179947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.145033 restraints weight = 15727.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 1.78
r_work: 0.3615 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3491 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13320  Z= 0.141
  Angle     :  0.492   7.366  17944  Z= 0.259
  Chirality :  0.041   0.139   1948
  Planarity :  0.004   0.038   2276
  Dihedral  :  5.471  54.891   1768
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.04 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.21), residues: 1576
  helix:  1.37 (0.18), residues: 864
  sheet:  1.19 (0.40), residues: 156
  loop : -0.70 (0.24), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 400 
 HIS   0.004   0.001   HIS A 224 
 PHE   0.017   0.002   PHE D  15 
 TYR   0.008   0.001   TYR B 162 
 ARG   0.003   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  665)
  hydrogen bonds       : angle       4.20360 ( 1935)
  covalent geometry    : bond        0.00319 (13320)
  covalent geometry    : angle       0.49153 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 127
  time to evaluate  : 2.104 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5784 (mp0)
REVERT: A  358 THR cc_start: 0.7868 (m) cc_final: 0.7338 (t)
REVERT: B  285 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5852 (mp0)
REVERT: B  358 THR cc_start: 0.7869 (m) cc_final: 0.7383 (t)
REVERT: B  410 GLN cc_start: 0.7264 (pt0) cc_final: 0.6677 (tt0)
REVERT: C  132 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7659 (tt0)
REVERT: C  213 MET cc_start: 0.3162 (ttt) cc_final: 0.2492 (ptp)
REVERT: C  285 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5790 (mp0)
REVERT: C  358 THR cc_start: 0.7856 (m) cc_final: 0.7338 (t)
REVERT: C  410 GLN cc_start: 0.7221 (pt0) cc_final: 0.6738 (tt0)
REVERT: D  213 MET cc_start: 0.3263 (ttt) cc_final: 0.2321 (ptt)
REVERT: D  285 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5610 (mp0)
REVERT: D  302 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.4417 (tt0)
REVERT: D  334 LYS cc_start: 0.6555 (ptpp) cc_final: 0.6340 (pttp)
REVERT: D  358 THR cc_start: 0.7885 (m) cc_final: 0.7393 (t)
REVERT: D  372 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7215 (mtm-85)
REVERT: D  410 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6926 (tt0)
  outliers start: 45
  outliers final: 25
  residues processed: 151
  average time/residue: 1.4134
  time to fit residues: 232.5885
Evaluate side-chains
  155 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   69 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   91 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue   69 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   91 MET
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  287 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  410 GLN
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 116 optimal weight:    0.9980
   chunk 114 optimal weight:    6.9990
   chunk 163 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 102 optimal weight:    0.4980
   chunk 90 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 41 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.6984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.179718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.144663 restraints weight = 15617.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 1.77
r_work: 0.3608 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13320  Z= 0.152
  Angle     :  0.502   7.514  17944  Z= 0.265
  Chirality :  0.041   0.139   1948
  Planarity :  0.004   0.038   2276
  Dihedral  :  5.487  52.942   1768
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.21 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.21), residues: 1576
  helix:  1.34 (0.18), residues: 864
  sheet:  0.75 (0.38), residues: 172
  loop : -0.77 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 400 
 HIS   0.004   0.001   HIS A 313 
 PHE   0.019   0.002   PHE C  15 
 TYR   0.009   0.001   TYR B 408 
 ARG   0.003   0.000   ARG D 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04207 (  665)
  hydrogen bonds       : angle       4.25952 ( 1935)
  covalent geometry    : bond        0.00346 (13320)
  covalent geometry    : angle       0.50217 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 124
  time to evaluate  : 2.033 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5739 (mp0)
REVERT: A  358 THR cc_start: 0.7899 (m) cc_final: 0.7391 (t)
REVERT: B  132 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7687 (tt0)
REVERT: B  285 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5777 (mp0)
REVERT: B  358 THR cc_start: 0.7878 (m) cc_final: 0.7399 (t)
REVERT: B  410 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6764 (tt0)
REVERT: C  132 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7660 (tt0)
REVERT: C  285 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5730 (mp0)
REVERT: C  358 THR cc_start: 0.7888 (m) cc_final: 0.7397 (t)
REVERT: C  410 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6791 (tt0)
REVERT: D  167 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7846 (mmp80)
REVERT: D  285 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5669 (mp0)
REVERT: D  302 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.4386 (tt0)
REVERT: D  334 LYS cc_start: 0.6496 (ptpp) cc_final: 0.6276 (pttp)
REVERT: D  358 THR cc_start: 0.7890 (m) cc_final: 0.7406 (t)
REVERT: D  372 ARG cc_start: 0.7681 (tpp80) cc_final: 0.7214 (mtm-85)
REVERT: D  410 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6951 (tt0)
  outliers start: 49
  outliers final: 28
  residues processed: 154
  average time/residue: 1.5693
  time to fit residues: 262.5977
Evaluate side-chains
  160 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   69 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   91 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue   69 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   91 MET
Chi-restraints excluded: chain D residue  167 ARG
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  287 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  410 GLN
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 132 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 105 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    1.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.179527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.144630 restraints weight = 15588.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 1.77
r_work: 0.3610 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13320  Z= 0.155
  Angle     :  0.506   7.607  17944  Z= 0.267
  Chirality :  0.041   0.138   1948
  Planarity :  0.004   0.038   2276
  Dihedral  :  5.484  51.393   1768
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 15.59 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.21), residues: 1576
  helix:  1.33 (0.18), residues: 864
  sheet:  0.76 (0.38), residues: 172
  loop : -0.78 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 400 
 HIS   0.004   0.001   HIS A 224 
 PHE   0.018   0.002   PHE A  15 
 TYR   0.008   0.001   TYR C 408 
 ARG   0.003   0.000   ARG D 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  665)
  hydrogen bonds       : angle       4.28392 ( 1935)
  covalent geometry    : bond        0.00353 (13320)
  covalent geometry    : angle       0.50642 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 118
  time to evaluate  : 1.534 
Fit side-chains
REVERT: A  285 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6107 (pp20)
REVERT: A  358 THR cc_start: 0.7879 (m) cc_final: 0.7374 (t)
REVERT: A  410 GLN cc_start: 0.7381 (pt0) cc_final: 0.6915 (tt0)
REVERT: B  285 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5968 (pp20)
REVERT: B  334 LYS cc_start: 0.6529 (ptpp) cc_final: 0.6316 (pttp)
REVERT: B  358 THR cc_start: 0.7889 (m) cc_final: 0.7403 (t)
REVERT: B  410 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6821 (tt0)
REVERT: C  132 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7647 (tt0)
REVERT: C  285 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6076 (pp20)
REVERT: C  358 THR cc_start: 0.7897 (m) cc_final: 0.7407 (t)
REVERT: C  410 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6762 (tt0)
REVERT: D  167 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7846 (mmp80)
REVERT: D  285 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5661 (mp0)
REVERT: D  302 GLU cc_start: 0.5416 (OUTLIER) cc_final: 0.4420 (tt0)
REVERT: D  358 THR cc_start: 0.7903 (m) cc_final: 0.7416 (t)
REVERT: D  372 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7214 (mtm-85)
REVERT: D  410 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7005 (tt0)
  outliers start: 45
  outliers final: 26
  residues processed: 143
  average time/residue: 1.4629
  time to fit residues: 227.7706
Evaluate side-chains
  149 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   69 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   91 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue   69 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   91 MET
Chi-restraints excluded: chain D residue  167 ARG
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  287 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  410 GLN
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 109 optimal weight:    4.9990
   chunk 151 optimal weight:   10.0000
   chunk 130 optimal weight:    0.0670
   chunk 17 optimal weight:    8.9990
   overall best weight:    1.9722

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.179213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.144151 restraints weight = 15596.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 1.78
r_work: 0.3603 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13320  Z= 0.168
  Angle     :  0.525   7.774  17944  Z= 0.277
  Chirality :  0.042   0.139   1948
  Planarity :  0.004   0.038   2276
  Dihedral  :  5.529  48.977   1768
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.96 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.21), residues: 1576
  helix:  1.27 (0.18), residues: 864
  sheet:  0.73 (0.37), residues: 172
  loop : -0.78 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 400 
 HIS   0.004   0.001   HIS A 224 
 PHE   0.022   0.002   PHE D  15 
 TYR   0.010   0.001   TYR D 408 
 ARG   0.003   0.001   ARG D 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04379 (  665)
  hydrogen bonds       : angle       4.37271 ( 1935)
  covalent geometry    : bond        0.00386 (13320)
  covalent geometry    : angle       0.52548 (17944)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 1.354 
Fit side-chains
REVERT: A  358 THR cc_start: 0.7888 (m) cc_final: 0.7387 (t)
REVERT: A  410 GLN cc_start: 0.7353 (pt0) cc_final: 0.6869 (tt0)
REVERT: B  132 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7679 (tt0)
REVERT: B  358 THR cc_start: 0.7917 (m) cc_final: 0.7710 (m)
REVERT: B  410 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6883 (tt0)
REVERT: C  132 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7657 (tt0)
REVERT: C  358 THR cc_start: 0.7925 (m) cc_final: 0.7455 (t)
REVERT: C  410 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6881 (tt0)
REVERT: D  167 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7854 (mmp80)
REVERT: D  285 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5693 (mp0)
REVERT: D  302 GLU cc_start: 0.5445 (OUTLIER) cc_final: 0.4450 (tt0)
REVERT: D  358 THR cc_start: 0.7938 (m) cc_final: 0.7466 (t)
REVERT: D  372 ARG cc_start: 0.7704 (tpp80) cc_final: 0.7233 (mtm-85)
REVERT: D  410 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6891 (tt0)
  outliers start: 41
  outliers final: 28
  residues processed: 134
  average time/residue: 1.4501
  time to fit residues: 210.9853
Evaluate side-chains
  143 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 107
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue   69 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   91 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  285 GLU
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  430 ASN
Chi-restraints excluded: chain D residue   69 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   91 MET
Chi-restraints excluded: chain D residue  167 ARG
Chi-restraints excluded: chain D residue  285 GLU
Chi-restraints excluded: chain D residue  287 GLU
Chi-restraints excluded: chain D residue  302 GLU
Chi-restraints excluded: chain D residue  402 GLU
Chi-restraints excluded: chain D residue  410 GLN
Chi-restraints excluded: chain D residue  430 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 110 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 127 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0020
   chunk 61 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9980
   overall best weight:    0.7388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.182053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.147095 restraints weight = 15684.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 1.81
r_work: 0.3643 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  13320  Z= 0.099
  Angle     :  0.448   7.337  17944  Z= 0.236
  Chirality :  0.039   0.139   1948
  Planarity :  0.003   0.038   2276
  Dihedral  :  5.224  50.286   1768
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.94 %
    Favored  : 80.80 %
  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:  1.15 (0.21), residues: 1576
  helix:  1.53 (0.18), residues: 868
  sheet:  1.55 (0.40), residues: 152
  loop : -0.66 (0.24), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 400 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.017   0.001   PHE B  15 
 TYR   0.004   0.001   TYR C 378 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  665)
  hydrogen bonds       : angle       4.07595 ( 1935)
  covalent geometry    : bond        0.00214 (13320)
  covalent geometry    : angle       0.44806 (17944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11294.75 seconds
wall clock time: 200 minutes 18.71 seconds (12018.71 seconds total)