Starting phenix.real_space_refine
on Thu Sep 18 10:09:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymt_39407/09_2025/8ymt_39407.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymt_39407/09_2025/8ymt_39407.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymt_39407/09_2025/8ymt_39407.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymt_39407/09_2025/8ymt_39407.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ymt_39407/09_2025/8ymt_39407.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymt_39407/09_2025/8ymt_39407.map"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.045
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: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5652      2.51       5
     N    1482      2.21       5
     O    1611      1.98       5
     H    7173      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15975
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 5325
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 17, 'TRANS': 344}
    Chain: "B"
      Number of atoms: 5325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 5325
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 17, 'TRANS': 344}
    Chain: "C"
      Number of atoms: 5325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 5325
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 17, 'TRANS': 344}
  Time building chain proxies: 3.42, per 1000 atoms: 0.21
  Number of scatterers: 15975
  At special positions: 0
  Unit cell: (100.44, 93.93, 121.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     O    1611      8.00
     N    1482      7.00
     C    5652      6.00
     H    7173      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 188 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 273 " - pdb=" SG  CYS A 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 106 " - pdb=" SG  CYS B 188 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 273 " - pdb=" SG  CYS B 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 282 " - pdb=" SG  CYS B 337 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 299 " - pdb=" SG  CYS B 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 106 " - pdb=" SG  CYS C 188 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 273 " - pdb=" SG  CYS C 341 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 282 " - pdb=" SG  CYS C 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 299 " - pdb=" SG  CYS C 311 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 452.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2088

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 13 sheets defined
      37.4% alpha, 27.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 83
      removed outlier: 3.702A  pdb=" N   ILE A  74 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   MET A  76 " --> pdb=" O   HIS A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 113
    Processing helix  chain 'A' and resid 115 through 122
    Processing helix  chain 'A' and resid 129 through 136
      removed outlier: 3.515A  pdb=" N   LEU A 133 " --> pdb=" O   PHE A 130 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE A 134 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 147
    Processing helix  chain 'A' and resid 240 through 245
    Processing helix  chain 'A' and resid 275 through 296
      removed outlier: 3.806A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 330
      removed outlier: 3.612A  pdb=" N   ASN A 330 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 335
      removed outlier: 4.162A  pdb=" N   GLU A 334 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 396
    Processing helix  chain 'A' and resid 401 through 413
    Processing helix  chain 'B' and resid 54 through 83
      removed outlier: 3.754A  pdb=" N   ILE B  74 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA B  75 " --> pdb=" O   ALA B  71 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   MET B  76 " --> pdb=" O   HIS B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 113
    Processing helix  chain 'B' and resid 115 through 122
    Processing helix  chain 'B' and resid 129 through 136
      removed outlier: 3.602A  pdb=" N   LEU B 133 " --> pdb=" O   PHE B 130 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE B 134 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 240 through 245
    Processing helix  chain 'B' and resid 275 through 293
    Processing helix  chain 'B' and resid 313 through 330
      removed outlier: 3.614A  pdb=" N   ASN B 330 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 396
    Processing helix  chain 'B' and resid 401 through 413
    Processing helix  chain 'C' and resid 54 through 83
      removed outlier: 3.781A  pdb=" N   ILE C  74 " --> pdb=" O   SER C  70 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA C  75 " --> pdb=" O   ALA C  71 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET C  76 " --> pdb=" O   HIS C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 113
    Processing helix  chain 'C' and resid 115 through 122
    Processing helix  chain 'C' and resid 129 through 136
      removed outlier: 3.639A  pdb=" N   LEU C 133 " --> pdb=" O   PHE C 130 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE C 134 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 147
    Processing helix  chain 'C' and resid 240 through 245
    Processing helix  chain 'C' and resid 275 through 293
    Processing helix  chain 'C' and resid 313 through 330
      removed outlier: 3.628A  pdb=" N   ASN C 330 " --> pdb=" O   ASP C 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 335
      removed outlier: 3.915A  pdb=" N   GLU C 334 " --> pdb=" O   ASN C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 396
    Processing helix  chain 'C' and resid 401 through 413
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94
      removed outlier: 8.183A  pdb=" N   TYR A 371 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   PHE A 260 " --> pdb=" O   TYR A 371 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   PHE A 254 " --> pdb=" O   SER A 364 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   TYR A 366 " --> pdb=" O   PHE A 254 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   PHE A 256 " --> pdb=" O   TYR A 366 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU A 161 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   TYR A 170 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94
      removed outlier: 8.183A  pdb=" N   TYR A 371 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   PHE A 260 " --> pdb=" O   TYR A 371 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 183
      removed outlier: 3.730A  pdb=" N   ILE A 103 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 94
      removed outlier: 14.696A  pdb=" N   TYR B 371 " --> pdb=" O   PHE B 256 " (cutoff:3.500A)
      removed outlier: 10.955A  pdb=" N   ILE B 258 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
      removed outlier: 9.734A  pdb=" N   GLN B 373 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   PHE B 260 " --> pdb=" O   GLN B 373 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ALA B 375 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLN B 262 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   GLU B 377 " --> pdb=" O   GLN B 262 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASN B 264 " --> pdb=" O   GLU B 377 " (cutoff:3.500A)
      removed outlier: 9.128A  pdb=" N   LEU B 379 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   PHE B 256 " --> pdb=" O   TYR B 366 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLU B 161 " --> pdb=" O   TYR B 170 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TYR B 170 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 94
      removed outlier: 14.696A  pdb=" N   TYR B 371 " --> pdb=" O   PHE B 256 " (cutoff:3.500A)
      removed outlier: 10.955A  pdb=" N   ILE B 258 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
      removed outlier: 9.734A  pdb=" N   GLN B 373 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   PHE B 260 " --> pdb=" O   GLN B 373 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ALA B 375 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLN B 262 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   GLU B 377 " --> pdb=" O   GLN B 262 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASN B 264 " --> pdb=" O   GLU B 377 " (cutoff:3.500A)
      removed outlier: 9.128A  pdb=" N   LEU B 379 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183
      removed outlier: 3.625A  pdb=" N   ILE B 103 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 94
      removed outlier: 14.605A  pdb=" N   TYR C 371 " --> pdb=" O   PHE C 256 " (cutoff:3.500A)
      removed outlier: 10.956A  pdb=" N   ILE C 258 " --> pdb=" O   TYR C 371 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   GLN C 373 " --> pdb=" O   ILE C 258 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   PHE C 260 " --> pdb=" O   GLN C 373 " (cutoff:3.500A)
      removed outlier: 8.407A  pdb=" N   ALA C 375 " --> pdb=" O   PHE C 260 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   GLN C 262 " --> pdb=" O   ALA C 375 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   GLU C 377 " --> pdb=" O   GLN C 262 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ASN C 264 " --> pdb=" O   GLU C 377 " (cutoff:3.500A)
      removed outlier: 9.107A  pdb=" N   LEU C 379 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   PHE C 256 " --> pdb=" O   TYR C 366 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 94
      removed outlier: 14.605A  pdb=" N   TYR C 371 " --> pdb=" O   PHE C 256 " (cutoff:3.500A)
      removed outlier: 10.956A  pdb=" N   ILE C 258 " --> pdb=" O   TYR C 371 " (cutoff:3.500A)
      removed outlier: 9.869A  pdb=" N   GLN C 373 " --> pdb=" O   ILE C 258 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   PHE C 260 " --> pdb=" O   GLN C 373 " (cutoff:3.500A)
      removed outlier: 8.407A  pdb=" N   ALA C 375 " --> pdb=" O   PHE C 260 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   GLN C 262 " --> pdb=" O   ALA C 375 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   GLU C 377 " --> pdb=" O   GLN C 262 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ASN C 264 " --> pdb=" O   GLU C 377 " (cutoff:3.500A)
      removed outlier: 9.107A  pdb=" N   LEU C 379 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98
    Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 183
      removed outlier: 3.679A  pdb=" N   ILE C 103 " --> pdb=" O   ILE C 191 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 223 through 226

    438 hydrogen bonds defined for protein.
    1215 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: 3.23

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 7170
        1.04 -     1.23: 241
        1.23 -     1.43: 3659
        1.43 -     1.63: 5040
        1.63 -     1.82: 81
  Bond restraints: 16191
  Sorted by residual:
  bond pdb=" CA  ILE C 347 "
       pdb=" CB  ILE C 347 "
    ideal  model  delta    sigma   weight residual
    1.540  1.526  0.014 1.36e-02 5.41e+03 1.06e+00
  bond pdb=" CG1 ILE A 258 "
       pdb=" CD1 ILE A 258 "
    ideal  model  delta    sigma   weight residual
    1.513  1.475  0.038 3.90e-02 6.57e+02 9.32e-01
  bond pdb=" CB  CYS B 188 "
       pdb=" SG  CYS B 188 "
    ideal  model  delta    sigma   weight residual
    1.808  1.777  0.031 3.30e-02 9.18e+02 8.56e-01
  bond pdb=" CA  GLU C  97 "
       pdb=" C   GLU C  97 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.010 1.08e-02 8.57e+03 8.41e-01
  bond pdb=" CG1 ILE B 166 "
       pdb=" CD1 ILE B 166 "
    ideal  model  delta    sigma   weight residual
    1.513  1.478  0.035 3.90e-02 6.57e+02 8.16e-01
  ... (remaining 16186 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.93: 28337
       10.93 -    21.86: 22
       21.86 -    32.79: 114
       32.79 -    43.72: 33
       43.72 -    54.65: 24
  Bond angle restraints: 28530
  Sorted by residual:
  angle pdb=" C   ASP C 316 "
        pdb=" N   ALA C 317 "
        pdb=" H   ALA C 317 "
      ideal   model   delta    sigma   weight residual
     125.01   70.36   54.65 3.00e+00 1.11e-01 3.32e+02
  angle pdb=" C   ASP A 316 "
        pdb=" N   ALA A 317 "
        pdb=" H   ALA A 317 "
      ideal   model   delta    sigma   weight residual
     125.01   70.41   54.60 3.00e+00 1.11e-01 3.31e+02
  angle pdb=" C   ASP B 316 "
        pdb=" N   ALA B 317 "
        pdb=" H   ALA B 317 "
      ideal   model   delta    sigma   weight residual
     125.01   70.42   54.59 3.00e+00 1.11e-01 3.31e+02
  angle pdb=" CA  ALA C 317 "
        pdb=" N   ALA C 317 "
        pdb=" H   ALA C 317 "
      ideal   model   delta    sigma   weight residual
     114.71   60.19   54.52 3.00e+00 1.11e-01 3.30e+02
  angle pdb=" CA  ALA B 317 "
        pdb=" N   ALA B 317 "
        pdb=" H   ALA B 317 "
      ideal   model   delta    sigma   weight residual
     114.71   60.34   54.37 3.00e+00 1.11e-01 3.28e+02
  ... (remaining 28525 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 7079
       17.29 -    34.57: 573
       34.57 -    51.86: 147
       51.86 -    69.15: 47
       69.15 -    86.43: 14
  Dihedral angle restraints: 7860
    sinusoidal: 4116
      harmonic: 3744
  Sorted by residual:
  dihedral pdb=" CB  CYS C 273 "
           pdb=" SG  CYS C 273 "
           pdb=" SG  CYS C 341 "
           pdb=" CB  CYS C 341 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.79   55.21     1      1.00e+01 1.00e-02 4.12e+01
  dihedral pdb=" CB  CYS B 299 "
           pdb=" SG  CYS B 299 "
           pdb=" SG  CYS B 311 "
           pdb=" CB  CYS B 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.74   51.26     1      1.00e+01 1.00e-02 3.59e+01
  dihedral pdb=" CA  CYS C 341 "
           pdb=" C   CYS C 341 "
           pdb=" N   GLU C 342 "
           pdb=" CA  GLU C 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.97   28.03     0      5.00e+00 4.00e-02 3.14e+01
  ... (remaining 7857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.346: 1350
       0.346 -    0.692: 12
       0.692 -    1.038: 0
       1.038 -    1.384: 0
       1.384 -    1.730: 3
  Chirality restraints: 1365
  Sorted by residual:
  chirality pdb=" CG  LEU B 394 "
            pdb=" CB  LEU B 394 "
            pdb=" CD1 LEU B 394 "
            pdb=" CD2 LEU B 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.86   -1.73 2.00e-01 2.50e+01 7.48e+01
  chirality pdb=" CG  LEU A 394 "
            pdb=" CB  LEU A 394 "
            pdb=" CD1 LEU A 394 "
            pdb=" CD2 LEU A 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.92   -1.67 2.00e-01 2.50e+01 6.98e+01
  chirality pdb=" CG  LEU C 394 "
            pdb=" CB  LEU C 394 "
            pdb=" CD1 LEU C 394 "
            pdb=" CD2 LEU C 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.92   -1.67 2.00e-01 2.50e+01 6.95e+01
  ... (remaining 1362 not shown)

  Planarity restraints: 2436
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 321 "    0.026 2.00e-02 2.50e+03   1.35e-02 5.50e+00
        pdb=" CG  PHE C 321 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 321 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 321 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 321 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 321 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 321 "    0.002 2.00e-02 2.50e+03
        pdb=" HD1 PHE C 321 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 PHE C 321 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE C 321 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 PHE C 321 "    0.005 2.00e-02 2.50e+03
        pdb=" HZ  PHE C 321 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 321 "    0.024 2.00e-02 2.50e+03   1.27e-02 4.86e+00
        pdb=" CG  PHE A 321 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 321 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 321 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 321 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 321 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 321 "    0.002 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 321 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 321 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 321 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 321 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 321 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 305 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO C 306 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C 306 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 306 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2433 not shown)

  Histogram of nonbonded interaction distances:
        1.41 -     2.05: 350
        2.05 -     2.69: 22910
        2.69 -     3.33: 44082
        3.33 -     3.96: 59271
        3.96 -     4.60: 90825
  Nonbonded interactions: 217438
  Sorted by model distance:
  nonbonded pdb=" H   HIS C 235 "
            pdb=" HA  HIS C 235 "
     model   vdw
     1.413 1.816
  nonbonded pdb=" H   HIS A 235 "
            pdb=" HA  HIS A 235 "
     model   vdw
     1.415 1.816
  nonbonded pdb=" H   HIS B 235 "
            pdb=" HA  HIS B 235 "
     model   vdw
     1.416 1.816
  nonbonded pdb=" H   ILE B 115 "
            pdb=" HA  ILE B 115 "
     model   vdw
     1.459 1.816
  nonbonded pdb=" H   ILE C 115 "
            pdb=" HA  ILE C 115 "
     model   vdw
     1.460 1.816
  ... (remaining 217433 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.100
  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:             0.100
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.280
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
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      :  0.004   0.038   9030  Z= 0.175
  Angle     :  0.935  18.865  12276  Z= 0.574
  Chirality :  0.099   1.730   1365
  Planarity :  0.005   0.050   1581
  Dihedral  : 13.437  86.431   3306
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 19.62
  Ramachandran Plot:
    Outliers :  1.20 %
    Allowed  :  6.39 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.25), residues: 1080
  helix:  0.38 (0.27), residues: 393
  sheet: -2.16 (0.30), residues: 267
  loop : -2.82 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 207 
 TYR   0.007   0.001   TYR B 279 
 PHE   0.038   0.002   PHE C 321 
 TRP   0.018   0.001   TRP A 145 
 HIS   0.005   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9018)
  covalent geometry    : angle       0.93495 (12252)
  SS BOND              : bond        0.00613 (   12)
  SS BOND              : angle       1.04924 (   24)
  hydrogen bonds       : bond        0.14395 (  409)
  hydrogen bonds       : angle       7.19762 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.6783 (mmt) cc_final: 0.6511 (mmt)
REVERT: A  128 MET cc_start: 0.7061 (mmm) cc_final: 0.6714 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 1.1276
  time to fit residues: 150.6793
Evaluate side-chains
  89 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   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  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.213253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.175474 restraints weight = 23289.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 1.75
r_work: 0.3839 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9030  Z= 0.171
  Angle     :  0.844  18.825  12276  Z= 0.460
  Chirality :  0.099   1.719   1365
  Planarity :  0.005   0.047   1581
  Dihedral  :  5.499  20.646   1206
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  7.22 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  7.24 %
    Favored  : 90.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.25), residues: 1080
  helix:  0.63 (0.27), residues: 402
  sheet: -2.04 (0.30), residues: 267
  loop : -2.75 (0.26), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 220 
 TYR   0.009   0.001   TYR C 246 
 PHE   0.013   0.002   PHE C 367 
 TRP   0.018   0.001   TRP A 145 
 HIS   0.006   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 9018)
  covalent geometry    : angle       0.84414 (12252)
  SS BOND              : bond        0.00461 (   12)
  SS BOND              : angle       1.00294 (   24)
  hydrogen bonds       : bond        0.03108 (  409)
  hydrogen bonds       : angle       5.26714 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.8083 (mmt) cc_final: 0.7810 (mmt)
REVERT: A  145 TRP cc_start: 0.7379 (m100) cc_final: 0.6352 (m-10)
REVERT: A  278 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7203 (mp0)
REVERT: B  119 MET cc_start: 0.8055 (mmt) cc_final: 0.7796 (mmt)
REVERT: B  129 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7855 (mtpp)
REVERT: B  220 ARG cc_start: 0.7662 (pmm150) cc_final: 0.7083 (mmt-90)
REVERT: C  278 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7267 (mp0)
  outliers start: 19
  outliers final: 6
  residues processed: 107
  average time/residue: 1.1783
  time to fit residues: 135.0998
Evaluate side-chains
  98 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  278 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 79 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 262 GLN
C 264 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.210868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.173647 restraints weight = 23252.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 1.73
r_work: 0.3799 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3659 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9030  Z= 0.174
  Angle     :  0.837  18.757  12276  Z= 0.456
  Chirality :  0.099   1.724   1365
  Planarity :  0.005   0.042   1581
  Dihedral  :  5.368  20.770   1206
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  7.22 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.60 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.25), residues: 1080
  helix:  0.81 (0.27), residues: 402
  sheet: -1.93 (0.31), residues: 264
  loop : -2.73 (0.26), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.008   0.001   TYR C 279 
 PHE   0.013   0.001   PHE A 367 
 TRP   0.013   0.001   TRP A 145 
 HIS   0.007   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9018)
  covalent geometry    : angle       0.83667 (12252)
  SS BOND              : bond        0.00664 (   12)
  SS BOND              : angle       0.97651 (   24)
  hydrogen bonds       : bond        0.02869 (  409)
  hydrogen bonds       : angle       4.88257 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.8059 (mmt) cc_final: 0.7826 (mmt)
REVERT: A  145 TRP cc_start: 0.7454 (m100) cc_final: 0.6380 (m-10)
REVERT: A  278 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7183 (mp0)
REVERT: A  319 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7671 (mttp)
REVERT: A  326 ASP cc_start: 0.8156 (t70) cc_final: 0.7604 (m-30)
REVERT: B   76 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.5981 (mpp)
REVERT: B  100 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7509 (pt)
REVERT: B  119 MET cc_start: 0.8050 (mmt) cc_final: 0.7769 (mmt)
REVERT: B  129 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7876 (mtpp)
REVERT: B  166 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6217 (pt)
REVERT: B  220 ARG cc_start: 0.7664 (pmm150) cc_final: 0.7128 (mmt-90)
  outliers start: 21
  outliers final: 6
  residues processed: 108
  average time/residue: 1.1049
  time to fit residues: 128.2871
Evaluate side-chains
  102 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  209 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   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  55 GLN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.211048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.172911 restraints weight = 23130.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 1.76
r_work: 0.3807 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3672 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9030  Z= 0.165
  Angle     :  0.828  19.069  12276  Z= 0.450
  Chirality :  0.098   1.720   1365
  Planarity :  0.004   0.038   1581
  Dihedral  :  5.378  34.371   1206
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  1.20 %
    Allowed  :  7.69 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 11.42 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.25), residues: 1080
  helix:  0.96 (0.27), residues: 402
  sheet: -1.90 (0.31), residues: 264
  loop : -2.70 (0.26), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 108 
 TYR   0.006   0.001   TYR C 246 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.011   0.001   TRP A 145 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9018)
  covalent geometry    : angle       0.82681 (12252)
  SS BOND              : bond        0.00499 (   12)
  SS BOND              : angle       1.37631 (   24)
  hydrogen bonds       : bond        0.02692 (  409)
  hydrogen bonds       : angle       4.71931 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 MET cc_start: 0.7981 (mmt) cc_final: 0.7747 (mmt)
REVERT: A  145 TRP cc_start: 0.7562 (m100) cc_final: 0.6391 (m-10)
REVERT: A  278 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.5837 (mp0)
REVERT: A  319 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7615 (mttp)
REVERT: A  326 ASP cc_start: 0.8122 (t70) cc_final: 0.7580 (m-30)
REVERT: A  349 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7647 (mm-30)
REVERT: B   76 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.5941 (mpp)
REVERT: B  100 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7561 (pt)
REVERT: B  119 MET cc_start: 0.8039 (mmt) cc_final: 0.7771 (mmt)
REVERT: B  129 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7873 (mtpp)
REVERT: B  166 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6433 (pt)
REVERT: B  220 ARG cc_start: 0.7678 (pmm150) cc_final: 0.7185 (mmt-90)
REVERT: B  349 GLU cc_start: 0.8574 (pm20) cc_final: 0.8292 (mm-30)
REVERT: C  100 ILE cc_start: 0.8054 (mm) cc_final: 0.7573 (pt)
REVERT: C  340 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7232 (mtpt)
  outliers start: 24
  outliers final: 6
  residues processed: 111
  average time/residue: 1.0958
  time to fit residues: 130.8447
Evaluate side-chains
  105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  341 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 105 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.208072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.169404 restraints weight = 23068.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.76
r_work: 0.3772 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3636 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9030  Z= 0.206
  Angle     :  0.852  18.647  12276  Z= 0.463
  Chirality :  0.099   1.729   1365
  Planarity :  0.005   0.046   1581
  Dihedral  :  5.473  28.048   1206
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  1.20 %
    Allowed  :  7.69 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 12.03 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.25), residues: 1080
  helix:  0.90 (0.27), residues: 402
  sheet: -1.93 (0.32), residues: 264
  loop : -2.71 (0.26), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.006   0.001   TYR B 292 
 PHE   0.016   0.002   PHE A 367 
 TRP   0.012   0.001   TRP A 145 
 HIS   0.008   0.002   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 9018)
  covalent geometry    : angle       0.84953 (12252)
  SS BOND              : bond        0.00559 (   12)
  SS BOND              : angle       1.63673 (   24)
  hydrogen bonds       : bond        0.02817 (  409)
  hydrogen bonds       : angle       4.73941 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8275 (m)
REVERT: A  278 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7154 (mp0)
REVERT: A  319 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7618 (mttp)
REVERT: A  398 LEU cc_start: 0.4369 (OUTLIER) cc_final: 0.3881 (tp)
REVERT: B  100 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7709 (pt)
REVERT: B  119 MET cc_start: 0.8185 (mmt) cc_final: 0.7887 (mmt)
REVERT: B  129 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8006 (mtpp)
REVERT: B  166 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6685 (pt)
REVERT: B  220 ARG cc_start: 0.7699 (pmm150) cc_final: 0.7196 (mmt-90)
REVERT: C  108 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7806 (mtp180)
REVERT: C  340 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7313 (mtpt)
  outliers start: 30
  outliers final: 9
  residues processed: 111
  average time/residue: 1.0958
  time to fit residues: 130.8474
Evaluate side-chains
  106 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  233 HIS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  341 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 106 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0980
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 GLN
C 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.207886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.169680 restraints weight = 23052.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 1.75
r_work: 0.3779 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9030  Z= 0.189
  Angle     :  0.838  18.986  12276  Z= 0.455
  Chirality :  0.098   1.727   1365
  Planarity :  0.004   0.040   1581
  Dihedral  :  5.409  27.792   1206
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  1.20 %
    Allowed  :  7.41 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 12.64 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.26), residues: 1080
  helix:  1.10 (0.27), residues: 396
  sheet: -1.90 (0.32), residues: 264
  loop : -2.68 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 339 
 TYR   0.006   0.001   TYR A 279 
 PHE   0.014   0.002   PHE A 205 
 TRP   0.011   0.001   TRP A 145 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 9018)
  covalent geometry    : angle       0.83645 (12252)
  SS BOND              : bond        0.00552 (   12)
  SS BOND              : angle       1.34852 (   24)
  hydrogen bonds       : bond        0.02691 (  409)
  hydrogen bonds       : angle       4.63471 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLN cc_start: 0.5131 (OUTLIER) cc_final: 0.4208 (mp10)
REVERT: A  274 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8141 (m)
REVERT: A  278 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7104 (mp0)
REVERT: A  319 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7607 (mttp)
REVERT: B  100 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7716 (pt)
REVERT: B  119 MET cc_start: 0.8231 (mmt) cc_final: 0.7934 (mmt)
REVERT: B  128 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6692 (mpm)
REVERT: B  129 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8006 (mtpp)
REVERT: B  166 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6951 (pt)
REVERT: B  349 GLU cc_start: 0.8591 (pm20) cc_final: 0.8315 (mm-30)
REVERT: C  108 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7837 (mtp180)
REVERT: C  340 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7364 (mtpt)
  outliers start: 28
  outliers final: 9
  residues processed: 106
  average time/residue: 1.0734
  time to fit residues: 121.8893
Evaluate side-chains
  104 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  128 MET
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  233 HIS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  341 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.208960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.170968 restraints weight = 23011.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 1.75
r_work: 0.3747 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3603 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9030  Z= 0.159
  Angle     :  0.824  19.197  12276  Z= 0.447
  Chirality :  0.098   1.723   1365
  Planarity :  0.004   0.037   1581
  Dihedral  :  5.361  26.869   1206
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  7.31 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.56 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.26), residues: 1080
  helix:  1.29 (0.27), residues: 393
  sheet: -1.67 (0.33), residues: 252
  loop : -2.74 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.005   0.001   TYR A 279 
 PHE   0.013   0.001   PHE A 367 
 TRP   0.010   0.001   TRP A 145 
 HIS   0.005   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 9018)
  covalent geometry    : angle       0.82232 (12252)
  SS BOND              : bond        0.00536 (   12)
  SS BOND              : angle       1.43268 (   24)
  hydrogen bonds       : bond        0.02592 (  409)
  hydrogen bonds       : angle       4.52380 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLN cc_start: 0.4930 (OUTLIER) cc_final: 0.4167 (mp10)
REVERT: A  220 ARG cc_start: 0.5887 (mmt-90) cc_final: 0.5439 (pmm150)
REVERT: A  274 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8053 (m)
REVERT: A  278 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7054 (mp0)
REVERT: A  319 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7603 (mttp)
REVERT: B   73 GLN cc_start: 0.4661 (OUTLIER) cc_final: 0.3256 (mp10)
REVERT: B  100 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7679 (pt)
REVERT: B  119 MET cc_start: 0.8261 (mmt) cc_final: 0.7971 (mmt)
REVERT: B  128 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6694 (mpm)
REVERT: B  129 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7987 (mtpp)
REVERT: B  349 GLU cc_start: 0.8575 (pm20) cc_final: 0.8283 (mm-30)
REVERT: C  108 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7822 (mtp180)
REVERT: C  236 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6756 (mt)
REVERT: C  340 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7401 (mtpt)
  outliers start: 29
  outliers final: 11
  residues processed: 106
  average time/residue: 0.9833
  time to fit residues: 112.4494
Evaluate side-chains
  108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  128 MET
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  233 HIS
Chi-restraints excluded: chain C residue  108 ARG
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  233 HIS
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  278 GLU
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  341 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0870
   chunk 26 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 36 optimal weight:   20.0000
   chunk 43 optimal weight:    0.0670
   chunk 79 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
A 262 GLN
A 264 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 154 ASN
B 262 GLN
B 264 ASN
** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.211354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.173673 restraints weight = 23101.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 1.75
r_work: 0.3785 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9030  Z= 0.117
  Angle     :  0.814  19.711  12276  Z= 0.440
  Chirality :  0.098   1.720   1365
  Planarity :  0.004   0.037   1581
  Dihedral  :  5.247  34.985   1206
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  6.85 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.17 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.26), residues: 1080
  helix:  1.29 (0.28), residues: 402
  sheet: -1.69 (0.33), residues: 252
  loop : -2.68 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 318 
 TYR   0.006   0.001   TYR C 246 
 PHE   0.013   0.001   PHE A 367 
 TRP   0.009   0.001   TRP A 145 
 HIS   0.003   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9018)
  covalent geometry    : angle       0.81276 (12252)
  SS BOND              : bond        0.00484 (   12)
  SS BOND              : angle       1.27973 (   24)
  hydrogen bonds       : bond        0.02393 (  409)
  hydrogen bonds       : angle       4.35361 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLN cc_start: 0.4924 (OUTLIER) cc_final: 0.4176 (mp10)
REVERT: A  220 ARG cc_start: 0.5912 (mmt-90) cc_final: 0.5580 (pmm150)
REVERT: A  278 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.5901 (mp0)
REVERT: B   73 GLN cc_start: 0.4628 (OUTLIER) cc_final: 0.3270 (mp10)
REVERT: B  100 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7607 (pt)
REVERT: B  113 ASN cc_start: 0.8629 (t0) cc_final: 0.8411 (t0)
REVERT: B  119 MET cc_start: 0.8211 (mmt) cc_final: 0.7935 (mmt)
REVERT: B  129 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7959 (mtpp)
REVERT: B  349 GLU cc_start: 0.8533 (pm20) cc_final: 0.8256 (mm-30)
REVERT: C   73 GLN cc_start: 0.4573 (OUTLIER) cc_final: 0.3193 (mp10)
REVERT: C  236 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6669 (mt)
REVERT: C  340 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7544 (mtpt)
  outliers start: 26
  outliers final: 13
  residues processed: 111
  average time/residue: 1.1084
  time to fit residues: 131.8579
Evaluate side-chains
  107 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  128 MET
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  233 HIS
Chi-restraints excluded: chain B residue  341 CYS
Chi-restraints excluded: chain C residue   73 GLN
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  233 HIS
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  278 GLU
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  341 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   chunk 36 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 74 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 106 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
A 262 GLN
A 264 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 ASN
** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.211385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.173982 restraints weight = 22866.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 1.73
r_work: 0.3824 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9030  Z= 0.128
  Angle     :  0.808  19.568  12276  Z= 0.437
  Chirality :  0.098   1.719   1365
  Planarity :  0.004   0.037   1581
  Dihedral  :  5.112  28.635   1206
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  7.50 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.68 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.26), residues: 1080
  helix:  1.37 (0.28), residues: 399
  sheet: -1.82 (0.32), residues: 258
  loop : -2.56 (0.27), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 339 
 TYR   0.007   0.001   TYR B 265 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.009   0.001   TRP A 145 
 HIS   0.004   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9018)
  covalent geometry    : angle       0.80608 (12252)
  SS BOND              : bond        0.00461 (   12)
  SS BOND              : angle       1.50710 (   24)
  hydrogen bonds       : bond        0.02353 (  409)
  hydrogen bonds       : angle       4.29489 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLN cc_start: 0.4977 (OUTLIER) cc_final: 0.4289 (mp10)
REVERT: A  220 ARG cc_start: 0.5953 (mmt-90) cc_final: 0.5645 (pmm150)
REVERT: A  278 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.5945 (mp0)
REVERT: B   73 GLN cc_start: 0.4708 (OUTLIER) cc_final: 0.3334 (mp10)
REVERT: B  100 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7596 (pt)
REVERT: B  129 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7890 (mtpp)
REVERT: C   73 GLN cc_start: 0.4598 (OUTLIER) cc_final: 0.3227 (mp10)
REVERT: C  135 ASP cc_start: 0.7962 (t0) cc_final: 0.7482 (t0)
REVERT: C  236 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6610 (mt)
REVERT: C  340 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7539 (mtpt)
  outliers start: 23
  outliers final: 10
  residues processed: 103
  average time/residue: 1.0745
  time to fit residues: 118.9708
Evaluate side-chains
  103 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  233 HIS
Chi-restraints excluded: chain B residue  341 CYS
Chi-restraints excluded: chain C residue   73 GLN
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  233 HIS
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  341 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 98 optimal weight:    0.2980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 ASN
** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.211391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.173562 restraints weight = 22908.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 1.76
r_work: 0.3789 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3659 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9030  Z= 0.131
  Angle     :  0.810  19.597  12276  Z= 0.438
  Chirality :  0.098   1.719   1365
  Planarity :  0.004   0.037   1581
  Dihedral  :  5.065  27.245   1206
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  7.22 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.98 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.26), residues: 1080
  helix:  1.36 (0.27), residues: 402
  sheet: -1.84 (0.32), residues: 258
  loop : -2.56 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 214 
 TYR   0.006   0.001   TYR C 246 
 PHE   0.012   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 145 
 HIS   0.004   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9018)
  covalent geometry    : angle       0.80882 (12252)
  SS BOND              : bond        0.00466 (   12)
  SS BOND              : angle       1.33457 (   24)
  hydrogen bonds       : bond        0.02332 (  409)
  hydrogen bonds       : angle       4.26929 ( 1215)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLN cc_start: 0.4975 (OUTLIER) cc_final: 0.4286 (mp10)
REVERT: A  278 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.5921 (mp0)
REVERT: B   73 GLN cc_start: 0.4683 (OUTLIER) cc_final: 0.3352 (mp10)
REVERT: B  100 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7569 (pt)
REVERT: B  119 MET cc_start: 0.8320 (mmt) cc_final: 0.8114 (mmt)
REVERT: B  129 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7906 (mtpp)
REVERT: C  135 ASP cc_start: 0.8001 (t0) cc_final: 0.7529 (t0)
REVERT: C  236 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6596 (mt)
REVERT: C  340 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7534 (mtpt)
  outliers start: 23
  outliers final: 11
  residues processed: 99
  average time/residue: 1.0093
  time to fit residues: 107.6010
Evaluate side-chains
  101 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  233 HIS
Chi-restraints excluded: chain B residue  341 CYS
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  233 HIS
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  341 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:   20.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 ASN
** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.211328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.173516 restraints weight = 23108.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 1.77
r_work: 0.3790 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9030  Z= 0.128
  Angle     :  0.804  19.636  12276  Z= 0.435
  Chirality :  0.097   1.718   1365
  Planarity :  0.004   0.036   1581
  Dihedral  :  5.034  26.086   1206
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.50 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.39 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.26), residues: 1080
  helix:  1.46 (0.27), residues: 399
  sheet: -1.82 (0.32), residues: 258
  loop : -2.51 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 214 
 TYR   0.006   0.001   TYR C 246 
 PHE   0.017   0.001   PHE A 367 
 TRP   0.009   0.001   TRP A 145 
 HIS   0.004   0.001   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9018)
  covalent geometry    : angle       0.80272 (12252)
  SS BOND              : bond        0.00458 (   12)
  SS BOND              : angle       1.30078 (   24)
  hydrogen bonds       : bond        0.02315 (  409)
  hydrogen bonds       : angle       4.23982 ( 1215)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5564.90 seconds
wall clock time: 95 minutes 1.16 seconds (5701.16 seconds total)