Starting phenix.real_space_refine
on Thu Sep 18 00:22:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v1y_31630/09_2025/7v1y_31630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v1y_31630/09_2025/7v1y_31630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v1y_31630/09_2025/7v1y_31630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v1y_31630/09_2025/7v1y_31630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v1y_31630/09_2025/7v1y_31630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v1y_31630/09_2025/7v1y_31630.cif"
  }
  resolution = 2.82
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    8032      2.51       5
     N    2104      2.21       5
     O    2324      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 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: 12524
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3113
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 3113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3113
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 3113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3113
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 3113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3113
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 18
          Unusual residues: {'B3S': 1}
          Classifications: {'peptide': 2, 'undetermined': 1}
          Link IDs: {'TRANS': 2}
    Chain: "F"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 18
          Unusual residues: {'B3S': 1}
          Classifications: {'peptide': 2, 'undetermined': 1}
          Link IDs: {'TRANS': 2}
    Chain: "G"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 18
          Unusual residues: {'B3S': 1}
          Classifications: {'peptide': 2, 'undetermined': 1}
          Link IDs: {'TRANS': 2}
    Chain: "H"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 18
          Unusual residues: {'B3S': 1}
          Classifications: {'peptide': 2, 'undetermined': 1}
          Link IDs: {'TRANS': 2}
  Time building chain proxies: 3.03, per 1000 atoms: 0.24
  Number of scatterers: 12524
  At special positions: 0
  Unit cell: (117.284, 80.7, 153.868, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    2324      8.00
     N    2104      7.00
     C    8032      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 548.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  B3S E   3 "
        pdb=" CB  B3S F   3 "
        pdb=" CB  B3S G   3 "
        pdb=" CB  B3S H   3 "
  Number of C-beta restraints generated:  2936

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 12 sheets defined
      40.8% alpha, 12.7% 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 104 through 123
    Processing helix  chain 'A' and resid 165 through 180
      removed outlier: 3.627A  pdb=" N   LEU A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 192
    Processing helix  chain 'A' and resid 209 through 215
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 290 through 294
      removed outlier: 3.716A  pdb=" N   LEU A 294 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 305
    Processing helix  chain 'A' and resid 306 through 308
      No H-bonds generated for 'chain 'A' and resid 306 through 308'
    Processing helix  chain 'A' and resid 325 through 340
      removed outlier: 3.631A  pdb=" N   GLY A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 354
    Processing helix  chain 'A' and resid 394 through 399
      removed outlier: 3.609A  pdb=" N   GLY A 398 " --> pdb=" O   LYS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 424
      removed outlier: 3.675A  pdb=" N   LEU A 407 " --> pdb=" O   THR A 403 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   GLY A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   LEU A 422 " --> pdb=" O   TYR A 418 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE A 423 " --> pdb=" O   GLN A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 444
    Processing helix  chain 'A' and resid 504 through 511
    Processing helix  chain 'A' and resid 530 through 545
    Processing helix  chain 'C' and resid 104 through 123
    Processing helix  chain 'C' and resid 165 through 180
      removed outlier: 3.627A  pdb=" N   LEU C 169 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 192
    Processing helix  chain 'C' and resid 209 through 215
    Processing helix  chain 'C' and resid 226 through 235
    Processing helix  chain 'C' and resid 290 through 294
      removed outlier: 3.717A  pdb=" N   LEU C 294 " --> pdb=" O   GLU C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 305
    Processing helix  chain 'C' and resid 306 through 308
      No H-bonds generated for 'chain 'C' and resid 306 through 308'
    Processing helix  chain 'C' and resid 325 through 340
      removed outlier: 3.631A  pdb=" N   GLY C 340 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 342 through 354
    Processing helix  chain 'C' and resid 394 through 399
    Processing helix  chain 'C' and resid 403 through 424
      removed outlier: 3.674A  pdb=" N   LEU C 407 " --> pdb=" O   THR C 403 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   GLY C 421 " --> pdb=" O   GLY C 417 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   LEU C 422 " --> pdb=" O   TYR C 418 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE C 423 " --> pdb=" O   GLN C 419 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 436 through 444
    Processing helix  chain 'C' and resid 504 through 511
    Processing helix  chain 'C' and resid 530 through 545
    Processing helix  chain 'B' and resid 104 through 123
    Processing helix  chain 'B' and resid 165 through 180
      removed outlier: 3.626A  pdb=" N   LEU B 169 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 192
    Processing helix  chain 'B' and resid 209 through 215
    Processing helix  chain 'B' and resid 226 through 235
    Processing helix  chain 'B' and resid 290 through 294
      removed outlier: 3.717A  pdb=" N   LEU B 294 " --> pdb=" O   GLU B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 305
    Processing helix  chain 'B' and resid 306 through 308
      No H-bonds generated for 'chain 'B' and resid 306 through 308'
    Processing helix  chain 'B' and resid 325 through 340
      removed outlier: 3.632A  pdb=" N   GLY B 340 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 354
    Processing helix  chain 'B' and resid 394 through 399
    Processing helix  chain 'B' and resid 403 through 424
      removed outlier: 3.676A  pdb=" N   LEU B 407 " --> pdb=" O   THR B 403 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   GLY B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   LEU B 422 " --> pdb=" O   TYR B 418 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE B 423 " --> pdb=" O   GLN B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 444
    Processing helix  chain 'B' and resid 504 through 511
    Processing helix  chain 'B' and resid 530 through 545
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'D' and resid 165 through 180
      removed outlier: 3.627A  pdb=" N   LEU D 169 " --> pdb=" O   ILE D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 192
    Processing helix  chain 'D' and resid 209 through 215
    Processing helix  chain 'D' and resid 226 through 235
    Processing helix  chain 'D' and resid 290 through 294
      removed outlier: 3.717A  pdb=" N   LEU D 294 " --> pdb=" O   GLU D 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 300 through 305
    Processing helix  chain 'D' and resid 306 through 308
      No H-bonds generated for 'chain 'D' and resid 306 through 308'
    Processing helix  chain 'D' and resid 325 through 340
      removed outlier: 3.631A  pdb=" N   GLY D 340 " --> pdb=" O   GLU D 336 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 342 through 354
    Processing helix  chain 'D' and resid 394 through 399
    Processing helix  chain 'D' and resid 403 through 424
      removed outlier: 3.675A  pdb=" N   LEU D 407 " --> pdb=" O   THR D 403 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   GLY D 421 " --> pdb=" O   GLY D 417 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   LEU D 422 " --> pdb=" O   TYR D 418 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE D 423 " --> pdb=" O   GLN D 419 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 436 through 444
    Processing helix  chain 'D' and resid 504 through 511
    Processing helix  chain 'D' and resid 530 through 545
    Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153
      removed outlier: 5.211A  pdb=" N   GLU A 137 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL A 133 " --> pdb=" O   GLU A 137 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 361
    Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 377
    Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153
      removed outlier: 5.212A  pdb=" N   GLU C 137 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL C 133 " --> pdb=" O   GLU C 137 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 360 through 361
    Processing sheet with id=AA6, first strand: chain 'C' and resid 375 through 377
    Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153
      removed outlier: 5.211A  pdb=" N   GLU B 137 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL B 133 " --> pdb=" O   GLU B 137 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 160 through 161
    Processing sheet with id=AA9, first strand: chain 'B' and resid 375 through 377
    Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153
      removed outlier: 5.212A  pdb=" N   GLU D 137 " --> pdb=" O   VAL D 133 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL D 133 " --> pdb=" O   GLU D 137 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 360 through 361
    Processing sheet with id=AB3, first strand: chain 'D' and resid 375 through 377

    553 hydrogen bonds defined for protein.
    1548 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: 2.00

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2064
        1.31 -     1.43: 3305
        1.43 -     1.56: 7315
        1.56 -     1.68: 4
        1.68 -     1.81: 108
  Bond restraints: 12796
  Sorted by residual:
  bond pdb=" C   ALA G   2 "
       pdb=" N   B3S G   3 "
    ideal  model  delta    sigma   weight residual
    1.329  1.450 -0.121 1.40e-02 5.10e+03 7.48e+01
  bond pdb=" C   ALA H   2 "
       pdb=" N   B3S H   3 "
    ideal  model  delta    sigma   weight residual
    1.329  1.450 -0.121 1.40e-02 5.10e+03 7.48e+01
  bond pdb=" C   ALA E   2 "
       pdb=" N   B3S E   3 "
    ideal  model  delta    sigma   weight residual
    1.329  1.450 -0.121 1.40e-02 5.10e+03 7.43e+01
  bond pdb=" C   ALA F   2 "
       pdb=" N   B3S F   3 "
    ideal  model  delta    sigma   weight residual
    1.329  1.449 -0.120 1.40e-02 5.10e+03 7.37e+01
  bond pdb=" C   ALA H   1 "
       pdb=" N   ALA H   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.448 -0.119 1.40e-02 5.10e+03 7.24e+01
  ... (remaining 12791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 16696
        1.81 -     3.63: 476
        3.63 -     5.44: 56
        5.44 -     7.25: 43
        7.25 -     9.06: 25
  Bond angle restraints: 17296
  Sorted by residual:
  angle pdb=" N   ILE D 165 "
        pdb=" CA  ILE D 165 "
        pdb=" C   ILE D 165 "
      ideal   model   delta    sigma   weight residual
     113.00  104.01    8.99 1.30e+00 5.92e-01 4.78e+01
  angle pdb=" N   ILE C 165 "
        pdb=" CA  ILE C 165 "
        pdb=" C   ILE C 165 "
      ideal   model   delta    sigma   weight residual
     113.00  104.04    8.96 1.30e+00 5.92e-01 4.75e+01
  angle pdb=" N   ILE A 165 "
        pdb=" CA  ILE A 165 "
        pdb=" C   ILE A 165 "
      ideal   model   delta    sigma   weight residual
     113.00  104.05    8.95 1.30e+00 5.92e-01 4.74e+01
  angle pdb=" N   ILE B 165 "
        pdb=" CA  ILE B 165 "
        pdb=" C   ILE B 165 "
      ideal   model   delta    sigma   weight residual
     113.00  104.07    8.93 1.30e+00 5.92e-01 4.72e+01
  angle pdb=" N   ILE D 162 "
        pdb=" CA  ILE D 162 "
        pdb=" C   ILE D 162 "
      ideal   model   delta    sigma   weight residual
     109.30  101.32    7.98 1.25e+00 6.40e-01 4.07e+01
  ... (remaining 17291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.55: 6805
       15.55 -    31.10: 681
       31.10 -    46.66: 152
       46.66 -    62.21: 22
       62.21 -    77.76: 12
  Dihedral angle restraints: 7672
    sinusoidal: 3080
      harmonic: 4592
  Sorted by residual:
  dihedral pdb=" CA  ALA G   2 "
           pdb=" C   ALA G   2 "
           pdb=" N   B3S G   3 "
           pdb=" CA  B3S G   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.43   42.57     0      5.00e+00 4.00e-02 7.25e+01
  dihedral pdb=" CA  ALA F   2 "
           pdb=" C   ALA F   2 "
           pdb=" N   B3S F   3 "
           pdb=" CA  B3S F   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.44   42.56     0      5.00e+00 4.00e-02 7.25e+01
  dihedral pdb=" CA  ALA H   2 "
           pdb=" C   ALA H   2 "
           pdb=" N   B3S H   3 "
           pdb=" CA  B3S H   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.44   42.56     0      5.00e+00 4.00e-02 7.24e+01
  ... (remaining 7669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 1692
       0.100 -    0.200: 169
       0.200 -    0.301: 34
       0.301 -    0.401: 0
       0.401 -    0.501: 5
  Chirality restraints: 1900
  Sorted by residual:
  chirality pdb=" CA  ALA F   2 "
            pdb=" N   ALA F   2 "
            pdb=" C   ALA F   2 "
            pdb=" CB  ALA F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.98    0.50 2.00e-01 2.50e+01 6.27e+00
  chirality pdb=" CA  ALA G   2 "
            pdb=" N   ALA G   2 "
            pdb=" C   ALA G   2 "
            pdb=" CB  ALA G   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.99    0.50 2.00e-01 2.50e+01 6.25e+00
  chirality pdb=" CA  ALA E   2 "
            pdb=" N   ALA E   2 "
            pdb=" C   ALA E   2 "
            pdb=" CB  ALA E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.99    0.50 2.00e-01 2.50e+01 6.22e+00
  ... (remaining 1897 not shown)

  Planarity restraints: 2200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 108 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.38e+00
        pdb=" C   ILE D 108 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ILE D 108 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLU D 109 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 108 "    0.008 2.00e-02 2.50e+03   1.52e-02 2.32e+00
        pdb=" C   ILE A 108 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ILE A 108 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLU A 109 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 108 "   -0.008 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" C   ILE C 108 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ILE C 108 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLU C 109 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2197 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2684
        2.78 -     3.31: 10867
        3.31 -     3.84: 19963
        3.84 -     4.37: 24569
        4.37 -     4.90: 42092
  Nonbonded interactions: 100175
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 358 "
            pdb=" OD2 ASP B 406 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR A 358 "
            pdb=" OD2 ASP A 406 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR C 358 "
            pdb=" OD2 ASP C 406 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR D 358 "
            pdb=" OD2 ASP D 406 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   VAL C 447 "
            pdb=" OG1 THR C 450 "
     model   vdw
     2.263 3.040
  ... (remaining 100170 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.250
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
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      :  0.006   0.167  12800  Z= 0.368
  Angle     :  0.783   9.065  17296  Z= 0.498
  Chirality :  0.065   0.501   1900
  Planarity :  0.003   0.033   2200
  Dihedral  : 13.037  77.760   4736
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.75 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.54 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 (0.21), residues: 1560
  helix:  2.59 (0.22), residues: 544
  sheet:  1.18 (0.50), residues: 116
  loop : -0.03 (0.20), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 221 
 TYR   0.012   0.001   TYR C 328 
 PHE   0.009   0.001   PHE B 298 
 TRP   0.008   0.001   TRP C 454 
 HIS   0.002   0.001   HIS B 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (12796)
  covalent geometry    : angle       0.78288 (17296)
  hydrogen bonds       : bond        0.18743 (  553)
  hydrogen bonds       : angle       6.13328 ( 1548)
  Misc. bond           : bond        0.03077 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 222
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.7459 (tp30) cc_final: 0.7232 (tp30)
REVERT: A  440 MET cc_start: 0.8819 (mmm) cc_final: 0.8502 (mmm)
REVERT: C  355 ASP cc_start: 0.7517 (t0) cc_final: 0.7238 (t0)
REVERT: C  525 MET cc_start: 0.8836 (tpt) cc_final: 0.8416 (tpp)
REVERT: B  227 ILE cc_start: 0.8332 (mt) cc_final: 0.8011 (tt)
REVERT: D  471 GLN cc_start: 0.8201 (tt0) cc_final: 0.7982 (tt0)
REVERT: D  477 ARG cc_start: 0.7666 (ttt90) cc_final: 0.6039 (mpp-170)
  outliers start: 2
  outliers final: 0
  residues processed: 224
  average time/residue: 0.8493
  time to fit residues: 202.0966
Evaluate side-chains
  121 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
C 289 GLN
C 479 GLN
B 289 GLN
D 289 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.093491 restraints weight = 15485.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.73
r_work: 0.2858 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12800  Z= 0.155
  Angle     :  0.579   7.783  17296  Z= 0.315
  Chirality :  0.044   0.149   1900
  Planarity :  0.004   0.037   2200
  Dihedral  :  4.403  30.096   1732
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  :  9.73 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.61 (0.21), residues: 1560
  helix:  2.78 (0.22), residues: 552
  sheet:  1.19 (0.48), residues: 116
  loop : -0.04 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 480 
 TYR   0.019   0.001   TYR C 328 
 PHE   0.012   0.001   PHE B 374 
 TRP   0.012   0.002   TRP A 464 
 HIS   0.006   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (12796)
  covalent geometry    : angle       0.57929 (17296)
  hydrogen bonds       : bond        0.05917 (  553)
  hydrogen bonds       : angle       4.60407 ( 1548)
  Misc. bond           : bond        0.00022 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.8322 (tp30) cc_final: 0.7887 (tp30)
REVERT: A  440 MET cc_start: 0.8934 (mmm) cc_final: 0.8627 (mmm)
REVERT: A  443 MET cc_start: 0.8615 (mtp) cc_final: 0.8355 (ttm)
REVERT: C  355 ASP cc_start: 0.8225 (t0) cc_final: 0.7852 (t0)
REVERT: C  540 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7525 (tt0)
REVERT: B  468 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7407 (mm-30)
  outliers start: 32
  outliers final: 12
  residues processed: 150
  average time/residue: 0.7773
  time to fit residues: 124.9485
Evaluate side-chains
  133 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  443 MET
Chi-restraints excluded: chain C residue  479 GLN
Chi-restraints excluded: chain C residue  540 GLU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  291 GLU
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  512 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 139 optimal weight:    0.8980
   chunk 143 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 53 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0770
   chunk 88 optimal weight:    9.9990
   chunk 8 optimal weight:    0.1980
   chunk 63 optimal weight:    3.9990
   chunk 128 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
C 479 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.126649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.097157 restraints weight = 15573.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 1.74
r_work: 0.2913 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12800  Z= 0.094
  Angle     :  0.479   5.935  17296  Z= 0.260
  Chirality :  0.041   0.159   1900
  Planarity :  0.003   0.035   2200
  Dihedral  :  4.104  38.274   1732
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.85 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.73 (0.21), residues: 1560
  helix:  2.90 (0.22), residues: 552
  sheet:  1.23 (0.49), residues: 116
  loop :  0.03 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 480 
 TYR   0.010   0.001   TYR B 328 
 PHE   0.009   0.001   PHE B 374 
 TRP   0.008   0.001   TRP D 454 
 HIS   0.003   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 (12796)
  covalent geometry    : angle       0.47947 (17296)
  hydrogen bonds       : bond        0.03935 (  553)
  hydrogen bonds       : angle       4.29406 ( 1548)
  Misc. bond           : bond        0.00022 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.8205 (tp30) cc_final: 0.7910 (tp30)
REVERT: A  440 MET cc_start: 0.8864 (mmm) cc_final: 0.8558 (mmm)
REVERT: C  355 ASP cc_start: 0.8135 (t0) cc_final: 0.7782 (t0)
REVERT: C  451 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7761 (mt-10)
REVERT: B  361 GLN cc_start: 0.8935 (pm20) cc_final: 0.8677 (pm20)
REVERT: D  543 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8006 (mtmm)
  outliers start: 26
  outliers final: 10
  residues processed: 146
  average time/residue: 0.7641
  time to fit residues: 119.7274
Evaluate side-chains
  132 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  451 GLU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain B residue  443 MET
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  512 VAL
Chi-restraints excluded: chain D residue  543 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 148 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 145 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 146 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 153 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 222 HIS
D 222 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.118632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.089115 restraints weight = 15536.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 1.71
r_work: 0.2782 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  12800  Z= 0.260
  Angle     :  0.665   7.123  17296  Z= 0.358
  Chirality :  0.048   0.145   1900
  Planarity :  0.005   0.039   2200
  Dihedral  :  4.669  40.527   1732
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.83 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.31 (0.21), residues: 1560
  helix:  2.54 (0.22), residues: 552
  sheet:  0.87 (0.45), residues: 116
  loop : -0.20 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 112 
 TYR   0.017   0.002   TYR C 328 
 PHE   0.014   0.002   PHE B 374 
 TRP   0.017   0.002   TRP A 464 
 HIS   0.010   0.002   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00647 (12796)
  covalent geometry    : angle       0.66452 (17296)
  hydrogen bonds       : bond        0.07403 (  553)
  hydrogen bonds       : angle       4.59607 ( 1548)
  Misc. bond           : bond        0.00066 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  342 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8252 (mtpt)
REVERT: A  440 MET cc_start: 0.8945 (mmm) cc_final: 0.8736 (mmm)
REVERT: C  355 ASP cc_start: 0.8268 (t0) cc_final: 0.7784 (t0)
REVERT: C  451 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7716 (mt-10)
REVERT: B  468 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7688 (mt-10)
REVERT: D  121 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7448 (tt0)
REVERT: D  336 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8183 (tt0)
REVERT: D  380 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8723 (mttp)
  outliers start: 33
  outliers final: 12
  residues processed: 154
  average time/residue: 0.7936
  time to fit residues: 130.6450
Evaluate side-chains
  132 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  342 LYS
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  451 GLU
Chi-restraints excluded: chain C residue  508 ILE
Chi-restraints excluded: chain C residue  544 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  380 LYS
Chi-restraints excluded: chain D residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 129 optimal weight:    0.6980
   chunk 134 optimal weight:    0.8980
   chunk 135 optimal weight:    2.9990
   chunk 9 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9980
   chunk 142 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.094653 restraints weight = 15585.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 1.68
r_work: 0.2882 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12800  Z= 0.104
  Angle     :  0.503   5.457  17296  Z= 0.273
  Chirality :  0.042   0.204   1900
  Planarity :  0.003   0.037   2200
  Dihedral  :  4.289  41.873   1732
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.02 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.53 (0.21), residues: 1560
  helix:  2.73 (0.22), residues: 552
  sheet:  0.87 (0.45), residues: 116
  loop : -0.05 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 106 
 TYR   0.011   0.001   TYR C 328 
 PHE   0.011   0.001   PHE D 374 
 TRP   0.009   0.001   TRP B 395 
 HIS   0.003   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (12796)
  covalent geometry    : angle       0.50343 (17296)
  hydrogen bonds       : bond        0.04249 (  553)
  hydrogen bonds       : angle       4.33517 ( 1548)
  Misc. bond           : bond        0.00119 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.8191 (tp30) cc_final: 0.7988 (tp30)
REVERT: A  226 ASP cc_start: 0.7075 (t70) cc_final: 0.6702 (m-30)
REVERT: A  288 GLU cc_start: 0.7848 (mp0) cc_final: 0.7028 (tm-30)
REVERT: A  440 MET cc_start: 0.8960 (mmm) cc_final: 0.8689 (mmm)
REVERT: C  355 ASP cc_start: 0.8180 (t0) cc_final: 0.7771 (t0)
REVERT: C  451 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7595 (mt-10)
REVERT: B  361 GLN cc_start: 0.9031 (pm20) cc_final: 0.8763 (pm20)
REVERT: D  336 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: D  380 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8610 (mttp)
  outliers start: 22
  outliers final: 12
  residues processed: 138
  average time/residue: 0.7766
  time to fit residues: 115.0123
Evaluate side-chains
  131 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain C residue  451 GLU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  380 LYS
Chi-restraints excluded: chain D residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 116 optimal weight:    0.8980
   chunk 144 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 52 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 154 optimal weight:    5.9990
   chunk 101 optimal weight:    0.7980
   chunk 149 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
C 479 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.120921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.092064 restraints weight = 15556.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 1.69
r_work: 0.2840 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12800  Z= 0.153
  Angle     :  0.550   5.739  17296  Z= 0.296
  Chirality :  0.043   0.139   1900
  Planarity :  0.004   0.037   2200
  Dihedral  :  4.359  41.041   1732
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.55 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.49 (0.21), residues: 1560
  helix:  2.69 (0.22), residues: 552
  sheet:  0.86 (0.44), residues: 116
  loop : -0.06 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 112 
 TYR   0.014   0.001   TYR C 328 
 PHE   0.012   0.001   PHE D 374 
 TRP   0.010   0.002   TRP D 454 
 HIS   0.006   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (12796)
  covalent geometry    : angle       0.55007 (17296)
  hydrogen bonds       : bond        0.05362 (  553)
  hydrogen bonds       : angle       4.35271 ( 1548)
  Misc. bond           : bond        0.00035 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.8221 (tp30) cc_final: 0.7980 (tp30)
REVERT: A  226 ASP cc_start: 0.7084 (t70) cc_final: 0.6703 (m-30)
REVERT: A  440 MET cc_start: 0.8948 (mmm) cc_final: 0.8670 (mmm)
REVERT: A  462 MET cc_start: 0.8949 (mtt) cc_final: 0.8722 (mtt)
REVERT: C  355 ASP cc_start: 0.8280 (t0) cc_final: 0.7726 (t0)
REVERT: C  451 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7707 (mt-10)
REVERT: C  540 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7613 (tt0)
REVERT: D  121 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7310 (tt0)
REVERT: D  543 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8051 (mtmm)
  outliers start: 23
  outliers final: 13
  residues processed: 138
  average time/residue: 0.7740
  time to fit residues: 114.4314
Evaluate side-chains
  134 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  451 GLU
Chi-restraints excluded: chain C residue  479 GLN
Chi-restraints excluded: chain C residue  540 GLU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  362 GLU
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  512 VAL
Chi-restraints excluded: chain D residue  543 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 150 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 149 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 121 optimal weight:    0.0270
   chunk 74 optimal weight:    7.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    1.5644

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
B 191 HIS
D 510 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.120614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.091564 restraints weight = 15490.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.68
r_work: 0.2831 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12800  Z= 0.161
  Angle     :  0.561   5.874  17296  Z= 0.302
  Chirality :  0.043   0.134   1900
  Planarity :  0.004   0.037   2200
  Dihedral  :  4.421  41.142   1732
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.85 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.43 (0.21), residues: 1560
  helix:  2.63 (0.22), residues: 552
  sheet:  0.80 (0.44), residues: 116
  loop : -0.09 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 480 
 TYR   0.013   0.001   TYR C 328 
 PHE   0.012   0.001   PHE D 374 
 TRP   0.010   0.002   TRP D 454 
 HIS   0.006   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12796)
  covalent geometry    : angle       0.56143 (17296)
  hydrogen bonds       : bond        0.05509 (  553)
  hydrogen bonds       : angle       4.39025 ( 1548)
  Misc. bond           : bond        0.00037 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.8242 (tp30) cc_final: 0.7990 (tp30)
REVERT: A  226 ASP cc_start: 0.7035 (t70) cc_final: 0.6657 (m-30)
REVERT: A  349 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8165 (ttmt)
REVERT: A  440 MET cc_start: 0.8989 (mmm) cc_final: 0.8715 (mmm)
REVERT: C  355 ASP cc_start: 0.8266 (t0) cc_final: 0.7760 (t0)
REVERT: C  451 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7697 (mt-10)
REVERT: D  121 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7336 (tt0)
REVERT: D  543 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8027 (mtmm)
  outliers start: 23
  outliers final: 14
  residues processed: 136
  average time/residue: 0.7251
  time to fit residues: 105.5983
Evaluate side-chains
  136 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  451 GLU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain D residue  109 GLU
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  362 GLU
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  512 VAL
Chi-restraints excluded: chain D residue  543 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 111 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 128 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 124 optimal weight:    0.4980
   chunk 143 optimal weight:    2.9990
   chunk 120 optimal weight:    0.0370
   overall best weight:    1.0662

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN
C 479 GLN
C 510 ASN
B 191 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.121444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.092575 restraints weight = 15445.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.68
r_work: 0.2856 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12800  Z= 0.128
  Angle     :  0.536   6.213  17296  Z= 0.290
  Chirality :  0.043   0.232   1900
  Planarity :  0.004   0.037   2200
  Dihedral  :  4.345  42.253   1732
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.30 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 (0.21), residues: 1560
  helix:  2.67 (0.22), residues: 552
  sheet:  0.81 (0.44), residues: 116
  loop : -0.06 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 106 
 TYR   0.012   0.001   TYR C 328 
 PHE   0.011   0.001   PHE D 374 
 TRP   0.010   0.001   TRP D 454 
 HIS   0.004   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (12796)
  covalent geometry    : angle       0.53556 (17296)
  hydrogen bonds       : bond        0.04831 (  553)
  hydrogen bonds       : angle       4.32915 ( 1548)
  Misc. bond           : bond        0.00038 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.8232 (tp30) cc_final: 0.8000 (tp30)
REVERT: A  226 ASP cc_start: 0.7016 (t70) cc_final: 0.6645 (m-30)
REVERT: A  440 MET cc_start: 0.8982 (mmm) cc_final: 0.8686 (mmm)
REVERT: C  355 ASP cc_start: 0.8211 (t0) cc_final: 0.7741 (t0)
REVERT: C  451 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7650 (mt-10)
REVERT: B  229 LYS cc_start: 0.7826 (tptm) cc_final: 0.7373 (tptp)
REVERT: B  469 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7866 (ptp90)
REVERT: D  121 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7277 (tt0)
REVERT: D  543 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7941 (mtmm)
  outliers start: 25
  outliers final: 13
  residues processed: 143
  average time/residue: 0.8014
  time to fit residues: 122.7339
Evaluate side-chains
  134 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  451 GLU
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain B residue  469 ARG
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  512 VAL
Chi-restraints excluded: chain D residue  543 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   chunk 83 optimal weight:    0.1980
   chunk 117 optimal weight:    5.9990
   chunk 132 optimal weight:    3.9990
   overall best weight:    2.4388

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

Flipped N/Q/H residues before XYZ refinement:
C 479 GLN
B 191 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.118355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.089831 restraints weight = 15635.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 1.78
r_work: 0.2787 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  12800  Z= 0.228
  Angle     :  0.640   6.692  17296  Z= 0.345
  Chirality :  0.047   0.235   1900
  Planarity :  0.004   0.038   2200
  Dihedral  :  4.686  45.595   1732
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.37 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.21 (0.21), residues: 1560
  helix:  2.43 (0.22), residues: 552
  sheet:  0.73 (0.43), residues: 116
  loop : -0.22 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 545 
 TYR   0.014   0.002   TYR D 328 
 PHE   0.013   0.002   PHE D 374 
 TRP   0.015   0.002   TRP C 464 
 HIS   0.007   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (12796)
  covalent geometry    : angle       0.64020 (17296)
  hydrogen bonds       : bond        0.06921 (  553)
  hydrogen bonds       : angle       4.54613 ( 1548)
  Misc. bond           : bond        0.00068 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 121
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 ASP cc_start: 0.7188 (t70) cc_final: 0.6796 (m-30)
REVERT: A  349 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8181 (ttmt)
REVERT: A  440 MET cc_start: 0.8970 (mmm) cc_final: 0.8737 (mmm)
REVERT: C  355 ASP cc_start: 0.8297 (t0) cc_final: 0.7770 (t0)
REVERT: C  451 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7700 (mt-10)
REVERT: C  540 GLU cc_start: 0.8017 (tt0) cc_final: 0.7800 (tt0)
REVERT: B  229 LYS cc_start: 0.7833 (tptm) cc_final: 0.7453 (tptp)
REVERT: B  469 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7874 (ptp90)
REVERT: D  121 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7452 (tt0)
REVERT: D  543 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8046 (mtmm)
  outliers start: 29
  outliers final: 18
  residues processed: 143
  average time/residue: 0.8103
  time to fit residues: 123.6719
Evaluate side-chains
  139 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  451 GLU
Chi-restraints excluded: chain C residue  479 GLN
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  191 HIS
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain B residue  469 ARG
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  362 GLU
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  512 VAL
Chi-restraints excluded: chain D residue  543 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 151 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 123 optimal weight:    2.9990
   chunk 142 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 130 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0570
   chunk 106 optimal weight:    0.8980
   chunk 144 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
A 289 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.122564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.094831 restraints weight = 15635.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.79
r_work: 0.2874 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12800  Z= 0.109
  Angle     :  0.524   6.699  17296  Z= 0.283
  Chirality :  0.042   0.216   1900
  Planarity :  0.003   0.037   2200
  Dihedral  :  4.423  47.904   1732
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 15.87 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.39 (0.21), residues: 1560
  helix:  2.61 (0.22), residues: 552
  sheet:  0.07 (0.37), residues: 156
  loop : -0.00 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 480 
 TYR   0.010   0.001   TYR A 328 
 PHE   0.010   0.001   PHE D 374 
 TRP   0.012   0.001   TRP B 395 
 HIS   0.005   0.001   HIS D 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (12796)
  covalent geometry    : angle       0.52385 (17296)
  hydrogen bonds       : bond        0.04313 (  553)
  hydrogen bonds       : angle       4.34710 ( 1548)
  Misc. bond           : bond        0.00049 (    4)

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 ASP cc_start: 0.6965 (t70) cc_final: 0.6609 (m-30)
REVERT: A  440 MET cc_start: 0.8987 (mmm) cc_final: 0.8687 (mmm)
REVERT: C  355 ASP cc_start: 0.8193 (t0) cc_final: 0.7748 (t0)
REVERT: C  451 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7604 (mt-10)
REVERT: C  540 GLU cc_start: 0.7947 (tt0) cc_final: 0.7717 (tt0)
REVERT: B  229 LYS cc_start: 0.7749 (tptm) cc_final: 0.7479 (tptp)
REVERT: B  469 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7802 (ptp90)
REVERT: D  336 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7829 (tm-30)
REVERT: D  543 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7911 (mtmm)
  outliers start: 17
  outliers final: 13
  residues processed: 132
  average time/residue: 0.7951
  time to fit residues: 112.3993
Evaluate side-chains
  132 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  544 ASP
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  451 GLU
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  316 LYS
Chi-restraints excluded: chain B residue  469 ARG
Chi-restraints excluded: chain D residue  379 LYS
Chi-restraints excluded: chain D residue  512 VAL
Chi-restraints excluded: chain D residue  543 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 133 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 108 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0670
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 41 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   chunk 151 optimal weight:    0.6980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 222 HIS
A 289 GLN
C 479 GLN
C 509 ASN
C 510 ASN
D 222 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.123506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.095788 restraints weight = 15613.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.79
r_work: 0.2898 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  12800  Z= 0.101
  Angle     :  0.506   7.634  17296  Z= 0.272
  Chirality :  0.042   0.209   1900
  Planarity :  0.003   0.037   2200
  Dihedral  :  4.228  50.101   1732
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.87 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.59 (0.22), residues: 1560
  helix:  2.69 (0.22), residues: 552
  sheet:  0.01 (0.37), residues: 188
  loop :  0.23 (0.22), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 106 
 TYR   0.011   0.001   TYR B 328 
 PHE   0.012   0.001   PHE D 374 
 TRP   0.011   0.001   TRP B 395 
 HIS   0.005   0.001   HIS D 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (12796)
  covalent geometry    : angle       0.50573 (17296)
  hydrogen bonds       : bond        0.03908 (  553)
  hydrogen bonds       : angle       4.19043 ( 1548)
  Misc. bond           : bond        0.00040 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4530.76 seconds
wall clock time: 78 minutes 5.70 seconds (4685.70 seconds total)