Starting phenix.real_space_refine
on Fri Aug 22 19:26:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r8d_18999/08_2025/8r8d_18999.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r8d_18999/08_2025/8r8d_18999.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r8d_18999/08_2025/8r8d_18999.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r8d_18999/08_2025/8r8d_18999.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r8d_18999/08_2025/8r8d_18999.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r8d_18999/08_2025/8r8d_18999.map"
  }
  resolution = 2.6
  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=   0.001 sd=   0.059
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      38      5.16       5
     C    4452      2.51       5
     N    1192      2.21       5
     O    1380      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7062
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "B"
      Number of atoms: 1664
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1664
          Classifications: {'peptide': 224}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 14, 'TRANS': 209}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "E"
      Number of atoms: 989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 989
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "I"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 798
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 989
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "L"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 798
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 1664
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1664
          Classifications: {'peptide': 224}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 14, 'TRANS': 209}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "C"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "D"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 2.08, per 1000 atoms: 0.29
  Number of scatterers: 7062
  At special positions: 0
  Unit cell: (128.115, 84.315, 86.505, 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      38     16.00
     O    1380      8.00
     N    1192      7.00
     C    4452      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  42 " - pdb=" SG  CYS B  58 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  77 " - pdb=" SG  CYS B  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 136 " - pdb=" SG  CYS B 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 168 " - pdb=" SG  CYS B 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 191 " - pdb=" SG  CYS B 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A  58 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 136 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 168 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 220 " 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
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
      " BMA D   3 " - " MAN D   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
      " BMA D   3 " - " MAN D   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    BETA1-6
      " NAG C   1 " - " FUC C   6 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
      " NAG D   1 " - " FUC D   6 "
    NAG-ASN
      " NAG C   1 " - " ASN B  74 "
      " NAG D   1 " - " ASN A  74 "
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 405.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1640

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 14 sheets defined
      9.0% alpha, 36.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'B' and resid 55 through 60
      removed outlier: 3.873A  pdb=" N   GLN B  60 " --> pdb=" O   HIS B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60D through 63
    Processing helix  chain 'B' and resid 164 through 169
    Processing helix  chain 'B' and resid 172 through 176
      removed outlier: 3.823A  pdb=" N   ILE B 176 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 242
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.593A  pdb=" N   THR E  91 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 80 through 84
      removed outlier: 3.795A  pdb=" N   GLU I  84 " --> pdb=" O   SER I  81 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.594A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.796A  pdb=" N   GLU L  84 " --> pdb=" O   SER L  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 60
      removed outlier: 3.874A  pdb=" N   GLN A  60 " --> pdb=" O   HIS A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60D through 63
    Processing helix  chain 'A' and resid 164 through 169
    Processing helix  chain 'A' and resid 172 through 176
      removed outlier: 3.823A  pdb=" N   ILE A 176 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 233
      No H-bonds generated for 'chain 'A' and resid 231 through 233'
    Processing helix  chain 'A' and resid 234 through 242
    Processing sheet with id=AA1, first strand: chain 'B' and resid 20 through 21
      removed outlier: 3.661A  pdb=" N   ALA B 139 " --> pdb=" O   PRO B 198 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LEU B 199 " --> pdb=" O   GLN B 210 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ILE B 213 " --> pdb=" O   THR B 229 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   THR B 229 " --> pdb=" O   ILE B 213 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   CYS B 182 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 37
      removed outlier: 6.549A  pdb=" N   TRP B  51 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B  87 " --> pdb=" O   ARG B 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 7
      removed outlier: 5.887A  pdb=" N   GLY E  16 " --> pdb=" O   SER E  85 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.807A  pdb=" N   MET E  34 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLY E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 12
      removed outlier: 6.300A  pdb=" N   TRP I  36 " --> pdb=" O   LEU I  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 9 through 12
      removed outlier: 4.009A  pdb=" N   ASP I  93 " --> pdb=" O   ARG I  97 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   ARG I  97 " --> pdb=" O   ASP I  93 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 18 through 23
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
      removed outlier: 5.887A  pdb=" N   GLY H  16 " --> pdb=" O   SER H  85 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.805A  pdb=" N   MET H  34 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLY H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.300A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12
      removed outlier: 4.011A  pdb=" N   ASP L  93 " --> pdb=" O   ARG L  97 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ARG L  97 " --> pdb=" O   ASP L  93 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AB4, first strand: chain 'A' and resid 20 through 21
      removed outlier: 3.661A  pdb=" N   ALA A 139 " --> pdb=" O   PRO A 198 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LEU A 199 " --> pdb=" O   GLN A 210 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ILE A 213 " --> pdb=" O   THR A 229 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   THR A 229 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   CYS A 182 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 30 through 37
      removed outlier: 6.550A  pdb=" N   TRP A  51 " --> pdb=" O   ILE A  47 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER A  87 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)

    246 hydrogen bonds defined for protein.
    582 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2258
        1.34 -     1.46: 1767
        1.46 -     1.58: 3149
        1.58 -     1.70: 0
        1.70 -     1.82: 44
  Bond restraints: 7218
  Sorted by residual:
  bond pdb=" C5  FUC C   6 "
       pdb=" O5  FUC C   6 "
    ideal  model  delta    sigma   weight residual
    1.423  1.458 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C5  FUC D   6 "
       pdb=" O5  FUC D   6 "
    ideal  model  delta    sigma   weight residual
    1.423  1.458 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C5  MAN D   5 "
       pdb=" O5  MAN D   5 "
    ideal  model  delta    sigma   weight residual
    1.418  1.445 -0.027 2.00e-02 2.50e+03 1.85e+00
  bond pdb=" C5  MAN C   5 "
       pdb=" O5  MAN C   5 "
    ideal  model  delta    sigma   weight residual
    1.418  1.445 -0.027 2.00e-02 2.50e+03 1.85e+00
  bond pdb=" C1  MAN C   5 "
       pdb=" C2  MAN C   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.552 -0.026 2.00e-02 2.50e+03 1.64e+00
  ... (remaining 7213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 9566
        1.72 -     3.44: 226
        3.44 -     5.16: 28
        5.16 -     6.88: 14
        6.88 -     8.60: 4
  Bond angle restraints: 9838
  Sorted by residual:
  angle pdb=" C   SER L  51 "
        pdb=" N   ASN L  52 "
        pdb=" CA  ASN L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.66   -6.12 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" C   SER I  51 "
        pdb=" N   ASN I  52 "
        pdb=" CA  ASN I  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.65   -6.11 1.91e+00 2.74e-01 1.02e+01
  angle pdb=" N   ARG H  67 "
        pdb=" CA  ARG H  67 "
        pdb=" C   ARG H  67 "
      ideal   model   delta    sigma   weight residual
     114.04  111.26    2.78 1.24e+00 6.50e-01 5.03e+00
  angle pdb=" N   ARG E  67 "
        pdb=" CA  ARG E  67 "
        pdb=" C   ARG E  67 "
      ideal   model   delta    sigma   weight residual
     114.04  111.29    2.75 1.24e+00 6.50e-01 4.93e+00
  angle pdb=" C3  BMA C   3 "
        pdb=" C2  BMA C   3 "
        pdb=" O2  BMA C   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.62    6.33 3.00e+00 1.11e-01 4.46e+00
  ... (remaining 9833 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.36: 4126
       21.36 -    42.72: 183
       42.72 -    64.08: 39
       64.08 -    85.44: 30
       85.44 -   106.80: 8
  Dihedral angle restraints: 4386
    sinusoidal: 1786
      harmonic: 2600
  Sorted by residual:
  dihedral pdb=" CB  CYS A 168 "
           pdb=" SG  CYS A 168 "
           pdb=" SG  CYS A 182 "
           pdb=" CB  CYS A 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.90  -65.90     1      1.00e+01 1.00e-02 5.68e+01
  dihedral pdb=" CB  CYS B 168 "
           pdb=" SG  CYS B 168 "
           pdb=" SG  CYS B 182 "
           pdb=" CB  CYS B 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.90  -65.90     1      1.00e+01 1.00e-02 5.68e+01
  dihedral pdb=" CB  CYS A  42 "
           pdb=" SG  CYS A  42 "
           pdb=" SG  CYS A  58 "
           pdb=" CB  CYS A  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.14  -57.14     1      1.00e+01 1.00e-02 4.39e+01
  ... (remaining 4383 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 917
       0.057 -    0.114: 171
       0.114 -    0.170: 30
       0.170 -    0.227: 0
       0.227 -    0.284: 2
  Chirality restraints: 1120
  Sorted by residual:
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.69e-01
  ... (remaining 1117 not shown)

  Planarity restraints: 1250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  48 "    0.031 5.00e-02 4.00e+02   4.69e-02 3.52e+00
        pdb=" N   PRO A  49 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A  49 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  49 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  48 "   -0.031 5.00e-02 4.00e+02   4.69e-02 3.52e+00
        pdb=" N   PRO B  49 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B  49 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B  49 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 115 "   -0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO A 116 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 116 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 116 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1247 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1068
        2.77 -     3.30: 6362
        3.30 -     3.83: 12223
        3.83 -     4.37: 15300
        4.37 -     4.90: 25681
  Nonbonded interactions: 60634
  Sorted by model distance:
  nonbonded pdb=" O   PRO A  60C"
            pdb=" OH  TYR A  88 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PRO B  60C"
            pdb=" OH  TYR B  88 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PRO E  41 "
            pdb=" NZ  LYS E  43 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   PRO H  41 "
            pdb=" NZ  LYS H  43 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   ARG A  24 "
            pdb=" NH1 ARG A  24 "
     model   vdw
     2.287 3.120
  ... (remaining 60629 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.180
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7246  Z= 0.155
  Angle     :  0.681   8.596   9906  Z= 0.318
  Chirality :  0.047   0.284   1120
  Planarity :  0.005   0.059   1248
  Dihedral  : 14.746 106.800   2698
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.28), residues: 900
  helix: -1.32 (0.75), residues: 42
  sheet:  0.41 (0.34), residues: 252
  loop :  0.10 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  98 
 TYR   0.026   0.002   TYR E 112 
 PHE   0.011   0.001   PHE E  29 
 TRP   0.015   0.002   TRP H  47 
 HIS   0.003   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7218)
  covalent geometry    : angle       0.66644 ( 9838)
  SS BOND              : bond        0.00304 (   16)
  SS BOND              : angle       1.48382 (   32)
  hydrogen bonds       : bond        0.22548 (  236)
  hydrogen bonds       : angle       9.51246 (  582)
  link_ALPHA1-3        : bond        0.00633 (    2)
  link_ALPHA1-3        : angle       1.82879 (    6)
  link_ALPHA1-6        : bond        0.00416 (    2)
  link_ALPHA1-6        : angle       1.64345 (    6)
  link_BETA1-4         : bond        0.00272 (    4)
  link_BETA1-4         : angle       2.44736 (   12)
  link_BETA1-6         : bond        0.00526 (    2)
  link_BETA1-6         : angle       2.11748 (    6)
  link_NAG-ASN         : bond        0.01029 (    2)
  link_NAG-ASN         : angle       1.47452 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   71 GLU cc_start: 0.8124 (tt0) cc_final: 0.7478 (tp30)
REVERT: I   83 ASP cc_start: 0.8661 (m-30) cc_final: 0.8346 (m-30)
REVERT: L   83 ASP cc_start: 0.8676 (m-30) cc_final: 0.8364 (m-30)
REVERT: A   71 GLU cc_start: 0.8131 (tt0) cc_final: 0.7473 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.6661
  time to fit residues: 97.6259
Evaluate side-chains
  120 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0050
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
I  54 GLN
L  54 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.157561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.135048 restraints weight = 6529.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.28
r_work: 0.3378 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.1165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7246  Z= 0.148
  Angle     :  0.666   6.868   9906  Z= 0.327
  Chirality :  0.046   0.147   1120
  Planarity :  0.005   0.039   1248
  Dihedral  :  8.406  61.285   1234
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  :  6.34 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.28), residues: 900
  helix: -0.91 (0.82), residues: 42
  sheet:  0.66 (0.33), residues: 238
  loop :  0.10 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 239 
 TYR   0.018   0.002   TYR E 112 
 PHE   0.011   0.001   PHE H  29 
 TRP   0.014   0.002   TRP H  47 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 7218)
  covalent geometry    : angle       0.65112 ( 9838)
  SS BOND              : bond        0.00469 (   16)
  SS BOND              : angle       1.39146 (   32)
  hydrogen bonds       : bond        0.03746 (  236)
  hydrogen bonds       : angle       6.42906 (  582)
  link_ALPHA1-3        : bond        0.00688 (    2)
  link_ALPHA1-3        : angle       1.90829 (    6)
  link_ALPHA1-6        : bond        0.00869 (    2)
  link_ALPHA1-6        : angle       1.32116 (    6)
  link_BETA1-4         : bond        0.00240 (    4)
  link_BETA1-4         : angle       2.85562 (   12)
  link_BETA1-6         : bond        0.00308 (    2)
  link_BETA1-6         : angle       1.13578 (    6)
  link_NAG-ASN         : bond        0.00728 (    2)
  link_NAG-ASN         : angle       1.77564 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   71 GLU cc_start: 0.8852 (tt0) cc_final: 0.7411 (tp30)
REVERT: I   83 ASP cc_start: 0.8551 (m-30) cc_final: 0.8307 (m-30)
REVERT: L   83 ASP cc_start: 0.8559 (m-30) cc_final: 0.8311 (m-30)
REVERT: A   71 GLU cc_start: 0.8851 (tt0) cc_final: 0.7466 (tp30)
  outliers start: 23
  outliers final: 10
  residues processed: 136
  average time/residue: 0.6469
  time to fit residues: 92.3009
Evaluate side-chains
  129 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain H residue  128 SER
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain A residue  153 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
A 109 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.147258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.122215 restraints weight = 7001.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.60
r_work: 0.3301 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7246  Z= 0.189
  Angle     :  0.700   7.483   9906  Z= 0.343
  Chirality :  0.048   0.177   1120
  Planarity :  0.005   0.040   1248
  Dihedral  :  7.216  46.224   1234
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.50 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.28), residues: 900
  helix: -1.02 (0.80), residues: 42
  sheet:  0.78 (0.33), residues: 238
  loop :  0.05 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 239 
 TYR   0.014   0.002   TYR B 117 
 PHE   0.013   0.002   PHE H  29 
 TRP   0.016   0.002   TRP H  47 
 HIS   0.004   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 7218)
  covalent geometry    : angle       0.68603 ( 9838)
  SS BOND              : bond        0.00567 (   16)
  SS BOND              : angle       1.51023 (   32)
  hydrogen bonds       : bond        0.03659 (  236)
  hydrogen bonds       : angle       6.16620 (  582)
  link_ALPHA1-3        : bond        0.01203 (    2)
  link_ALPHA1-3        : angle       1.04419 (    6)
  link_ALPHA1-6        : bond        0.00556 (    2)
  link_ALPHA1-6        : angle       2.13167 (    6)
  link_BETA1-4         : bond        0.00304 (    4)
  link_BETA1-4         : angle       2.74550 (   12)
  link_BETA1-6         : bond        0.00169 (    2)
  link_BETA1-6         : angle       1.35921 (    6)
  link_NAG-ASN         : bond        0.01202 (    2)
  link_NAG-ASN         : angle       1.67345 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: I   83 ASP cc_start: 0.8641 (m-30) cc_final: 0.8377 (m-30)
REVERT: L   83 ASP cc_start: 0.8629 (m-30) cc_final: 0.8364 (m-30)
  outliers start: 17
  outliers final: 15
  residues processed: 126
  average time/residue: 0.6791
  time to fit residues: 89.6216
Evaluate side-chains
  131 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 GLN
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain I residue   86 ASP
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain A residue  109 GLN
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  165 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0870
   chunk 37 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0770
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
I  54 GLN
L  54 GLN
A 109 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.150083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125348 restraints weight = 7025.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.59
r_work: 0.3336 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7246  Z= 0.122
  Angle     :  0.621   7.126   9906  Z= 0.305
  Chirality :  0.046   0.176   1120
  Planarity :  0.005   0.040   1248
  Dihedral  :  6.464  38.060   1234
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 11.02 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.28), residues: 900
  helix: -0.74 (0.83), residues: 42
  sheet:  0.81 (0.33), residues: 240
  loop :  0.11 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 239 
 TYR   0.010   0.001   TYR E 111 
 PHE   0.013   0.001   PHE E  29 
 TRP   0.015   0.002   TRP H  47 
 HIS   0.005   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7218)
  covalent geometry    : angle       0.60807 ( 9838)
  SS BOND              : bond        0.00460 (   16)
  SS BOND              : angle       1.30479 (   32)
  hydrogen bonds       : bond        0.02989 (  236)
  hydrogen bonds       : angle       5.81080 (  582)
  link_ALPHA1-3        : bond        0.01293 (    2)
  link_ALPHA1-3        : angle       1.31019 (    6)
  link_ALPHA1-6        : bond        0.00423 (    2)
  link_ALPHA1-6        : angle       1.94722 (    6)
  link_BETA1-4         : bond        0.00169 (    4)
  link_BETA1-4         : angle       2.49531 (   12)
  link_BETA1-6         : bond        0.00260 (    2)
  link_BETA1-6         : angle       1.20031 (    6)
  link_NAG-ASN         : bond        0.00646 (    2)
  link_NAG-ASN         : angle       1.54038 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.277 
Fit side-chains
REVERT: E   39 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8656 (mm-40)
REVERT: E   43 LYS cc_start: 0.8195 (mptt) cc_final: 0.7990 (mptt)
REVERT: I   83 ASP cc_start: 0.8585 (m-30) cc_final: 0.8363 (m-30)
REVERT: H   39 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8687 (mm-40)
REVERT: L   83 ASP cc_start: 0.8591 (m-30) cc_final: 0.8370 (m-30)
  outliers start: 19
  outliers final: 12
  residues processed: 129
  average time/residue: 0.6841
  time to fit residues: 92.4620
Evaluate side-chains
  136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue   39 GLN
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue   86 ASP
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  165 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 41 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0470
   chunk 3 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
I  54 GLN
L  54 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.149845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.125967 restraints weight = 7038.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.53
r_work: 0.3338 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7246  Z= 0.116
  Angle     :  0.602   7.212   9906  Z= 0.295
  Chirality :  0.045   0.149   1120
  Planarity :  0.005   0.041   1248
  Dihedral  :  5.785  33.107   1234
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.12 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.28), residues: 900
  helix: -0.85 (0.81), residues: 42
  sheet:  0.84 (0.33), residues: 240
  loop :  0.11 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 239 
 TYR   0.011   0.002   TYR E  80 
 PHE   0.011   0.001   PHE H  29 
 TRP   0.016   0.002   TRP H  47 
 HIS   0.005   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7218)
  covalent geometry    : angle       0.58971 ( 9838)
  SS BOND              : bond        0.00405 (   16)
  SS BOND              : angle       1.17459 (   32)
  hydrogen bonds       : bond        0.02783 (  236)
  hydrogen bonds       : angle       5.56280 (  582)
  link_ALPHA1-3        : bond        0.01255 (    2)
  link_ALPHA1-3        : angle       1.26944 (    6)
  link_ALPHA1-6        : bond        0.00398 (    2)
  link_ALPHA1-6        : angle       1.80748 (    6)
  link_BETA1-4         : bond        0.00240 (    4)
  link_BETA1-4         : angle       2.44346 (   12)
  link_BETA1-6         : bond        0.00289 (    2)
  link_BETA1-6         : angle       1.19004 (    6)
  link_NAG-ASN         : bond        0.00665 (    2)
  link_NAG-ASN         : angle       1.48283 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.303 
Fit side-chains
REVERT: I   83 ASP cc_start: 0.8598 (m-30) cc_final: 0.8382 (m-30)
REVERT: L   83 ASP cc_start: 0.8593 (m-30) cc_final: 0.8377 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 127
  average time/residue: 0.6732
  time to fit residues: 89.7275
Evaluate side-chains
  128 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  165 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 51 optimal weight:    0.1980
   chunk 1 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
I  54 GLN
L  54 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.148613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123865 restraints weight = 7085.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.59
r_work: 0.3313 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7246  Z= 0.148
  Angle     :  0.645   7.136   9906  Z= 0.316
  Chirality :  0.046   0.147   1120
  Planarity :  0.005   0.041   1248
  Dihedral  :  5.773  30.179   1234
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.67 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.28), residues: 900
  helix: -0.96 (0.78), residues: 42
  sheet:  0.79 (0.33), residues: 240
  loop :  0.09 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 239 
 TYR   0.013   0.002   TYR E 112 
 PHE   0.012   0.001   PHE E  29 
 TRP   0.015   0.002   TRP H  47 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7218)
  covalent geometry    : angle       0.63251 ( 9838)
  SS BOND              : bond        0.00488 (   16)
  SS BOND              : angle       1.31767 (   32)
  hydrogen bonds       : bond        0.03007 (  236)
  hydrogen bonds       : angle       5.66319 (  582)
  link_ALPHA1-3        : bond        0.01192 (    2)
  link_ALPHA1-3        : angle       1.18451 (    6)
  link_ALPHA1-6        : bond        0.00395 (    2)
  link_ALPHA1-6        : angle       1.77503 (    6)
  link_BETA1-4         : bond        0.00289 (    4)
  link_BETA1-4         : angle       2.56965 (   12)
  link_BETA1-6         : bond        0.00181 (    2)
  link_BETA1-6         : angle       1.35770 (    6)
  link_NAG-ASN         : bond        0.00872 (    2)
  link_NAG-ASN         : angle       1.46728 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.277 
Fit side-chains
REVERT: B  109 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7951 (tm-30)
REVERT: I   83 ASP cc_start: 0.8592 (m-30) cc_final: 0.8363 (m-30)
REVERT: L   83 ASP cc_start: 0.8588 (m-30) cc_final: 0.8353 (m-30)
REVERT: A  109 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7939 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 125
  average time/residue: 0.6666
  time to fit residues: 87.3440
Evaluate side-chains
  131 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain A residue  153 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 63 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 77 optimal weight:    0.4980
   chunk 48 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.150239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.125343 restraints weight = 6923.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.59
r_work: 0.3339 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7246  Z= 0.122
  Angle     :  0.616   7.166   9906  Z= 0.303
  Chirality :  0.045   0.174   1120
  Planarity :  0.005   0.038   1248
  Dihedral  :  5.584  28.871   1234
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.67 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.28), residues: 900
  helix: -0.77 (0.81), residues: 42
  sheet:  0.84 (0.33), residues: 240
  loop :  0.11 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 239 
 TYR   0.012   0.002   TYR E 112 
 PHE   0.012   0.001   PHE H  29 
 TRP   0.016   0.002   TRP H  47 
 HIS   0.005   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7218)
  covalent geometry    : angle       0.59913 ( 9838)
  SS BOND              : bond        0.00444 (   16)
  SS BOND              : angle       1.82443 (   32)
  hydrogen bonds       : bond        0.02774 (  236)
  hydrogen bonds       : angle       5.53350 (  582)
  link_ALPHA1-3        : bond        0.01208 (    2)
  link_ALPHA1-3        : angle       1.15090 (    6)
  link_ALPHA1-6        : bond        0.00367 (    2)
  link_ALPHA1-6        : angle       1.70523 (    6)
  link_BETA1-4         : bond        0.00229 (    4)
  link_BETA1-4         : angle       2.48664 (   12)
  link_BETA1-6         : bond        0.00231 (    2)
  link_BETA1-6         : angle       1.25163 (    6)
  link_NAG-ASN         : bond        0.00664 (    2)
  link_NAG-ASN         : angle       1.40564 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.273 
Fit side-chains
REVERT: B  109 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7922 (tm-30)
REVERT: B  157 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8046 (pt0)
REVERT: E   43 LYS cc_start: 0.8141 (mptt) cc_final: 0.7920 (mptt)
REVERT: I   83 ASP cc_start: 0.8569 (m-30) cc_final: 0.8332 (m-30)
REVERT: L   83 ASP cc_start: 0.8567 (m-30) cc_final: 0.8332 (m-30)
REVERT: A  109 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7933 (tm-30)
REVERT: A  157 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8063 (pt0)
  outliers start: 19
  outliers final: 14
  residues processed: 130
  average time/residue: 0.6575
  time to fit residues: 89.6196
Evaluate side-chains
  138 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain H residue  128 SER
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  165 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
I  54 GLN
L  54 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.149015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.124975 restraints weight = 7015.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.53
r_work: 0.3327 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7246  Z= 0.148
  Angle     :  0.651   7.118   9906  Z= 0.320
  Chirality :  0.046   0.150   1120
  Planarity :  0.005   0.041   1248
  Dihedral  :  5.643  27.457   1234
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.09 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.28), residues: 900
  helix: -0.83 (0.79), residues: 42
  sheet:  0.78 (0.33), residues: 240
  loop :  0.09 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 239 
 TYR   0.012   0.002   TYR E 112 
 PHE   0.012   0.001   PHE H  29 
 TRP   0.015   0.002   TRP H  47 
 HIS   0.005   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7218)
  covalent geometry    : angle       0.62997 ( 9838)
  SS BOND              : bond        0.00548 (   16)
  SS BOND              : angle       2.32571 (   32)
  hydrogen bonds       : bond        0.02849 (  236)
  hydrogen bonds       : angle       5.59912 (  582)
  link_ALPHA1-3        : bond        0.01199 (    2)
  link_ALPHA1-3        : angle       1.08767 (    6)
  link_ALPHA1-6        : bond        0.00401 (    2)
  link_ALPHA1-6        : angle       1.70930 (    6)
  link_BETA1-4         : bond        0.00288 (    4)
  link_BETA1-4         : angle       2.57587 (   12)
  link_BETA1-6         : bond        0.00188 (    2)
  link_BETA1-6         : angle       1.33965 (    6)
  link_NAG-ASN         : bond        0.00833 (    2)
  link_NAG-ASN         : angle       1.41810 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.248 
Fit side-chains
REVERT: I   83 ASP cc_start: 0.8609 (m-30) cc_final: 0.8386 (m-30)
REVERT: L   83 ASP cc_start: 0.8601 (m-30) cc_final: 0.8369 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 125
  average time/residue: 0.6878
  time to fit residues: 90.0766
Evaluate side-chains
  132 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain H residue  128 SER
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  153 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
I  54 GLN
A 109 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.149598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124791 restraints weight = 6997.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 1.58
r_work: 0.3330 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7246  Z= 0.151
  Angle     :  0.652   7.132   9906  Z= 0.321
  Chirality :  0.046   0.149   1120
  Planarity :  0.005   0.045   1248
  Dihedral  :  5.571  25.574   1234
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.22 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.28), residues: 900
  helix: -0.82 (0.79), residues: 42
  sheet:  0.77 (0.33), residues: 240
  loop :  0.10 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 107 
 TYR   0.013   0.002   TYR E 112 
 PHE   0.012   0.001   PHE H  29 
 TRP   0.016   0.002   TRP H  47 
 HIS   0.005   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7218)
  covalent geometry    : angle       0.63395 ( 9838)
  SS BOND              : bond        0.00560 (   16)
  SS BOND              : angle       2.04900 (   32)
  hydrogen bonds       : bond        0.02922 (  236)
  hydrogen bonds       : angle       5.61368 (  582)
  link_ALPHA1-3        : bond        0.01174 (    2)
  link_ALPHA1-3        : angle       0.98676 (    6)
  link_ALPHA1-6        : bond        0.00403 (    2)
  link_ALPHA1-6        : angle       1.68101 (    6)
  link_BETA1-4         : bond        0.00303 (    4)
  link_BETA1-4         : angle       2.59548 (   12)
  link_BETA1-6         : bond        0.00162 (    2)
  link_BETA1-6         : angle       1.36479 (    6)
  link_NAG-ASN         : bond        0.00869 (    2)
  link_NAG-ASN         : angle       1.41311 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.277 
Fit side-chains
REVERT: I   83 ASP cc_start: 0.8579 (m-30) cc_final: 0.8331 (m-30)
REVERT: L   83 ASP cc_start: 0.8577 (m-30) cc_final: 0.8346 (m-30)
  outliers start: 17
  outliers final: 15
  residues processed: 123
  average time/residue: 0.6711
  time to fit residues: 86.5404
Evaluate side-chains
  134 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue  109 GLN
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain H residue  128 SER
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  109 GLN
Chi-restraints excluded: chain A residue  153 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 35 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
I  54 GLN
L  54 GLN
A 109 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.149531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.124452 restraints weight = 6946.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.60
r_work: 0.3328 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099   7246  Z= 0.205
  Angle     :  1.256  59.192   9906  Z= 0.730
  Chirality :  0.046   0.149   1120
  Planarity :  0.005   0.045   1248
  Dihedral  :  5.566  25.622   1234
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.09 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.28), residues: 900
  helix: -0.82 (0.79), residues: 42
  sheet:  0.77 (0.33), residues: 240
  loop :  0.09 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 107 
 TYR   0.011   0.002   TYR E 112 
 PHE   0.012   0.001   PHE H  29 
 TRP   0.016   0.002   TRP H  47 
 HIS   0.005   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 7218)
  covalent geometry    : angle       1.24989 ( 9838)
  SS BOND              : bond        0.00546 (   16)
  SS BOND              : angle       2.01363 (   32)
  hydrogen bonds       : bond        0.02917 (  236)
  hydrogen bonds       : angle       5.61165 (  582)
  link_ALPHA1-3        : bond        0.00967 (    2)
  link_ALPHA1-3        : angle       1.05125 (    6)
  link_ALPHA1-6        : bond        0.00449 (    2)
  link_ALPHA1-6        : angle       1.73401 (    6)
  link_BETA1-4         : bond        0.00312 (    4)
  link_BETA1-4         : angle       2.66113 (   12)
  link_BETA1-6         : bond        0.00208 (    2)
  link_BETA1-6         : angle       1.36939 (    6)
  link_NAG-ASN         : bond        0.00831 (    2)
  link_NAG-ASN         : angle       1.41515 (    6)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.275 
Fit side-chains
REVERT: I   83 ASP cc_start: 0.8581 (m-30) cc_final: 0.8332 (m-30)
REVERT: L   83 ASP cc_start: 0.8580 (m-30) cc_final: 0.8348 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 123
  average time/residue: 0.6780
  time to fit residues: 87.3813
Evaluate side-chains
  131 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain E residue  128 SER
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   57 SER
Chi-restraints excluded: chain I residue   86 ASP
Chi-restraints excluded: chain H residue  107 ILE
Chi-restraints excluded: chain H residue  128 SER
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  153 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0770
   chunk 76 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0980
   chunk 83 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 9 optimal weight:   50.0000
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.4740

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  54 GLN
** A 109 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 = 0.3697 r_free = 0.3697 target = 0.149520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.124680 restraints weight = 6918.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.58
r_work: 0.3329 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7246  Z= 0.227
  Angle     :  1.252  59.200   9906  Z= 0.729
  Chirality :  0.047   0.206   1120
  Planarity :  0.005   0.045   1248
  Dihedral  :  5.550  25.564   1234
  Min Nonbonded Distance : 1.739

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.77 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.28), residues: 900
  helix: -0.82 (0.79), residues: 42
  sheet:  0.77 (0.33), residues: 240
  loop :  0.09 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 107 
 TYR   0.010   0.002   TYR H 111 
 PHE   0.012   0.001   PHE H  29 
 TRP   0.016   0.002   TRP H  47 
 HIS   0.005   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 7218)
  covalent geometry    : angle       1.24584 ( 9838)
  SS BOND              : bond        0.00526 (   16)
  SS BOND              : angle       2.00165 (   32)
  hydrogen bonds       : bond        0.02915 (  236)
  hydrogen bonds       : angle       5.61057 (  582)
  link_ALPHA1-3        : bond        0.01155 (    2)
  link_ALPHA1-3        : angle       1.14677 (    6)
  link_ALPHA1-6        : bond        0.00690 (    2)
  link_ALPHA1-6        : angle       1.69676 (    6)
  link_BETA1-4         : bond        0.01077 (    4)
  link_BETA1-4         : angle       2.50138 (   12)
  link_BETA1-6         : bond        0.00152 (    2)
  link_BETA1-6         : angle       1.32408 (    6)
  link_NAG-ASN         : bond        0.00798 (    2)
  link_NAG-ASN         : angle       1.41681 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2995.03 seconds
wall clock time: 51 minutes 54.78 seconds (3114.78 seconds total)