Starting phenix.real_space_refine
on Tue Feb  3 18:13:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pzx_72085/02_2026/9pzx_72085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pzx_72085/02_2026/9pzx_72085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pzx_72085/02_2026/9pzx_72085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pzx_72085/02_2026/9pzx_72085.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pzx_72085/02_2026/9pzx_72085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pzx_72085/02_2026/9pzx_72085.map"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      26      5.16       5
     C    3770      2.51       5
     N     999      2.21       5
     O    1123      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5918
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1413
          Classifications: {'peptide': 191}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 12, 'TRANS': 178}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "B"
      Number of atoms: 2721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 360, 2721
          Classifications: {'peptide': 360}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 15, 'TRANS': 344}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 166
          Unresolved non-hydrogen dihedrals: 109
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 102
    Chain: "J"
      Number of atoms: 906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 906
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "K"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 794
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.21, per 1000 atoms: 0.20
  Number of scatterers: 5918
  At special positions: 0
  Unit cell: (95.45, 112.05, 85.49, 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      26     16.00
     O    1123      8.00
     N     999      7.00
     C    3770      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  79 " - pdb=" SG  CYS A 308 " distance=1.35
    Simple disulfide: pdb=" SG  CYS B  87 " - pdb=" SG  CYS B 320 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  41 " - pdb=" SG  CYS J 115 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K  43 " - pdb=" SG  CYS K 112 " distance=2.04

  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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A 901 " - " ASN A  61 "
      " NAG B 901 " - " ASN B  75 "
      " NAG B 902 " - " ASN B 380 "
      " NAG B 903 " - " ASN B 340 "
      " NAG C   1 " - " ASN A 276 "
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 334.3 milliseconds
  

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1446

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 10 sheets defined
      25.9% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 54
      removed outlier: 3.640A  pdb=" N   GLN A  40 " --> pdb=" O   ARG A  36 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   HIS A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY A  54 " --> pdb=" O   ASN A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 82
    Processing helix  chain 'A' and resid 83 through 85
      No H-bonds generated for 'chain 'A' and resid 83 through 85'
    Processing helix  chain 'A' and resid 104 through 113
    Processing helix  chain 'A' and resid 125 through 130
    Processing helix  chain 'A' and resid 277 through 296
      removed outlier: 3.620A  pdb=" N   SER A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 327
    Processing helix  chain 'B' and resid 47 through 53
      removed outlier: 3.625A  pdb=" N   LEU B  51 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG B  52 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 59
      removed outlier: 3.970A  pdb=" N   GLU B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 93
      removed outlier: 3.893A  pdb=" N   ILE B  83 " --> pdb=" O   PRO B  79 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ALA B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 121
    Processing helix  chain 'B' and resid 150 through 165
    Processing helix  chain 'B' and resid 179 through 192
    Processing helix  chain 'B' and resid 215 through 220
    Processing helix  chain 'B' and resid 232 through 247
      removed outlier: 4.417A  pdb=" N   LEU B 238 " --> pdb=" O   ASP B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 310
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65
      removed outlier: 5.977A  pdb=" N   ILE A  29 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   VAL A  65 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ALA A  31 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ASN A  28 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ALA A  89 " --> pdb=" O   ASN A  28 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   LEU A 119 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ILE A  90 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 74
      removed outlier: 3.636A  pdb=" N   GLY B  97 " --> pdb=" O   ASN B  35 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B  37 " --> pdb=" O   GLY B  97 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 203 through 205
      removed outlier: 6.357A  pdb=" N   LEU B 172 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   VAL B 279 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   LEU B 361 " --> pdb=" O   TRP B 378 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   VAL B 365 " --> pdb=" O   LYS B 374 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   LYS B 374 " --> pdb=" O   VAL B 365 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLU B 379 " --> pdb=" O   THR B 382 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 23 through 25
    Processing sheet with id=AA5, first strand: chain 'J' and resid 29 through 30
      removed outlier: 3.586A  pdb=" N   ALA J 134 " --> pdb=" O   TYR J 113 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR J 113 " --> pdb=" O   ALA J 134 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLY J  68 " --> pdb=" O   TRP J  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'J' and resid 29 through 30
      removed outlier: 3.586A  pdb=" N   ALA J 134 " --> pdb=" O   TYR J 113 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR J 113 " --> pdb=" O   ALA J 134 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR J 129 " --> pdb=" O   ARG J 117 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 26 through 27
      removed outlier: 3.658A  pdb=" N   SER K  42 " --> pdb=" O   SER K  27 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 30 through 31
    Processing sheet with id=AA9, first strand: chain 'K' and resid 50 through 51
    Processing sheet with id=AB1, first strand: chain 'K' and resid 77 through 78
      removed outlier: 6.439A  pdb=" N   TRP K  59 " --> pdb=" O   LEU K  71 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   MET K 109 " --> pdb=" O   GLN K  62 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   THR K 121 " --> pdb=" O   GLN K 114 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    621 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: 0.53

  Time building geometry restraints manager: 0.62 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: 1837
        1.34 -     1.46: 1081
        1.46 -     1.58: 3089
        1.58 -     1.70: 0
        1.70 -     1.82: 43
  Bond restraints: 6050
  Sorted by residual:
  bond pdb=" N   ILE B 222 "
       pdb=" CA  ILE B 222 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.17e-02 7.31e+03 9.21e+00
  bond pdb=" N   VAL B 226 "
       pdb=" CA  VAL B 226 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.22e-02 6.72e+03 9.21e+00
  bond pdb=" N   LYS J  32 "
       pdb=" CA  LYS J  32 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.033 1.16e-02 7.43e+03 8.23e+00
  bond pdb=" N   LYS B 221 "
       pdb=" CA  LYS B 221 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.19e-02 7.06e+03 7.77e+00
  bond pdb=" N   VAL A 141 "
       pdb=" CA  VAL A 141 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.23e-02 6.61e+03 7.00e+00
  ... (remaining 6045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 7864
        1.35 -     2.71: 300
        2.71 -     4.06: 64
        4.06 -     5.41: 15
        5.41 -     6.76: 3
  Bond angle restraints: 8246
  Sorted by residual:
  angle pdb=" C   PHE B 195 "
        pdb=" N   VAL B 196 "
        pdb=" CA  VAL B 196 "
      ideal   model   delta    sigma   weight residual
     120.88  125.61   -4.73 1.22e+00 6.72e-01 1.51e+01
  angle pdb=" N   ASN B 193 "
        pdb=" CA  ASN B 193 "
        pdb=" C   ASN B 193 "
      ideal   model   delta    sigma   weight residual
     109.56  116.32   -6.76 1.84e+00 2.95e-01 1.35e+01
  angle pdb=" CA  ARG B 360 "
        pdb=" C   ARG B 360 "
        pdb=" O   ARG B 360 "
      ideal   model   delta    sigma   weight residual
     122.13  118.28    3.85 1.13e+00 7.83e-01 1.16e+01
  angle pdb=" CA  VAL B 226 "
        pdb=" C   VAL B 226 "
        pdb=" O   VAL B 226 "
      ideal   model   delta    sigma   weight residual
     121.23  117.87    3.36 1.07e+00 8.73e-01 9.89e+00
  angle pdb=" C   PRO A 143 "
        pdb=" CA  PRO A 143 "
        pdb=" CB  PRO A 143 "
      ideal   model   delta    sigma   weight residual
     113.09  108.89    4.20 1.36e+00 5.41e-01 9.52e+00
  ... (remaining 8241 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.76: 3487
       23.76 -    47.51: 123
       47.51 -    71.27: 20
       71.27 -    95.02: 7
       95.02 -   118.78: 3
  Dihedral angle restraints: 3640
    sinusoidal: 1394
      harmonic: 2246
  Sorted by residual:
  dihedral pdb=" N2  NAG A 901 "
           pdb=" C1  NAG A 901 "
           pdb=" C2  NAG A 901 "
           pdb=" O5  NAG A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -59.41 -118.78     1      3.00e+01 1.11e-03 1.58e+01
  dihedral pdb=" C3  NAG A 901 "
           pdb=" C1  NAG A 901 "
           pdb=" C2  NAG A 901 "
           pdb=" O5  NAG A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.55   62.55 -118.10     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" C2  NAG A 901 "
           pdb=" C1  NAG A 901 "
           pdb=" O5  NAG A 901 "
           pdb=" C5  NAG A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   39.16 -102.12     1      3.00e+01 1.11e-03 1.29e+01
  ... (remaining 3637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 810
       0.060 -    0.120: 142
       0.120 -    0.180: 17
       0.180 -    0.240: 4
       0.240 -    0.299: 2
  Chirality restraints: 975
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-02 2.50e+03 9.23e+01
  chirality pdb=" C1  NAG B 901 "
            pdb=" ND2 ASN B  75 "
            pdb=" C2  NAG B 901 "
            pdb=" O5  NAG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 276 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 972 not shown)

  Planarity restraints: 1044
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.347 2.00e-02 2.50e+03   3.00e-01 1.12e+03
        pdb=" C7  NAG C   1 "   -0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.098 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.533 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.170 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 901 "   -0.207 2.00e-02 2.50e+03   1.71e-01 3.67e+02
        pdb=" C7  NAG A 901 "    0.057 2.00e-02 2.50e+03
        pdb=" C8  NAG A 901 "   -0.149 2.00e-02 2.50e+03
        pdb=" N2  NAG A 901 "    0.279 2.00e-02 2.50e+03
        pdb=" O7  NAG A 901 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG J  59 "   -0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO J  60 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO J  60 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO J  60 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1041 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 971
        2.77 -     3.30: 5360
        3.30 -     3.83: 9103
        3.83 -     4.37: 10273
        4.37 -     4.90: 18574
  Nonbonded interactions: 44281
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  73 "
            pdb=" O6  NAG B 901 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OD1 ASP B 347 "
            pdb=" OG  SER B 349 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   LYS B 188 "
            pdb=" CG1 VAL B 191 "
     model   vdw
     2.319 3.460
  nonbonded pdb=" O   MET B 133 "
            pdb=" NE2 GLN B 146 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   GLN K  37 "
            pdb=" ND1 HIS K 100 "
     model   vdw
     2.347 3.120
  ... (remaining 44276 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             10.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.700
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:5.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
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      :  0.010   0.677   6060  Z= 0.488
  Angle     :  0.892  48.238   8272  Z= 0.464
  Chirality :  0.049   0.299    975
  Planarity :  0.012   0.300   1039
  Dihedral  : 13.342 118.777   2182
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  9.95 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -1.03 (0.31), residues: 765
  helix:  1.38 (0.41), residues: 176
  sheet: -0.44 (0.37), residues: 219
  loop : -1.91 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 244 
 TYR   0.009   0.001   TYR B 180 
 PHE   0.011   0.001   PHE A  42 
 TRP   0.008   0.001   TRP J 130 
 HIS   0.003   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6050)
  covalent geometry    : angle       0.63371 ( 8246)
  SS BOND              : bond        0.33876 (    4)
  SS BOND              : angle      19.23398 (    8)
  hydrogen bonds       : bond        0.22903 (  222)
  hydrogen bonds       : angle       7.42265 (  621)
  link_BETA1-4         : bond        0.01381 (    1)
  link_BETA1-4         : angle       2.66635 (    3)
  link_NAG-ASN         : bond        0.00670 (    5)
  link_NAG-ASN         : angle       4.38649 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  251 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.2962 (m-10)
REVERT: B  286 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6897 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 105
  average time/residue: 0.5385
  time to fit residues: 58.6599
Evaluate side-chains
  70 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain J residue  105 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 134 HIS
A 311 ASN
B 358 HIS
J  58 GLN
J 132 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.081757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.069253 restraints weight = 21283.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 3.68
r_work: 0.3364 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6060  Z= 0.163
  Angle     :  0.698  12.176   8272  Z= 0.349
  Chirality :  0.048   0.362    975
  Planarity :  0.005   0.068   1039
  Dihedral  :  9.740 103.792    958
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 15.75 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.71 (0.31), residues: 765
  helix:  1.47 (0.39), residues: 191
  sheet: -0.13 (0.37), residues: 220
  loop : -1.83 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 244 
 TYR   0.010   0.001   TYR K  51 
 PHE   0.012   0.001   PHE A 102 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.004   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6050)
  covalent geometry    : angle       0.66387 ( 8246)
  SS BOND              : bond        0.00667 (    4)
  SS BOND              : angle       1.79791 (    8)
  hydrogen bonds       : bond        0.05209 (  222)
  hydrogen bonds       : angle       5.52341 (  621)
  link_BETA1-4         : bond        0.00381 (    1)
  link_BETA1-4         : angle       1.20191 (    3)
  link_NAG-ASN         : bond        0.00704 (    5)
  link_NAG-ASN         : angle       4.96685 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  297 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8160 (mp0)
REVERT: B  251 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.2551 (m-10)
REVERT: B  286 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7945 (t80)
REVERT: J   78 ASN cc_start: 0.8248 (m-40) cc_final: 0.7961 (m-40)
  outliers start: 25
  outliers final: 8
  residues processed: 89
  average time/residue: 0.4947
  time to fit residues: 46.0427
Evaluate side-chains
  73 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   58 GLN
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  123 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0870
   chunk 56 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.1962

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

Flipped N/Q/H residues before XYZ refinement:
J  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.080867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.068209 restraints weight = 20594.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 3.68
r_work: 0.3340 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6060  Z= 0.159
  Angle     :  0.634  12.026   8272  Z= 0.323
  Chirality :  0.046   0.287    975
  Planarity :  0.005   0.055   1039
  Dihedral  :  9.134 100.103    958
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.24 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.65 (0.31), residues: 765
  helix:  1.47 (0.39), residues: 191
  sheet:  0.05 (0.37), residues: 218
  loop : -1.87 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  52 
 TYR   0.008   0.001   TYR K  51 
 PHE   0.010   0.001   PHE A  42 
 TRP   0.009   0.001   TRP J 130 
 HIS   0.004   0.001   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6050)
  covalent geometry    : angle       0.60471 ( 8246)
  SS BOND              : bond        0.00577 (    4)
  SS BOND              : angle       1.18275 (    8)
  hydrogen bonds       : bond        0.04772 (  222)
  hydrogen bonds       : angle       5.08989 (  621)
  link_BETA1-4         : bond        0.00834 (    1)
  link_BETA1-4         : angle       0.48165 (    3)
  link_NAG-ASN         : bond        0.00581 (    5)
  link_NAG-ASN         : angle       4.44970 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8725 (mp)
REVERT: A  297 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8206 (mp0)
REVERT: B   48 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8485 (tm-30)
REVERT: B  251 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.2427 (m-10)
REVERT: B  286 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.7680 (t80)
REVERT: J   78 ASN cc_start: 0.8240 (m-40) cc_final: 0.7951 (m-40)
REVERT: J  100 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7841 (tpt)
REVERT: K   99 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8494 (pp)
  outliers start: 22
  outliers final: 7
  residues processed: 82
  average time/residue: 0.4394
  time to fit residues: 37.8015
Evaluate side-chains
  73 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue  100 MET
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  123 ILE
Chi-restraints excluded: chain J residue  135 LEU
Chi-restraints excluded: chain K residue   99 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0570
   chunk 67 optimal weight:    0.0570
   chunk 71 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.4416

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.081642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.069108 restraints weight = 20716.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 3.69
r_work: 0.3359 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6060  Z= 0.105
  Angle     :  0.588  11.947   8272  Z= 0.295
  Chirality :  0.045   0.291    975
  Planarity :  0.004   0.062   1039
  Dihedral  :  8.601  95.928    958
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.57 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.40 (0.31), residues: 765
  helix:  1.72 (0.40), residues: 191
  sheet:  0.27 (0.36), residues: 217
  loop : -1.80 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  52 
 TYR   0.008   0.001   TYR B 180 
 PHE   0.008   0.001   PHE A  42 
 TRP   0.008   0.001   TRP J 130 
 HIS   0.003   0.000   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6050)
  covalent geometry    : angle       0.55850 ( 8246)
  SS BOND              : bond        0.00390 (    4)
  SS BOND              : angle       1.13571 (    8)
  hydrogen bonds       : bond        0.03542 (  222)
  hydrogen bonds       : angle       4.76626 (  621)
  link_BETA1-4         : bond        0.00841 (    1)
  link_BETA1-4         : angle       0.54523 (    3)
  link_NAG-ASN         : bond        0.00675 (    5)
  link_NAG-ASN         : angle       4.26181 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6346 (m-40)
REVERT: A   73 GLN cc_start: 0.8572 (mp10) cc_final: 0.8365 (mp10)
REVERT: A   79 CYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (t)
REVERT: A  297 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8185 (mp0)
REVERT: B  251 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.2615 (m-80)
REVERT: B  286 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7694 (t80)
REVERT: B  379 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8676 (tm-30)
REVERT: J   78 ASN cc_start: 0.8238 (m-40) cc_final: 0.8000 (m-40)
REVERT: K   50 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8400 (mp0)
REVERT: K   99 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8438 (pp)
  outliers start: 19
  outliers final: 9
  residues processed: 85
  average time/residue: 0.4144
  time to fit residues: 37.0112
Evaluate side-chains
  76 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  312 TYR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  135 LEU
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   99 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0000
   chunk 61 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0170
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.2028

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.080226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.067688 restraints weight = 20921.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 3.68
r_work: 0.3328 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6060  Z= 0.163
  Angle     :  0.626  11.334   8272  Z= 0.317
  Chirality :  0.046   0.294    975
  Planarity :  0.005   0.059   1039
  Dihedral  :  8.454  93.171    958
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 18.74 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.37 (0.31), residues: 765
  helix:  1.65 (0.40), residues: 191
  sheet:  0.30 (0.37), residues: 219
  loop : -1.74 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.025   0.001   TYR B 312 
 PHE   0.011   0.001   PHE A  42 
 TRP   0.007   0.001   TRP B 198 
 HIS   0.004   0.001   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 6050)
  covalent geometry    : angle       0.60038 ( 8246)
  SS BOND              : bond        0.00655 (    4)
  SS BOND              : angle       1.14948 (    8)
  hydrogen bonds       : bond        0.04420 (  222)
  hydrogen bonds       : angle       4.74756 (  621)
  link_BETA1-4         : bond        0.00601 (    1)
  link_BETA1-4         : angle       0.47500 (    3)
  link_NAG-ASN         : bond        0.00598 (    5)
  link_NAG-ASN         : angle       4.15081 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   48 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8382 (tm-30)
REVERT: B  251 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.2445 (m-10)
REVERT: B  286 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8079 (t80)
REVERT: B  360 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8305 (mtm-85)
REVERT: B  379 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: J   78 ASN cc_start: 0.8245 (m-40) cc_final: 0.7998 (m-40)
REVERT: J  100 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7904 (tpt)
REVERT: K   50 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8394 (mp0)
REVERT: K   66 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7677 (mm-40)
REVERT: K   99 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8479 (pp)
  outliers start: 26
  outliers final: 11
  residues processed: 82
  average time/residue: 0.5421
  time to fit residues: 46.3389
Evaluate side-chains
  74 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  202 ASN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  360 ARG
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue  100 MET
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  135 LEU
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   99 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 59 optimal weight:    0.2980
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.079554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.067048 restraints weight = 20793.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 3.65
r_work: 0.3316 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6060  Z= 0.159
  Angle     :  0.627  11.168   8272  Z= 0.319
  Chirality :  0.046   0.288    975
  Planarity :  0.005   0.063   1039
  Dihedral  :  8.297  90.460    958
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 18.41 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.37 (0.31), residues: 765
  helix:  1.57 (0.40), residues: 191
  sheet:  0.36 (0.37), residues: 219
  loop : -1.72 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  52 
 TYR   0.008   0.001   TYR B 165 
 PHE   0.016   0.001   PHE A 102 
 TRP   0.007   0.001   TRP J  66 
 HIS   0.004   0.001   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6050)
  covalent geometry    : angle       0.60234 ( 8246)
  SS BOND              : bond        0.00476 (    4)
  SS BOND              : angle       1.17308 (    8)
  hydrogen bonds       : bond        0.04435 (  222)
  hydrogen bonds       : angle       4.74644 (  621)
  link_BETA1-4         : bond        0.00778 (    1)
  link_BETA1-4         : angle       0.47329 (    3)
  link_NAG-ASN         : bond        0.00563 (    5)
  link_NAG-ASN         : angle       4.03928 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 60
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7975 (mm-30)
REVERT: B  251 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.2393 (m-10)
REVERT: B  286 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8097 (t80)
REVERT: B  360 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8289 (mtm-85)
REVERT: B  379 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: J   78 ASN cc_start: 0.8241 (m-40) cc_final: 0.7975 (m-40)
REVERT: J  100 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.7900 (tpt)
REVERT: K   50 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8450 (mp0)
REVERT: K   99 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8466 (pp)
  outliers start: 29
  outliers final: 12
  residues processed: 86
  average time/residue: 0.4382
  time to fit residues: 39.5941
Evaluate side-chains
  74 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  202 ASN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  360 ARG
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue  100 MET
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  135 LEU
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   99 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0970
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.080356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.067852 restraints weight = 20998.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.70
r_work: 0.3337 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6060  Z= 0.115
  Angle     :  0.624  11.115   8272  Z= 0.312
  Chirality :  0.045   0.291    975
  Planarity :  0.004   0.061   1039
  Dihedral  :  7.959  87.753    958
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.07 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.24 (0.31), residues: 765
  helix:  1.70 (0.41), residues: 191
  sheet:  0.45 (0.37), residues: 219
  loop : -1.68 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  52 
 TYR   0.008   0.001   TYR B 180 
 PHE   0.009   0.001   PHE A  42 
 TRP   0.008   0.001   TRP B 198 
 HIS   0.004   0.001   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6050)
  covalent geometry    : angle       0.60031 ( 8246)
  SS BOND              : bond        0.00385 (    4)
  SS BOND              : angle       1.01905 (    8)
  hydrogen bonds       : bond        0.03648 (  222)
  hydrogen bonds       : angle       4.53838 (  621)
  link_BETA1-4         : bond        0.00801 (    1)
  link_BETA1-4         : angle       0.50371 (    3)
  link_NAG-ASN         : bond        0.00628 (    5)
  link_NAG-ASN         : angle       3.99879 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   48 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8490 (tm-30)
REVERT: B  251 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.2543 (m-80)
REVERT: B  286 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8085 (t80)
REVERT: B  360 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8265 (mtm-85)
REVERT: B  379 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: J   78 ASN cc_start: 0.8208 (m-40) cc_final: 0.7988 (m-40)
REVERT: J  100 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8012 (tpt)
REVERT: K   66 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7649 (mm-40)
REVERT: K   99 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8456 (pp)
  outliers start: 21
  outliers final: 12
  residues processed: 77
  average time/residue: 0.5382
  time to fit residues: 43.2628
Evaluate side-chains
  73 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain B residue   74 MET
Chi-restraints excluded: chain B residue  171 SER
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  360 ARG
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue  100 MET
Chi-restraints excluded: chain J residue  105 LEU
Chi-restraints excluded: chain J residue  135 LEU
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   99 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   chunk 3 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
J 132 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.079414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.066993 restraints weight = 20809.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 3.63
r_work: 0.3316 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6060  Z= 0.146
  Angle     :  0.637  10.764   8272  Z= 0.322
  Chirality :  0.046   0.292    975
  Planarity :  0.005   0.063   1039
  Dihedral  :  7.837  84.664    958
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.56 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.26 (0.31), residues: 765
  helix:  1.64 (0.40), residues: 191
  sheet:  0.45 (0.37), residues: 220
  loop : -1.67 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  52 
 TYR   0.007   0.001   TYR B 165 
 PHE   0.015   0.001   PHE A 102 
 TRP   0.006   0.001   TRP J  66 
 HIS   0.003   0.001   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6050)
  covalent geometry    : angle       0.61500 ( 8246)
  SS BOND              : bond        0.00449 (    4)
  SS BOND              : angle       1.10140 (    8)
  hydrogen bonds       : bond        0.04175 (  222)
  hydrogen bonds       : angle       4.58510 (  621)
  link_BETA1-4         : bond        0.00750 (    1)
  link_BETA1-4         : angle       0.49455 (    3)
  link_NAG-ASN         : bond        0.00571 (    5)
  link_NAG-ASN         : angle       3.91740 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  251 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.2394 (m-10)
REVERT: B  286 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8095 (t80)
REVERT: B  360 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8247 (mtm-85)
REVERT: B  379 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: J   78 ASN cc_start: 0.8194 (m-40) cc_final: 0.7987 (m-40)
REVERT: J  100 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7919 (tpt)
REVERT: K   50 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8425 (mp0)
REVERT: K   66 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7568 (mm-40)
REVERT: K   99 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8471 (pp)
  outliers start: 19
  outliers final: 12
  residues processed: 77
  average time/residue: 0.4248
  time to fit residues: 34.3754
Evaluate side-chains
  74 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain B residue   74 MET
Chi-restraints excluded: chain B residue  171 SER
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  202 ASN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  360 ARG
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue  100 MET
Chi-restraints excluded: chain J residue  135 LEU
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   99 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 40 optimal weight:    0.1980
   chunk 63 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.079029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.066600 restraints weight = 21025.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 3.64
r_work: 0.3305 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6060  Z= 0.165
  Angle     :  0.668  10.437   8272  Z= 0.336
  Chirality :  0.046   0.295    975
  Planarity :  0.005   0.062   1039
  Dihedral  :  7.643  81.448    956
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.06 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.19 (0.31), residues: 765
  helix:  1.84 (0.41), residues: 184
  sheet:  0.40 (0.37), residues: 221
  loop : -1.57 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  52 
 TYR   0.009   0.001   TYR B 165 
 PHE   0.011   0.001   PHE A  42 
 TRP   0.007   0.001   TRP J  66 
 HIS   0.004   0.001   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6050)
  covalent geometry    : angle       0.64679 ( 8246)
  SS BOND              : bond        0.00489 (    4)
  SS BOND              : angle       1.19846 (    8)
  hydrogen bonds       : bond        0.04471 (  222)
  hydrogen bonds       : angle       4.64609 (  621)
  link_BETA1-4         : bond        0.00901 (    1)
  link_BETA1-4         : angle       0.50711 (    3)
  link_NAG-ASN         : bond        0.00549 (    5)
  link_NAG-ASN         : angle       3.86850 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  251 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.2380 (m-10)
REVERT: B  286 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8098 (t80)
REVERT: B  360 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8239 (mtm-85)
REVERT: J   78 ASN cc_start: 0.8206 (m-40) cc_final: 0.8002 (m-40)
REVERT: J  100 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.7876 (tpt)
REVERT: K   50 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8442 (mp0)
REVERT: K   66 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7660 (mm-40)
REVERT: K   99 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8494 (pp)
  outliers start: 21
  outliers final: 11
  residues processed: 78
  average time/residue: 0.5248
  time to fit residues: 42.7657
Evaluate side-chains
  73 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  171 SER
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  202 ASN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  360 ARG
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue  100 MET
Chi-restraints excluded: chain J residue  135 LEU
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   99 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.078753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.066381 restraints weight = 21082.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 3.64
r_work: 0.3307 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6060  Z= 0.155
  Angle     :  0.689  10.445   8272  Z= 0.348
  Chirality :  0.046   0.293    975
  Planarity :  0.005   0.063   1039
  Dihedral  :  7.523  79.553    956
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.23 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.16 (0.31), residues: 765
  helix:  1.86 (0.41), residues: 184
  sheet:  0.42 (0.37), residues: 221
  loop : -1.55 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  52 
 TYR   0.008   0.001   TYR B 165 
 PHE   0.016   0.001   PHE A 102 
 TRP   0.007   0.001   TRP J  66 
 HIS   0.004   0.001   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6050)
  covalent geometry    : angle       0.66950 ( 8246)
  SS BOND              : bond        0.00466 (    4)
  SS BOND              : angle       1.14598 (    8)
  hydrogen bonds       : bond        0.04281 (  222)
  hydrogen bonds       : angle       4.62529 (  621)
  link_BETA1-4         : bond        0.00789 (    1)
  link_BETA1-4         : angle       0.44830 (    3)
  link_NAG-ASN         : bond        0.00539 (    5)
  link_NAG-ASN         : angle       3.86194 (   15)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  251 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.2372 (m-10)
REVERT: B  286 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8101 (t80)
REVERT: B  360 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8251 (mtm-85)
REVERT: J  100 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.7919 (tpt)
REVERT: K   50 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8424 (mp0)
REVERT: K   66 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7687 (mm-40)
REVERT: K   99 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8451 (pp)
  outliers start: 19
  outliers final: 13
  residues processed: 78
  average time/residue: 0.5595
  time to fit residues: 45.6415
Evaluate side-chains
  78 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  171 SER
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  202 ASN
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  360 ARG
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue  100 MET
Chi-restraints excluded: chain J residue  135 LEU
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   99 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0050
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.079400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.067026 restraints weight = 20792.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.67
r_work: 0.3321 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6060  Z= 0.129
  Angle     :  0.662  10.394   8272  Z= 0.331
  Chirality :  0.045   0.296    975
  Planarity :  0.005   0.062   1039
  Dihedral  :  7.337  77.597    956
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.89 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 are not related in a simple way.
  whole: -0.11 (0.31), residues: 765
  helix:  1.91 (0.41), residues: 184
  sheet:  0.54 (0.37), residues: 216
  loop : -1.57 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  52 
 TYR   0.007   0.001   TYR B 180 
 PHE   0.010   0.001   PHE A  42 
 TRP   0.012   0.001   TRP B 198 
 HIS   0.004   0.001   HIS J  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6050)
  covalent geometry    : angle       0.64095 ( 8246)
  SS BOND              : bond        0.00410 (    4)
  SS BOND              : angle       1.04131 (    8)
  hydrogen bonds       : bond        0.03807 (  222)
  hydrogen bonds       : angle       4.51673 (  621)
  link_BETA1-4         : bond        0.00821 (    1)
  link_BETA1-4         : angle       0.48450 (    3)
  link_NAG-ASN         : bond        0.00579 (    5)
  link_NAG-ASN         : angle       3.85580 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2042.70 seconds
wall clock time: 35 minutes 29.29 seconds (2129.29 seconds total)