Starting phenix.real_space_refine
on Sat Dec 28 12:49:57 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wfs_37498/12_2024/8wfs_37498.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wfs_37498/12_2024/8wfs_37498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wfs_37498/12_2024/8wfs_37498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wfs_37498/12_2024/8wfs_37498.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wfs_37498/12_2024/8wfs_37498.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wfs_37498/12_2024/8wfs_37498.cif"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2864 atoms to isotropic.
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      54      5.16       5
     C    3973      2.51       5
     N    1123      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 6274
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "c"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 884
          Classifications: {'peptide': 118}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 882
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 117, 877
          Classifications: {'peptide': 117}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 102}
      Conformer: "B"
        Number of residues, atoms: 117, 877
          Classifications: {'peptide': 117}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 102}
          bond proxies already assigned to first conformer: 894
    Chain: "E"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 957
          Classifications: {'peptide': 125}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 113}
    Chain: "B"
      Number of atoms: 1035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1035
          Classifications: {'peptide': 140}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 123}
    Chain: "b"
      Number of atoms: 1035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1035
          Classifications: {'peptide': 140}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 123}
    Chain: "X"
      Number of atoms: 1112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1112
          Classifications: {'peptide': 146}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 133}
    Chain: "a"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 179
          Classifications: {'peptide': 22}
          Link IDs: {'PTRANS': 1, 'TRANS': 20}
    Chain: "A"
      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: "D"
      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: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "H"
      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: "I"
      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
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AALA C 114 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA C 114 " occ=0.50
  Time building chain proxies: 5.16, per 1000 atoms: 0.82
  Number of scatterers: 6274
  At special positions: 0
  Unit cell: (83.7876, 97.7522, 134.275, 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      54     16.00
     O    1124      8.00
     N    1123      7.00
     C    3973      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=26, symmetry=0
    Simple disulfide: pdb=" SG  CYS c   1 " - pdb=" SG  CYS c   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS c   5 " - pdb=" SG  CYS c  14 " distance=2.03
    Simple disulfide: pdb=" SG  CYS c  68 " - pdb=" SG  CYS c  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS c  70 " - pdb=" SG  CYS c 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   1 " - pdb=" SG  CYS C   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   5 " - pdb=" SG  CYS C  14 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  68 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  70 " - pdb=" SG  CYS C 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   4 " - pdb=" SG  CYS E  10 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   8 " - pdb=" SG  CYS E  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  73 " - pdb=" SG  CYS E  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  75 " - pdb=" SG  CYS E 119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   1 " - pdb=" SG  CYS B   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   5 " - pdb=" SG  CYS B  14 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  68 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  70 " - pdb=" SG  CYS B 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 122 " - pdb=" SG  CYS a 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b   1 " - pdb=" SG  CYS b   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b   5 " - pdb=" SG  CYS b  14 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  68 " - pdb=" SG  CYS b  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  70 " - pdb=" SG  CYS b 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 122 " - pdb=" SG  CYS a 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X   4 " - pdb=" SG  CYS X  10 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X   8 " - pdb=" SG  CYS X  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X  73 " - pdb=" SG  CYS X  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X  75 " - pdb=" SG  CYS X 119 " 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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
    NAG-ASN
      " NAG A   1 " - " ASN c  41 "
      " NAG D   1 " - " ASN C  41 "
      " NAG F   1 " - " ASN E  44 "
      " NAG G   1 " - " ASN B  41 "
      " NAG H   1 " - " ASN b  41 "
      " NAG I   1 " - " ASN X  44 "
  Time building additional restraints: 1.78
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 11 sheets defined
      31.2% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'c' and resid 49 through 53
      removed outlier: 3.545A  pdb=" N   ALA c  52 " --> pdb=" O   LEU c  49 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 69 through 71
      No H-bonds generated for 'chain 'c' and resid 69 through 71'
    Processing helix  chain 'c' and resid 72 through 81
      removed outlier: 4.190A  pdb=" N   GLY c  81 " --> pdb=" O   ALA c  77 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 85 through 89
      removed outlier: 3.541A  pdb=" N   TYR c  88 " --> pdb=" O   ARG c  85 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG c  89 " --> pdb=" O   ALA c  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'c' and resid 85 through 89'
    Processing helix  chain 'c' and resid 96 through 100
      removed outlier: 3.662A  pdb=" N   ARG c 100 " --> pdb=" O   PRO c  97 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 108 through 115
    Processing helix  chain 'C' and resid 69 through 71
      No H-bonds generated for 'chain 'C' and resid 69 through 71'
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 96 through 100
      removed outlier: 3.651A  pdb=" N   ARG C 100 " --> pdb=" O   PRO C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 107
    Processing helix  chain 'C' and resid 108 through 115
      removed outlier: 3.754A  pdb=" N   LEU C 112 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA C 115 " --> pdb=" O   GLU C 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 77 through 85
    Processing helix  chain 'E' and resid 88 through 95
      removed outlier: 4.089A  pdb=" N   VAL E  95 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 71
      No H-bonds generated for 'chain 'B' and resid 69 through 71'
    Processing helix  chain 'B' and resid 72 through 80
      removed outlier: 3.594A  pdb=" N   ALA B  80 " --> pdb=" O   ARG B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 89
      removed outlier: 3.524A  pdb=" N   TYR B  88 " --> pdb=" O   ARG B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 100
      removed outlier: 3.589A  pdb=" N   ARG B 100 " --> pdb=" O   PRO B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 107
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 4.135A  pdb=" N   ALA B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 140
      removed outlier: 3.829A  pdb=" N   GLN B 129 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ALA B 131 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 49 through 53
      removed outlier: 3.908A  pdb=" N   LEU b  53 " --> pdb=" O   LEU b  50 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 69 through 71
      No H-bonds generated for 'chain 'b' and resid 69 through 71'
    Processing helix  chain 'b' and resid 72 through 81
      removed outlier: 3.505A  pdb=" N   GLY b  81 " --> pdb=" O   ALA b  77 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 96 through 100
      removed outlier: 3.551A  pdb=" N   ARG b 100 " --> pdb=" O   PRO b  97 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 103 through 107
    Processing helix  chain 'b' and resid 108 through 116
      removed outlier: 3.798A  pdb=" N   LEU b 112 " --> pdb=" O   ALA b 108 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   CYS b 116 " --> pdb=" O   LEU b 112 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 125 through 140
    Processing helix  chain 'X' and resid 74 through 76
      No H-bonds generated for 'chain 'X' and resid 74 through 76'
    Processing helix  chain 'X' and resid 77 through 88
    Processing helix  chain 'X' and resid 89 through 94
    Processing helix  chain 'X' and resid 130 through 146
      removed outlier: 3.662A  pdb=" N   ALA X 137 " --> pdb=" O   LEU X 133 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLY X 145 " --> pdb=" O   VAL X 141 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU X 146 " --> pdb=" O   ALA X 142 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 483 through 503
      removed outlier: 3.688A  pdb=" N   LEU a 487 " --> pdb=" O   PHE a 483 " (cutoff:3.500A)
      Proline residue:  a 488  - end of helix
      removed outlier: 4.359A  pdb=" N   PHE a 491 " --> pdb=" O   LEU a 487 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL a 493 " --> pdb=" O   LEU a 489 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'c' and resid 6 through 8
    Processing sheet with id=AA2, first strand: chain 'c' and resid 66 through 67
      removed outlier: 7.480A  pdb=" N   TRP c  66 " --> pdb=" O   VAL c  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 8
      removed outlier: 3.658A  pdb=" N   VAL C  36 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 67
      removed outlier: 7.132A  pdb=" N   TRP C  66 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 9 through 13
      removed outlier: 3.660A  pdb=" N   GLY E  17 " --> pdb=" O   LEU E  13 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   LEU E  18 " --> pdb=" O   HIS E  39 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU E  41 " --> pdb=" O   LEU E  18 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL E  20 " --> pdb=" O   LEU E  41 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   LEU E  40 " --> pdb=" O   ASP E  65 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 71 through 72
      removed outlier: 7.077A  pdb=" N   TRP E  71 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 8
      removed outlier: 6.827A  pdb=" N   LEU B  35 " --> pdb=" O   HIS B  60 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'b' and resid 6 through 8
      removed outlier: 3.522A  pdb=" N   VAL b  36 " --> pdb=" O   VAL b  12 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   LEU b  35 " --> pdb=" O   HIS b  60 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'b' and resid 66 through 67
      removed outlier: 7.041A  pdb=" N   TRP b  66 " --> pdb=" O   VAL b  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'X' and resid 9 through 13
      removed outlier: 6.947A  pdb=" N   LEU X  18 " --> pdb=" O   ARG X  38 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   LEU X  40 " --> pdb=" O   LEU X  18 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL X  20 " --> pdb=" O   LEU X  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'X' and resid 71 through 72
      removed outlier: 6.640A  pdb=" N   TRP X  71 " --> pdb=" O   ALA X  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    149 hydrogen bonds defined for protein.
    351 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: 1.44

  Time building geometry restraints manager: 2.00 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: 2060
        1.34 -     1.47: 1427
        1.47 -     1.59: 2898
        1.59 -     1.71: 1
        1.71 -     1.83: 56
  Bond restraints: 6442
  Sorted by residual:
  bond pdb=" CB  PRO c  29 "
       pdb=" CG  PRO c  29 "
    ideal  model  delta    sigma   weight residual
    1.492  1.651 -0.159 5.00e-02 4.00e+02 1.01e+01
  bond pdb=" CB  PRO C   2 "
       pdb=" CG  PRO C   2 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.54e+00
  bond pdb=" C   ALA B  86 "
       pdb=" N   PRO B  87 "
    ideal  model  delta    sigma   weight residual
    1.334  1.347 -0.013 8.40e-03 1.42e+04 2.38e+00
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.548 -0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" CG  PRO C   2 "
       pdb=" CD  PRO C   2 "
    ideal  model  delta    sigma   weight residual
    1.503  1.551 -0.048 3.40e-02 8.65e+02 1.95e+00
  ... (remaining 6437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 8639
        2.61 -     5.22: 181
        5.22 -     7.83: 18
        7.83 -    10.45: 9
       10.45 -    13.06: 1
  Bond angle restraints: 8848
  Sorted by residual:
  angle pdb=" CA  PRO c  29 "
        pdb=" N   PRO c  29 "
        pdb=" CD  PRO c  29 "
      ideal   model   delta    sigma   weight residual
     112.00   98.94   13.06 1.40e+00 5.10e-01 8.70e+01
  angle pdb=" N   GLY b 124 "
        pdb=" CA  GLY b 124 "
        pdb=" C   GLY b 124 "
      ideal   model   delta    sigma   weight residual
     115.66  105.40   10.26 1.56e+00 4.11e-01 4.33e+01
  angle pdb=" CA  PRO C   2 "
        pdb=" N   PRO C   2 "
        pdb=" CD  PRO C   2 "
      ideal   model   delta    sigma   weight residual
     112.00  106.47    5.53 1.40e+00 5.10e-01 1.56e+01
  angle pdb=" N   PRO c  29 "
        pdb=" CD  PRO c  29 "
        pdb=" CG  PRO c  29 "
      ideal   model   delta    sigma   weight residual
     103.20   98.14    5.06 1.50e+00 4.44e-01 1.14e+01
  angle pdb=" N   PRO c  29 "
        pdb=" CA  PRO c  29 "
        pdb=" C   PRO c  29 "
      ideal   model   delta    sigma   weight residual
     111.68  116.99   -5.31 1.67e+00 3.59e-01 1.01e+01
  ... (remaining 8843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.26: 3602
       22.26 -    44.52: 419
       44.52 -    66.78: 71
       66.78 -    89.03: 20
       89.03 -   111.29: 16
  Dihedral angle restraints: 4128
    sinusoidal: 1818
      harmonic: 2310
  Sorted by residual:
  dihedral pdb=" CB  CYS X  73 "
           pdb=" SG  CYS X  73 "
           pdb=" SG  CYS X  97 "
           pdb=" CB  CYS X  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   14.03   78.97     1      1.00e+01 1.00e-02 7.76e+01
  dihedral pdb=" CB  CYS b 122 "
           pdb=" SG  CYS b 122 "
           pdb=" SG  CYS a 485 "
           pdb=" CB  CYS a 485 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.92  -78.92     1      1.00e+01 1.00e-02 7.76e+01
  dihedral pdb=" CB  CYS B 122 "
           pdb=" SG  CYS B 122 "
           pdb=" SG  CYS a 484 "
           pdb=" CB  CYS a 484 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.07  -75.07     1      1.00e+01 1.00e-02 7.13e+01
  ... (remaining 4125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 870
       0.056 -    0.111: 160
       0.111 -    0.167: 22
       0.167 -    0.223: 3
       0.223 -    0.278: 5
  Chirality restraints: 1060
  Sorted by residual:
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  PRO c  29 "
            pdb=" N   PRO c  29 "
            pdb=" C   PRO c  29 "
            pdb=" CB  PRO c  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 1057 not shown)

  Planarity restraints: 1135
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE c  28 "    0.089 5.00e-02 4.00e+02   1.24e-01 2.47e+01
        pdb=" N   PRO c  29 "   -0.214 5.00e-02 4.00e+02
        pdb=" CA  PRO c  29 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO c  29 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C   1 "   -0.059 5.00e-02 4.00e+02   8.78e-02 1.23e+01
        pdb=" N   PRO C   2 "    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO C   2 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C   2 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO X  51 "   -0.053 5.00e-02 4.00e+02   8.04e-02 1.04e+01
        pdb=" N   PRO X  52 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO X  52 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO X  52 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1132 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1511
        2.79 -     3.32: 5736
        3.32 -     3.84: 10220
        3.84 -     4.37: 11281
        4.37 -     4.90: 19207
  Nonbonded interactions: 47955
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG c 102 "
            pdb=" OE2 GLU c 111 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NH1 ARG c  67 "
            pdb=" OD2 ASP c  69 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   SER X 126 "
            pdb=" OG  SER X 126 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" NH1 ARG C  89 "
            pdb=" OD1 ASP E  86 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   CYS b 122 "
            pdb=" N   GLY b 124 "
     model   vdw
     2.330 3.120
  ... (remaining 47950 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'b'
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 113 or resid 115 through 117))
  selection = (chain 'c' and (resid 1 through 113 or resid 115 through 117))
}
ncs_group {
  reference = chain 'E'
  selection = (chain 'X' and resid 1 through 125)
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.180
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
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      :  0.005   0.159   6442  Z= 0.293
  Angle     :  0.866  13.057   8848  Z= 0.414
  Chirality :  0.048   0.278   1060
  Planarity :  0.008   0.124   1129
  Dihedral  : 19.138 111.292   2556
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 32.97 %
    Favored  : 66.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.29), residues: 797
  helix: -1.26 (0.39), residues: 161
  sheet: -1.45 (0.69), residues: 68
  loop : -1.15 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP b 123 
 HIS   0.002   0.001   HIS E  72 
 PHE   0.008   0.001   PHE c  28 
 TYR   0.032   0.002   TYR a 492 
 ARG   0.008   0.001   ARG b  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: b  113 ARG cc_start: 0.7548 (mtp85) cc_final: 0.7257 (mtp85)
  outliers start: 6
  outliers final: 2
  residues processed: 134
  average time/residue: 0.3919
  time to fit residues: 60.1977
Evaluate side-chains
  132 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0020
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
c  64 ASN
** C  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 115 GLN
B  64 ASN
b  40 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.0786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6442  Z= 0.278
  Angle     :  0.802   9.761   8848  Z= 0.367
  Chirality :  0.046   0.179   1060
  Planarity :  0.006   0.064   1129
  Dihedral  : 12.657  87.122   1177
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 30.14 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.30), residues: 797
  helix: -0.25 (0.41), residues: 165
  sheet: -1.48 (0.68), residues: 68
  loop : -1.10 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP b 123 
 HIS   0.003   0.001   HIS c  60 
 PHE   0.005   0.001   PHE X  55 
 TYR   0.035   0.002   TYR a 492 
 ARG   0.010   0.001   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   21 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.6473 (t70)
REVERT: E   36 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7118 (ptt90)
REVERT: b   76 ARG cc_start: 0.7969 (tpt90) cc_final: 0.7754 (tmt170)
REVERT: b  113 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7331 (mtp85)
REVERT: b  138 LEU cc_start: -0.3155 (OUTLIER) cc_final: -0.3631 (tp)
REVERT: X   62 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7472 (pt0)
  outliers start: 23
  outliers final: 7
  residues processed: 147
  average time/residue: 0.3687
  time to fit residues: 62.5141
Evaluate side-chains
  138 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   36 ARG
Chi-restraints excluded: chain b residue  138 LEU
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  116 LEU
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0770
   chunk 48 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 70 optimal weight:    0.4980
   chunk 76 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
C  40 ASN
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6442  Z= 0.234
  Angle     :  0.754   9.390   8848  Z= 0.344
  Chirality :  0.044   0.213   1060
  Planarity :  0.006   0.056   1129
  Dihedral  :  9.998  73.866   1176
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 28.10 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.30), residues: 797
  helix:  0.07 (0.41), residues: 165
  sheet: -1.58 (0.66), residues: 68
  loop : -1.04 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP b 123 
 HIS   0.002   0.001   HIS B  60 
 PHE   0.004   0.001   PHE a 491 
 TYR   0.029   0.002   TYR a 492 
 ARG   0.012   0.001   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 133
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   21 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6437 (t70)
REVERT: E   95 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7786 (t)
REVERT: b   76 ARG cc_start: 0.7977 (tpt90) cc_final: 0.7764 (tmt170)
REVERT: b  138 LEU cc_start: -0.3529 (OUTLIER) cc_final: -0.3951 (tp)
REVERT: X  124 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6635 (pp30)
  outliers start: 36
  outliers final: 18
  residues processed: 158
  average time/residue: 0.3579
  time to fit residues: 65.5263
Evaluate side-chains
  146 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain b residue  138 LEU
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  116 LEU
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.1980
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 20 optimal weight:    0.3980
   chunk 62 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.3518

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6442  Z= 0.228
  Angle     :  0.752   9.858   8848  Z= 0.341
  Chirality :  0.044   0.220   1060
  Planarity :  0.006   0.051   1129
  Dihedral  :  8.776  63.735   1176
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 29.51 %
    Favored  : 65.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.29), residues: 797
  helix:  0.09 (0.41), residues: 165
  sheet: -1.62 (0.66), residues: 68
  loop : -1.05 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP b 123 
 HIS   0.002   0.001   HIS B  60 
 PHE   0.004   0.001   PHE c  28 
 TYR   0.029   0.002   TYR a 492 
 ARG   0.010   0.000   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   21 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6434 (t70)
REVERT: E   95 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7805 (t)
REVERT: B   17 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.7013 (mtm-85)
REVERT: b   21 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.7751 (t-100)
REVERT: X  124 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6533 (pp30)
  outliers start: 33
  outliers final: 22
  residues processed: 155
  average time/residue: 0.3577
  time to fit residues: 64.2887
Evaluate side-chains
  150 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  116 LEU
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0470
   chunk 67 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6442  Z= 0.286
  Angle     :  0.766   9.594   8848  Z= 0.351
  Chirality :  0.046   0.230   1060
  Planarity :  0.006   0.050   1129
  Dihedral  :  7.913  59.081   1176
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 29.51 %
    Favored  : 64.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.30), residues: 797
  helix:  0.13 (0.42), residues: 159
  sheet: -1.55 (0.67), residues: 68
  loop : -1.10 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP b 123 
 HIS   0.003   0.001   HIS B  60 
 PHE   0.006   0.001   PHE c  28 
 TYR   0.028   0.002   TYR a 492 
 ARG   0.011   0.001   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   95 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7776 (t)
REVERT: b   21 TRP cc_start: 0.8266 (OUTLIER) cc_final: 0.7765 (t-100)
REVERT: X  124 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6538 (pp30)
  outliers start: 36
  outliers final: 23
  residues processed: 148
  average time/residue: 0.3518
  time to fit residues: 60.2702
Evaluate side-chains
  149 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue  112 THR
Chi-restraints excluded: chain X residue  115 GLN
Chi-restraints excluded: chain X residue  116 LEU
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0980
   chunk 75 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0370
   chunk 34 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.3980
   chunk 39 optimal weight:    0.7980
   chunk 72 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0980
   overall best weight:    0.2058

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6442  Z= 0.191
  Angle     :  0.738   9.522   8848  Z= 0.336
  Chirality :  0.043   0.239   1060
  Planarity :  0.006   0.048   1129
  Dihedral  :  7.145  58.432   1175
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 29.04 %
    Favored  : 65.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.30), residues: 797
  helix:  0.23 (0.42), residues: 159
  sheet: -1.53 (0.67), residues: 68
  loop : -1.12 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  78 
 HIS   0.001   0.000   HIS E  72 
 PHE   0.004   0.001   PHE c  28 
 TYR   0.025   0.001   TYR a 492 
 ARG   0.009   0.000   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   21 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6480 (t70)
REVERT: E   95 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7793 (t)
REVERT: B  109 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: b   21 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7759 (t-100)
REVERT: b  113 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6898 (mtp85)
REVERT: X   62 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7573 (pt0)
REVERT: X  124 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6635 (pp30)
  outliers start: 35
  outliers final: 20
  residues processed: 152
  average time/residue: 0.3673
  time to fit residues: 64.5163
Evaluate side-chains
  150 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   18 LEU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 75 optimal weight:    0.7980
   chunk 47 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0870
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** c  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6442  Z= 0.281
  Angle     :  0.771   9.397   8848  Z= 0.351
  Chirality :  0.046   0.274   1060
  Planarity :  0.006   0.048   1129
  Dihedral  :  6.858  57.940   1175
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 28.73 %
    Favored  : 65.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.30), residues: 797
  helix:  0.10 (0.41), residues: 159
  sheet: -1.53 (0.67), residues: 68
  loop : -1.13 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP a 498 
 HIS   0.004   0.001   HIS B 139 
 PHE   0.005   0.001   PHE c  28 
 TYR   0.024   0.002   TYR a 492 
 ARG   0.011   0.001   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   21 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6418 (t70)
REVERT: E   95 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7809 (t)
REVERT: b   21 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.7763 (t-100)
REVERT: X   62 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7572 (pt0)
REVERT: X  124 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6674 (pp30)
  outliers start: 35
  outliers final: 24
  residues processed: 156
  average time/residue: 0.3515
  time to fit residues: 63.6935
Evaluate side-chains
  157 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   18 LEU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   47 LEU
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0970
   chunk 72 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
c  40 ASN
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6442  Z= 0.297
  Angle     :  0.780   9.738   8848  Z= 0.357
  Chirality :  0.047   0.290   1060
  Planarity :  0.006   0.049   1129
  Dihedral  :  6.633  57.257   1175
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 29.36 %
    Favored  : 64.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.30), residues: 797
  helix: -0.12 (0.41), residues: 159
  sheet: -1.55 (0.67), residues: 68
  loop : -1.16 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP a 498 
 HIS   0.003   0.001   HIS E  72 
 PHE   0.006   0.001   PHE a 497 
 TYR   0.025   0.002   TYR a 492 
 ARG   0.011   0.001   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   21 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6394 (t70)
REVERT: B   17 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.6943 (mtm180)
REVERT: B   70 CYS cc_start: 0.5729 (t) cc_final: 0.5301 (t)
REVERT: b   21 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7771 (t-100)
REVERT: X   62 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7571 (pt0)
REVERT: X  124 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6758 (pp30)
  outliers start: 36
  outliers final: 26
  residues processed: 160
  average time/residue: 0.3385
  time to fit residues: 63.2583
Evaluate side-chains
  161 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   18 LEU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   47 LEU
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Chi-restraints excluded: chain a residue  501 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.0980
   chunk 55 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0980
   chunk 63 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0980
   chunk 45 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6442  Z= 0.225
  Angle     :  0.762  10.978   8848  Z= 0.345
  Chirality :  0.045   0.343   1060
  Planarity :  0.006   0.048   1129
  Dihedral  :  6.270  55.737   1175
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 28.89 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.30), residues: 797
  helix: -0.03 (0.41), residues: 159
  sheet: -1.55 (0.67), residues: 68
  loop : -1.15 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP a 498 
 HIS   0.002   0.001   HIS E  72 
 PHE   0.004   0.001   PHE a 491 
 TYR   0.024   0.001   TYR a 492 
 ARG   0.010   0.001   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.7951 (tpp-160) cc_final: 0.7695 (tpp80)
REVERT: C   72 LEU cc_start: 0.8604 (tp) cc_final: 0.8210 (tp)
REVERT: E   21 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6346 (t70)
REVERT: B   70 CYS cc_start: 0.5690 (t) cc_final: 0.5222 (t)
REVERT: b   21 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7767 (t-100)
REVERT: b   94 VAL cc_start: 0.7926 (p) cc_final: 0.7681 (p)
REVERT: X   11 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6791 (mtp180)
REVERT: X   62 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7569 (pt0)
REVERT: X  124 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6619 (pp30)
  outliers start: 33
  outliers final: 25
  residues processed: 156
  average time/residue: 0.3782
  time to fit residues: 69.3983
Evaluate side-chains
  159 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   18 LEU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   47 LEU
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Chi-restraints excluded: chain a residue  501 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0870
   chunk 57 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6442  Z= 0.261
  Angle     :  0.776  10.162   8848  Z= 0.351
  Chirality :  0.046   0.319   1060
  Planarity :  0.006   0.047   1129
  Dihedral  :  6.132  52.541   1175
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 29.67 %
    Favored  : 65.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.30), residues: 797
  helix:  0.06 (0.42), residues: 159
  sheet: -1.67 (0.66), residues: 68
  loop : -1.17 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP a 498 
 HIS   0.002   0.001   HIS E  72 
 PHE   0.006   0.001   PHE a 491 
 TYR   0.024   0.002   TYR a 492 
 ARG   0.009   0.001   ARG C  89 

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7689 (tpp80)
REVERT: C   72 LEU cc_start: 0.8523 (tp) cc_final: 0.8132 (tp)
REVERT: E   21 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6331 (t70)
REVERT: B   70 CYS cc_start: 0.5737 (t) cc_final: 0.5310 (t)
REVERT: b   21 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7759 (t-100)
REVERT: X   62 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7578 (pt0)
REVERT: X  124 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6651 (pp30)
  outliers start: 29
  outliers final: 25
  residues processed: 153
  average time/residue: 0.3443
  time to fit residues: 61.3766
Evaluate side-chains
  159 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue    6 SER
Chi-restraints excluded: chain c residue   26 THR
Chi-restraints excluded: chain c residue   35 LEU
Chi-restraints excluded: chain c residue   91 LEU
Chi-restraints excluded: chain C residue    5 CYS
Chi-restraints excluded: chain C residue    7 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain E residue   21 ASP
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain b residue   21 TRP
Chi-restraints excluded: chain X residue    4 CYS
Chi-restraints excluded: chain X residue   14 GLU
Chi-restraints excluded: chain X residue   15 THR
Chi-restraints excluded: chain X residue   16 MET
Chi-restraints excluded: chain X residue   18 LEU
Chi-restraints excluded: chain X residue   20 VAL
Chi-restraints excluded: chain X residue   47 LEU
Chi-restraints excluded: chain X residue   62 GLN
Chi-restraints excluded: chain X residue  110 ARG
Chi-restraints excluded: chain X residue  124 GLN
Chi-restraints excluded: chain X residue  146 LEU
Chi-restraints excluded: chain a residue  485 CYS
Chi-restraints excluded: chain a residue  501 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 3 optimal weight:    0.1980
   chunk 44 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 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 = 0.3775 r_free = 0.3775 target = 0.137083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.121380 restraints weight = 10082.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.50
r_work: 0.3452 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6442  Z= 0.273
  Angle     :  0.784  10.949   8848  Z= 0.356
  Chirality :  0.047   0.328   1060
  Planarity :  0.006   0.047   1129
  Dihedral  :  6.051  48.663   1175
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 29.51 %
    Favored  : 65.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.18 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.30), residues: 797
  helix:  0.01 (0.42), residues: 159
  sheet: -1.68 (0.67), residues: 68
  loop : -1.19 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP a 498 
 HIS   0.003   0.001   HIS E  72 
 PHE   0.006   0.001   PHE a 491 
 TYR   0.023   0.002   TYR a 492 
 ARG   0.009   0.001   ARG C  89 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2103.13 seconds
wall clock time: 38 minutes 33.19 seconds (2313.19 seconds total)