Starting phenix.real_space_refine
on Wed Apr 30 03:31:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r4a_18883/04_2025/8r4a_18883.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r4a_18883/04_2025/8r4a_18883.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r4a_18883/04_2025/8r4a_18883.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r4a_18883/04_2025/8r4a_18883.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r4a_18883/04_2025/8r4a_18883.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r4a_18883/04_2025/8r4a_18883.cif"
  }
  resolution = 2.8
  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=   0.003
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      90      5.16       5
     C    5679      2.51       5
     N    1800      2.21       5
     O    1656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9225
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
    Chain: "B"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
    Chain: "C"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
    Chain: "D"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
    Chain: "E"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
    Chain: "F"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
    Chain: "G"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
    Chain: "H"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
    Chain: "I"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 127}
  Time building chain proxies: 6.17, per 1000 atoms: 0.67
  Number of scatterers: 9225
  At special positions: 0
  Unit cell: (100.88, 96.72, 71.76, 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      90     16.00
     O    1656      8.00
     N    1800      7.00
     C    5679      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=36, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  30 " - pdb=" SG  CYS A 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A  65 " - pdb=" SG  CYS A  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   6 " - pdb=" SG  CYS B 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  30 " - pdb=" SG  CYS B 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  65 " - pdb=" SG  CYS B  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  77 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  30 " - pdb=" SG  CYS C 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  77 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   6 " - pdb=" SG  CYS D 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  30 " - pdb=" SG  CYS D 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS D  65 " - pdb=" SG  CYS D  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  77 " - pdb=" SG  CYS D  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   6 " - pdb=" SG  CYS E 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  30 " - pdb=" SG  CYS E 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  77 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   6 " - pdb=" SG  CYS F 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  30 " - pdb=" SG  CYS F 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS F  65 " - pdb=" SG  CYS F  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  77 " - pdb=" SG  CYS F  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G   6 " - pdb=" SG  CYS G 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  30 " - pdb=" SG  CYS G 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS G  65 " - pdb=" SG  CYS G  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  77 " - pdb=" SG  CYS G  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H   6 " - pdb=" SG  CYS H 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  30 " - pdb=" SG  CYS H 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS H  65 " - pdb=" SG  CYS H  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  77 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I   6 " - pdb=" SG  CYS I 128 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I  30 " - pdb=" SG  CYS I 116 " distance=2.01
    Simple disulfide: pdb=" SG  CYS I  65 " - pdb=" SG  CYS I  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  77 " - pdb=" SG  CYS I  95 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.59
  Conformation dependent library (CDL) restraints added in 980.0 milliseconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24
    Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35
    Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46
    Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56
      removed outlier: 6.725A  pdb=" N   ILE B  56 " --> pdb=" O   GLY A  55 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE C  56 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE D  56 " --> pdb=" O   GLY C  55 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE E  56 " --> pdb=" O   GLY D  55 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE F  56 " --> pdb=" O   GLY E  55 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE G  56 " --> pdb=" O   GLY F  55 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE H  56 " --> pdb=" O   GLY G  55 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE I  56 " --> pdb=" O   GLY H  55 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 66
      removed outlier: 6.534A  pdb=" N   ILE A  59 " --> pdb=" O   ASN B  60 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ARG B  62 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER A  61 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   TRP B  64 " --> pdb=" O   SER A  61 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR A  63 " --> pdb=" O   TRP B  64 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   ASN B  66 " --> pdb=" O   TYR A  63 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   CYS A  65 " --> pdb=" O   ASN B  66 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE B  59 " --> pdb=" O   ASN C  60 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ARG C  62 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER B  61 " --> pdb=" O   ARG C  62 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   TRP C  64 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR B  63 " --> pdb=" O   TRP C  64 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ASN C  66 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   CYS B  65 " --> pdb=" O   ASN C  66 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE C  59 " --> pdb=" O   ASN D  60 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ARG D  62 " --> pdb=" O   ILE C  59 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER C  61 " --> pdb=" O   ARG D  62 " (cutoff:3.500A)
      removed outlier: 8.439A  pdb=" N   TRP D  64 " --> pdb=" O   SER C  61 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR C  63 " --> pdb=" O   TRP D  64 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   ASN D  66 " --> pdb=" O   TYR C  63 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   CYS C  65 " --> pdb=" O   ASN D  66 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ILE D  59 " --> pdb=" O   ASN E  60 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ARG E  62 " --> pdb=" O   ILE D  59 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER D  61 " --> pdb=" O   ARG E  62 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   TRP E  64 " --> pdb=" O   SER D  61 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR D  63 " --> pdb=" O   TRP E  64 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ASN E  66 " --> pdb=" O   TYR D  63 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   CYS D  65 " --> pdb=" O   ASN E  66 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE E  59 " --> pdb=" O   ASN F  60 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ARG F  62 " --> pdb=" O   ILE E  59 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER E  61 " --> pdb=" O   ARG F  62 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   TRP F  64 " --> pdb=" O   SER E  61 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR E  63 " --> pdb=" O   TRP F  64 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ASN F  66 " --> pdb=" O   TYR E  63 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   CYS E  65 " --> pdb=" O   ASN F  66 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ILE F  59 " --> pdb=" O   ASN G  60 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ARG G  62 " --> pdb=" O   ILE F  59 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER F  61 " --> pdb=" O   ARG G  62 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   TRP G  64 " --> pdb=" O   SER F  61 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR F  63 " --> pdb=" O   TRP G  64 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ASN G  66 " --> pdb=" O   TYR F  63 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   CYS F  65 " --> pdb=" O   ASN G  66 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ILE G  59 " --> pdb=" O   ASN H  60 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ARG H  62 " --> pdb=" O   ILE G  59 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER G  61 " --> pdb=" O   ARG H  62 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   TRP H  64 " --> pdb=" O   SER G  61 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR G  63 " --> pdb=" O   TRP H  64 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ASN H  66 " --> pdb=" O   TYR G  63 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   CYS G  65 " --> pdb=" O   ASN H  66 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE H  59 " --> pdb=" O   ASN I  60 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ARG I  62 " --> pdb=" O   ILE H  59 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   SER H  61 " --> pdb=" O   ARG I  62 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   TRP I  64 " --> pdb=" O   SER H  61 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR H  63 " --> pdb=" O   TRP I  64 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   ASN I  66 " --> pdb=" O   TYR H  63 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   CYS H  65 " --> pdb=" O   ASN I  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 74 through 79
      removed outlier: 6.716A  pdb=" N   HIS B  78 " --> pdb=" O   CYS A  77 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU A  79 " --> pdb=" O   HIS B  78 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   HIS C  78 " --> pdb=" O   CYS B  77 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU B  79 " --> pdb=" O   HIS C  78 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   HIS D  78 " --> pdb=" O   CYS C  77 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU C  79 " --> pdb=" O   HIS D  78 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   HIS E  78 " --> pdb=" O   CYS D  77 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU D  79 " --> pdb=" O   HIS E  78 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   HIS F  78 " --> pdb=" O   CYS E  77 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU E  79 " --> pdb=" O   HIS F  78 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   HIS G  78 " --> pdb=" O   CYS F  77 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU F  79 " --> pdb=" O   HIS G  78 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   HIS H  78 " --> pdb=" O   CYS G  77 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU G  79 " --> pdb=" O   HIS H  78 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   HIS I  78 " --> pdb=" O   CYS H  77 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU H  79 " --> pdb=" O   HIS I  78 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 89 through 90
    Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 99
    Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AB1, first strand: chain 'A' and resid 124 through 126

    96 hydrogen bonds defined for protein.
    288 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1503
        1.30 -     1.43: 2718
        1.43 -     1.56: 5076
        1.56 -     1.69: 0
        1.69 -     1.82: 108
  Bond restraints: 9405
  Sorted by residual:
  bond pdb=" C   CYS D   6 "
       pdb=" O   CYS D   6 "
    ideal  model  delta    sigma   weight residual
    1.235  1.171  0.064 1.23e-02 6.61e+03 2.69e+01
  bond pdb=" C   CYS I   6 "
       pdb=" O   CYS I   6 "
    ideal  model  delta    sigma   weight residual
    1.235  1.171  0.064 1.23e-02 6.61e+03 2.69e+01
  bond pdb=" C   CYS F   6 "
       pdb=" O   CYS F   6 "
    ideal  model  delta    sigma   weight residual
    1.235  1.171  0.064 1.23e-02 6.61e+03 2.69e+01
  bond pdb=" C   CYS G   6 "
       pdb=" O   CYS G   6 "
    ideal  model  delta    sigma   weight residual
    1.235  1.171  0.064 1.23e-02 6.61e+03 2.68e+01
  bond pdb=" C   CYS E   6 "
       pdb=" O   CYS E   6 "
    ideal  model  delta    sigma   weight residual
    1.235  1.171  0.064 1.23e-02 6.61e+03 2.68e+01
  ... (remaining 9400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 8771
        1.87 -     3.75: 2561
        3.75 -     5.62: 1160
        5.62 -     7.50: 180
        7.50 -     9.37: 36
  Bond angle restraints: 12708
  Sorted by residual:
  angle pdb=" CA  ASP H 102 "
        pdb=" C   ASP H 102 "
        pdb=" N   PRO H 103 "
      ideal   model   delta    sigma   weight residual
     118.16  122.86   -4.70 7.00e-01 2.04e+00 4.50e+01
  angle pdb=" CA  ASP F 102 "
        pdb=" C   ASP F 102 "
        pdb=" N   PRO F 103 "
      ideal   model   delta    sigma   weight residual
     118.16  122.84   -4.68 7.00e-01 2.04e+00 4.47e+01
  angle pdb=" CA  ASP A 102 "
        pdb=" C   ASP A 102 "
        pdb=" N   PRO A 103 "
      ideal   model   delta    sigma   weight residual
     118.16  122.82   -4.66 7.00e-01 2.04e+00 4.43e+01
  angle pdb=" CA  ASP E 102 "
        pdb=" C   ASP E 102 "
        pdb=" N   PRO E 103 "
      ideal   model   delta    sigma   weight residual
     118.16  122.82   -4.66 7.00e-01 2.04e+00 4.43e+01
  angle pdb=" CA  ASP C 102 "
        pdb=" C   ASP C 102 "
        pdb=" N   PRO C 103 "
      ideal   model   delta    sigma   weight residual
     118.16  122.81   -4.65 7.00e-01 2.04e+00 4.42e+01
  ... (remaining 12703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.61: 5067
       15.61 -    31.22: 396
       31.22 -    46.83: 117
       46.83 -    62.43: 45
       62.43 -    78.04: 36
  Dihedral angle restraints: 5661
    sinusoidal: 2322
      harmonic: 3339
  Sorted by residual:
  dihedral pdb=" CA  ASN F  60 "
           pdb=" CB  ASN F  60 "
           pdb=" CG  ASN F  60 "
           pdb=" OD1 ASN F  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -159.22   69.22     2      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  ASN G  60 "
           pdb=" CB  ASN G  60 "
           pdb=" CG  ASN G  60 "
           pdb=" OD1 ASN G  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -159.22   69.22     2      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  ASN C  60 "
           pdb=" CB  ASN C  60 "
           pdb=" CG  ASN C  60 "
           pdb=" OD1 ASN C  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -159.21   69.21     2      2.00e+01 2.50e-03 1.05e+01
  ... (remaining 5658 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 561
       0.064 -    0.128: 440
       0.128 -    0.192: 205
       0.192 -    0.256: 90
       0.256 -    0.320: 9
  Chirality restraints: 1305
  Sorted by residual:
  chirality pdb=" CA  VAL C 121 "
            pdb=" N   VAL C 121 "
            pdb=" C   VAL C 121 "
            pdb=" CB  VAL C 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.76   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  VAL F 121 "
            pdb=" N   VAL F 121 "
            pdb=" C   VAL F 121 "
            pdb=" CB  VAL F 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.76   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  VAL B 121 "
            pdb=" N   VAL B 121 "
            pdb=" C   VAL B 121 "
            pdb=" CB  VAL B 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.76   -0.32 2.00e-01 2.50e+01 2.55e+00
  ... (remaining 1302 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  31 "    0.018 2.00e-02 2.50e+03   3.74e-02 1.40e+01
        pdb=" C   LEU C  31 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   LEU C  31 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ALA C  32 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU I  31 "    0.018 2.00e-02 2.50e+03   3.74e-02 1.40e+01
        pdb=" C   LEU I  31 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   LEU I  31 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ALA I  32 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  31 "    0.018 2.00e-02 2.50e+03   3.74e-02 1.40e+01
        pdb=" C   LEU B  31 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   LEU B  31 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ALA B  32 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 3880
        2.94 -     3.43: 9783
        3.43 -     3.92: 16519
        3.92 -     4.41: 20132
        4.41 -     4.90: 35789
  Nonbonded interactions: 86103
  Sorted by model distance:
  nonbonded pdb=" N   ASN G 118 "
            pdb=" O   ASN G 118 "
     model   vdw
     2.451 2.496
  nonbonded pdb=" N   ASN E 118 "
            pdb=" O   ASN E 118 "
     model   vdw
     2.451 2.496
  nonbonded pdb=" N   ASN H 118 "
            pdb=" O   ASN H 118 "
     model   vdw
     2.451 2.496
  nonbonded pdb=" N   ASN A 118 "
            pdb=" O   ASN A 118 "
     model   vdw
     2.451 2.496
  nonbonded pdb=" N   ASN B 118 "
            pdb=" O   ASN B 118 "
     model   vdw
     2.451 2.496
  ... (remaining 86098 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.710
  Find NCS groups from input model:        0.230
  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:12.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
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      :  0.013   0.064   9441  Z= 0.988
  Angle     :  2.161   9.371  12780  Z= 1.562
  Chirality :  0.105   0.320   1305
  Planarity :  0.011   0.037   1674
  Dihedral  : 15.072  78.043   3429
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.54 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -4.27 (0.13), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.10), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP G 112 
 HIS   0.007   0.005   HIS H  78 
 PHE   0.016   0.003   PHE H   3 
 TYR   0.018   0.003   TYR G  63 
 ARG   0.004   0.001   ARG I  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27857 (   96)
  hydrogen bonds       : angle       9.95736 (  288)
  SS BOND              : bond        0.01280 (   36)
  SS BOND              : angle       1.87167 (   72)
  covalent geometry    : bond        0.01314 ( 9405)
  covalent geometry    : angle       2.16272 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.934 
Fit side-chains
REVERT: B   67 ASP cc_start: 0.7893 (t0) cc_final: 0.7486 (t0)
REVERT: B   98 ARG cc_start: 0.7405 (ttm110) cc_final: 0.7056 (ttm170)
REVERT: C   98 ARG cc_start: 0.7339 (ttm110) cc_final: 0.6969 (ttm170)
REVERT: D   29 MET cc_start: 0.7516 (mtt) cc_final: 0.7214 (mtt)
REVERT: D   43 THR cc_start: 0.8798 (p) cc_final: 0.8503 (m)
REVERT: E   74 VAL cc_start: 0.8842 (p) cc_final: 0.8620 (t)
REVERT: F   29 MET cc_start: 0.7546 (mtt) cc_final: 0.7336 (mtt)
REVERT: G   74 VAL cc_start: 0.8791 (p) cc_final: 0.8554 (t)
REVERT: I   45 TYR cc_start: 0.9011 (m-80) cc_final: 0.8704 (m-80)
REVERT: I   97 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7743 (tmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 300
  average time/residue: 1.4458
  time to fit residues: 461.7881
Evaluate side-chains
  193 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  44 ASN
A  58 GLN
B  44 ASN
B  58 GLN
B 104 GLN
C  44 ASN
C  58 GLN
C  88 ASN
D  27 ASN
D  44 ASN
D  58 GLN
E  44 ASN
E  58 GLN
** E  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 104 GLN
F  44 ASN
** F  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 ASN
H  44 ASN
H  58 GLN
** H  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 104 GLN
I  44 ASN
I 104 GLN
I 114 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.112223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.095056 restraints weight = 10774.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.31
r_work: 0.3229 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9441  Z= 0.188
  Angle     :  0.834   9.993  12780  Z= 0.451
  Chirality :  0.052   0.167   1305
  Planarity :  0.004   0.029   1674
  Dihedral  :  7.774  51.157   1350
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 19.66 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -4.20 (0.15), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.12), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 112 
 HIS   0.003   0.001   HIS B  78 
 PHE   0.024   0.005   PHE D   3 
 TYR   0.015   0.002   TYR F  54 
 ARG   0.005   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08172 (   96)
  hydrogen bonds       : angle       5.67474 (  288)
  SS BOND              : bond        0.00340 (   36)
  SS BOND              : angle       0.66678 (   72)
  covalent geometry    : bond        0.00431 ( 9405)
  covalent geometry    : angle       0.83488 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 170
  time to evaluate  : 1.003 
Fit side-chains
REVERT: B   12 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7448 (tt)
REVERT: B   67 ASP cc_start: 0.8230 (t0) cc_final: 0.8007 (t0)
REVERT: C   12 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7581 (tt)
REVERT: C   62 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7805 (ttm170)
REVERT: C   98 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7718 (ttm170)
REVERT: C  106 ILE cc_start: 0.8661 (mp) cc_final: 0.8433 (mt)
REVERT: C  113 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8071 (mtm-85)
REVERT: D   29 MET cc_start: 0.8119 (mtt) cc_final: 0.7877 (mtt)
REVERT: D  113 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8245 (mtm-85)
REVERT: E   12 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7698 (tt)
REVERT: E   98 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7893 (ttm170)
REVERT: F  117 GLN cc_start: 0.8565 (pt0) cc_final: 0.8262 (pt0)
REVERT: I  115 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8083 (ttt90)
  outliers start: 54
  outliers final: 19
  residues processed: 206
  average time/residue: 1.0465
  time to fit residues: 233.7022
Evaluate side-chains
  181 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   25 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  113 ARG
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   52 THR
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue   59 ILE
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue  115 ARG
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 95 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.1544

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A  78 HIS
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  88 ASN
E  78 HIS
E  88 ASN
F  78 HIS
F  88 ASN
F 104 GLN
** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  88 ASN
H 114 ASN
I  78 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.105836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.087811 restraints weight = 10947.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.35
r_work: 0.3110 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   9441  Z= 0.242
  Angle     :  0.830  10.681  12780  Z= 0.443
  Chirality :  0.052   0.183   1305
  Planarity :  0.004   0.027   1674
  Dihedral  :  7.504  44.874   1350
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 21.47 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.26 (0.15), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.12), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 112 
 HIS   0.006   0.002   HIS B  78 
 PHE   0.019   0.003   PHE F   3 
 TYR   0.014   0.002   TYR B  54 
 ARG   0.008   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07825 (   96)
  hydrogen bonds       : angle       5.94232 (  288)
  SS BOND              : bond        0.00587 (   36)
  SS BOND              : angle       0.90704 (   72)
  covalent geometry    : bond        0.00553 ( 9405)
  covalent geometry    : angle       0.82977 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 152
  time to evaluate  : 1.080 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8135 (mt-10)
REVERT: B   12 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7656 (tt)
REVERT: B   67 ASP cc_start: 0.8391 (t0) cc_final: 0.8174 (t0)
REVERT: C   12 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7817 (tt)
REVERT: C   62 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7516 (ttm170)
REVERT: C   98 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7892 (ttm170)
REVERT: C  113 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8308 (mtm-85)
REVERT: D   14 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8395 (ttp80)
REVERT: D   29 MET cc_start: 0.8189 (mtt) cc_final: 0.7964 (mtt)
REVERT: D   62 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8086 (ttp-170)
REVERT: E   12 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7876 (tt)
REVERT: F  117 GLN cc_start: 0.8699 (pt0) cc_final: 0.8324 (pt0)
REVERT: H   12 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7901 (tt)
REVERT: I   10 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8284 (mtp-110)
  outliers start: 57
  outliers final: 26
  residues processed: 190
  average time/residue: 1.2732
  time to fit residues: 259.0130
Evaluate side-chains
  180 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   35 GLU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   14 ARG
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   59 ILE
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   59 ILE
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue   70 THR
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 63 optimal weight:    0.2980
   chunk 71 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 114 ASN
D 123 GLN
E  88 ASN
G  78 HIS
H  88 ASN
H 104 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.106195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.087424 restraints weight = 10474.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.39
r_work: 0.3090 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9441  Z= 0.212
  Angle     :  0.775   8.948  12780  Z= 0.414
  Chirality :  0.051   0.173   1305
  Planarity :  0.004   0.039   1674
  Dihedral  :  7.328  41.165   1350
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 23.40 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.32 (0.16), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.12), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 112 
 HIS   0.004   0.002   HIS G  78 
 PHE   0.017   0.003   PHE F   3 
 TYR   0.012   0.002   TYR F  54 
 ARG   0.008   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07335 (   96)
  hydrogen bonds       : angle       6.02807 (  288)
  SS BOND              : bond        0.00506 (   36)
  SS BOND              : angle       0.79817 (   72)
  covalent geometry    : bond        0.00474 ( 9405)
  covalent geometry    : angle       0.77463 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 152
  time to evaluate  : 0.886 
Fit side-chains
REVERT: B   12 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7670 (tt)
REVERT: B   67 ASP cc_start: 0.8377 (t0) cc_final: 0.8141 (t0)
REVERT: C   12 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7850 (tt)
REVERT: C   62 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7852 (ttp80)
REVERT: C   98 ARG cc_start: 0.8364 (ttm110) cc_final: 0.7948 (ttm170)
REVERT: C  113 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8280 (mtm-85)
REVERT: D   62 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8100 (ttp-170)
REVERT: E   12 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7783 (tt)
REVERT: F   12 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7936 (tt)
REVERT: F  117 GLN cc_start: 0.8758 (pt0) cc_final: 0.8412 (pt0)
REVERT: H   12 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7933 (tt)
REVERT: I   10 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8256 (mtp-110)
REVERT: I  115 ARG cc_start: 0.8329 (ttt90) cc_final: 0.8070 (ttt90)
  outliers start: 51
  outliers final: 32
  residues processed: 179
  average time/residue: 1.2081
  time to fit residues: 233.0203
Evaluate side-chains
  188 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 148
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   12 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   59 ILE
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   59 ILE
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   11 THR
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   52 THR
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue   70 THR
Chi-restraints excluded: chain I residue   97 LYS
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 62 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 95 optimal weight:    0.1980
   chunk 94 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 123 GLN
E  86 GLN
E  88 ASN
G  88 ASN
H 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.106575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.088507 restraints weight = 10720.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 1.34
r_work: 0.3128 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9441  Z= 0.141
  Angle     :  0.700   7.869  12780  Z= 0.377
  Chirality :  0.049   0.174   1305
  Planarity :  0.003   0.041   1674
  Dihedral  :  7.030  34.880   1350
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 23.18 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -4.36 (0.16), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.12), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 112 
 HIS   0.003   0.001   HIS B  78 
 PHE   0.016   0.002   PHE G   3 
 TYR   0.010   0.001   TYR A  54 
 ARG   0.010   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06600 (   96)
  hydrogen bonds       : angle       5.90481 (  288)
  SS BOND              : bond        0.00363 (   36)
  SS BOND              : angle       0.56204 (   72)
  covalent geometry    : bond        0.00311 ( 9405)
  covalent geometry    : angle       0.70104 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 153
  time to evaluate  : 1.896 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8167 (mmt)
REVERT: A   35 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8216 (mt-10)
REVERT: B   12 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7712 (tt)
REVERT: B   17 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8686 (mtm)
REVERT: B   67 ASP cc_start: 0.8239 (t0) cc_final: 0.7966 (t0)
REVERT: C   12 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7824 (tt)
REVERT: C   62 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7688 (ttp80)
REVERT: C   98 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7809 (ttm170)
REVERT: C  113 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8304 (mtm-85)
REVERT: D   62 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8106 (ttp-170)
REVERT: E   12 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7736 (tt)
REVERT: F   12 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7903 (tt)
REVERT: F  117 GLN cc_start: 0.8691 (pt0) cc_final: 0.8401 (pt0)
REVERT: H   17 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8679 (mtm)
REVERT: I   10 ARG cc_start: 0.8465 (mmm160) cc_final: 0.8249 (mtp-110)
  outliers start: 51
  outliers final: 27
  residues processed: 181
  average time/residue: 1.1185
  time to fit residues: 217.5230
Evaluate side-chains
  186 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   35 GLU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   12 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   70 THR
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue   12 LEU
Chi-restraints excluded: chain H residue   17 MET
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   52 THR
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  78 HIS
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  78 HIS
E  86 GLN
H  78 HIS
H 104 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.102592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.083787 restraints weight = 10596.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.37
r_work: 0.3041 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060   9441  Z= 0.369
  Angle     :  0.875  10.205  12780  Z= 0.463
  Chirality :  0.055   0.201   1305
  Planarity :  0.005   0.044   1674
  Dihedral  :  7.616  45.828   1350
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  7.48 %
    Allowed  : 21.37 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.27 (0.16), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.13), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 112 
 HIS   0.007   0.002   HIS B  78 
 PHE   0.019   0.003   PHE G   3 
 TYR   0.013   0.002   TYR F  54 
 ARG   0.012   0.001   ARG B  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08179 (   96)
  hydrogen bonds       : angle       6.22679 (  288)
  SS BOND              : bond        0.00759 (   36)
  SS BOND              : angle       1.07160 (   72)
  covalent geometry    : bond        0.00836 ( 9405)
  covalent geometry    : angle       0.87360 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 154
  time to evaluate  : 1.277 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8242 (mmt)
REVERT: A   35 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8262 (mt-10)
REVERT: B   12 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7728 (tt)
REVERT: B   67 ASP cc_start: 0.8309 (t0) cc_final: 0.8070 (t0)
REVERT: C   12 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8002 (tt)
REVERT: C   62 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7512 (ttm170)
REVERT: C  113 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8278 (mtm-85)
REVERT: D   62 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8102 (ttp-170)
REVERT: E   12 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7937 (tt)
REVERT: F   12 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8040 (tt)
REVERT: G   45 TYR cc_start: 0.9238 (m-80) cc_final: 0.9010 (m-80)
REVERT: I   35 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8147 (mp0)
REVERT: I   53 ASP cc_start: 0.8730 (p0) cc_final: 0.8484 (p0)
REVERT: I   62 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7880 (ttt90)
  outliers start: 70
  outliers final: 43
  residues processed: 190
  average time/residue: 1.0663
  time to fit residues: 218.2999
Evaluate side-chains
  201 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 147
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   11 THR
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   35 GLU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   11 THR
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  118 ASN
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   11 THR
Chi-restraints excluded: chain F residue   12 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   59 ILE
Chi-restraints excluded: chain F residue   70 THR
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   11 THR
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   52 THR
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue   62 ARG
Chi-restraints excluded: chain I residue   70 THR
Chi-restraints excluded: chain I residue   97 LYS
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   chunk 103 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  44 ASN
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  86 GLN
H 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.105100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.086609 restraints weight = 10823.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.38
r_work: 0.3094 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9441  Z= 0.163
  Angle     :  0.730   8.360  12780  Z= 0.393
  Chirality :  0.050   0.175   1305
  Planarity :  0.003   0.043   1674
  Dihedral  :  7.243  39.099   1350
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 24.04 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.20 (0.17), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.13), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 112 
 HIS   0.002   0.001   HIS E  78 
 PHE   0.014   0.002   PHE F   3 
 TYR   0.011   0.002   TYR B 124 
 ARG   0.013   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06917 (   96)
  hydrogen bonds       : angle       5.92154 (  288)
  SS BOND              : bond        0.00440 (   36)
  SS BOND              : angle       0.69527 (   72)
  covalent geometry    : bond        0.00358 ( 9405)
  covalent geometry    : angle       0.73009 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 157
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8187 (mmt)
REVERT: A   35 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8291 (mt-10)
REVERT: B   12 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7655 (tt)
REVERT: C   12 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7880 (tt)
REVERT: C   62 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7807 (ttp80)
REVERT: C   98 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7956 (ttm170)
REVERT: C  113 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8318 (mtm-85)
REVERT: D   62 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8160 (ttp-170)
REVERT: E   12 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7788 (tt)
REVERT: F   12 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7952 (tt)
REVERT: F   84 LEU cc_start: 0.8676 (mt) cc_final: 0.8471 (mm)
REVERT: F  117 GLN cc_start: 0.8797 (pt0) cc_final: 0.8442 (pt0)
REVERT: I   35 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8176 (mp0)
  outliers start: 51
  outliers final: 33
  residues processed: 183
  average time/residue: 1.0158
  time to fit residues: 201.1003
Evaluate side-chains
  194 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 151
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   12 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   59 ILE
Chi-restraints excluded: chain F residue   70 THR
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   52 THR
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue   70 THR
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 36 optimal weight:    0.4980
   chunk 113 optimal weight:    0.3980
   chunk 75 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0040
   chunk 70 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 123 GLN
E  86 GLN
H 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.107040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.088207 restraints weight = 10711.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.41
r_work: 0.3110 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9441  Z= 0.143
  Angle     :  0.699   8.945  12780  Z= 0.374
  Chirality :  0.049   0.170   1305
  Planarity :  0.003   0.054   1674
  Dihedral  :  6.994  33.270   1350
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 24.47 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -4.19 (0.17), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.13), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 112 
 HIS   0.001   0.001   HIS C  78 
 PHE   0.013   0.002   PHE F   3 
 TYR   0.012   0.001   TYR B 124 
 ARG   0.012   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06422 (   96)
  hydrogen bonds       : angle       5.71120 (  288)
  SS BOND              : bond        0.00358 (   36)
  SS BOND              : angle       0.59593 (   72)
  covalent geometry    : bond        0.00314 ( 9405)
  covalent geometry    : angle       0.69984 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 154
  time to evaluate  : 1.042 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8119 (mmt)
REVERT: A   35 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8245 (mt-10)
REVERT: B   12 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7681 (tt)
REVERT: C   12 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7847 (tt)
REVERT: C   62 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7819 (ttp80)
REVERT: C   98 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7900 (ttm170)
REVERT: C  113 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8345 (mtm-85)
REVERT: D   62 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8169 (ttp-170)
REVERT: E   12 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7793 (tt)
REVERT: F   12 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7878 (tt)
REVERT: F  117 GLN cc_start: 0.8740 (pt0) cc_final: 0.8393 (pt0)
REVERT: I   35 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8079 (mp0)
  outliers start: 46
  outliers final: 32
  residues processed: 181
  average time/residue: 1.0687
  time to fit residues: 209.3222
Evaluate side-chains
  195 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   12 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   59 ILE
Chi-restraints excluded: chain F residue   70 THR
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue   21 ARG
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   52 THR
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue   70 THR
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 72 optimal weight:    0.3980
   chunk 56 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 123 GLN
E  86 GLN
H 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.105927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.087325 restraints weight = 10693.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.38
r_work: 0.3108 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9441  Z= 0.164
  Angle     :  0.712   9.243  12780  Z= 0.380
  Chirality :  0.049   0.173   1305
  Planarity :  0.004   0.054   1674
  Dihedral  :  7.001  33.130   1350
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 24.36 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.23 (0.17), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.13), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 112 
 HIS   0.002   0.001   HIS C  78 
 PHE   0.013   0.002   PHE G   3 
 TYR   0.014   0.002   TYR B 124 
 ARG   0.015   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06570 (   96)
  hydrogen bonds       : angle       5.67626 (  288)
  SS BOND              : bond        0.00406 (   36)
  SS BOND              : angle       0.64172 (   72)
  covalent geometry    : bond        0.00362 ( 9405)
  covalent geometry    : angle       0.71231 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 152
  time to evaluate  : 1.023 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8140 (mmt)
REVERT: A   35 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8282 (mt-10)
REVERT: B   12 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7700 (tt)
REVERT: C   12 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7829 (tt)
REVERT: C   62 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7690 (ttp80)
REVERT: C  113 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8308 (mtm-85)
REVERT: D   62 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8179 (ttp-170)
REVERT: E   12 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: F   12 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7885 (tt)
REVERT: F  117 GLN cc_start: 0.8731 (pt0) cc_final: 0.8250 (pt0)
REVERT: I   35 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8173 (mp0)
  outliers start: 45
  outliers final: 35
  residues processed: 176
  average time/residue: 1.0500
  time to fit residues: 199.6138
Evaluate side-chains
  196 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 151
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   29 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   35 GLU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   12 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   59 ILE
Chi-restraints excluded: chain F residue   70 THR
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue   21 ARG
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   52 THR
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue   70 THR
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0060
   chunk 28 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0270
   chunk 32 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.5654

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

Flipped N/Q/H residues before XYZ refinement:
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  86 GLN
H 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.088177 restraints weight = 10802.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.39
r_work: 0.3123 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9441  Z= 0.140
  Angle     :  0.692   9.346  12780  Z= 0.370
  Chirality :  0.048   0.171   1305
  Planarity :  0.003   0.054   1674
  Dihedral  :  6.899  31.058   1350
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 25.21 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -4.24 (0.17), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.22 (0.13), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 112 
 HIS   0.001   0.001   HIS C  78 
 PHE   0.012   0.002   PHE D   3 
 TYR   0.013   0.001   TYR B 124 
 ARG   0.014   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06275 (   96)
  hydrogen bonds       : angle       5.58236 (  288)
  SS BOND              : bond        0.00338 (   36)
  SS BOND              : angle       0.56184 (   72)
  covalent geometry    : bond        0.00306 ( 9405)
  covalent geometry    : angle       0.69241 (12708)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 149
  time to evaluate  : 1.172 
Fit side-chains
REVERT: A   29 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8126 (mmt)
REVERT: A   35 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8274 (mt-10)
REVERT: C   12 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7773 (tt)
REVERT: C   62 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7802 (ttp80)
REVERT: C   98 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7917 (ttm170)
REVERT: C  113 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8299 (mtm-85)
REVERT: D   62 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8186 (ttp-170)
REVERT: E   12 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7774 (tt)
REVERT: F   12 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7863 (tt)
REVERT: F  117 GLN cc_start: 0.8666 (pt0) cc_final: 0.8198 (pt0)
REVERT: I   35 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8162 (mp0)
  outliers start: 42
  outliers final: 32
  residues processed: 172
  average time/residue: 1.2082
  time to fit residues: 223.7880
Evaluate side-chains
  187 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 146
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   59 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain F residue   12 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   59 ILE
Chi-restraints excluded: chain F residue   70 THR
Chi-restraints excluded: chain F residue  130 VAL
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue  130 VAL
Chi-restraints excluded: chain H residue   21 ARG
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  130 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   52 THR
Chi-restraints excluded: chain I residue   59 ILE
Chi-restraints excluded: chain I residue   70 THR
Chi-restraints excluded: chain I residue  130 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 72 optimal weight:    0.4980
   chunk 103 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 105 optimal weight:    0.0060
   chunk 85 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0770
   chunk 39 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  86 GLN
H 104 GLN
I  46 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.107435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.088764 restraints weight = 10674.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.38
r_work: 0.3139 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9441  Z= 0.129
  Angle     :  0.680   9.422  12780  Z= 0.363
  Chirality :  0.048   0.170   1305
  Planarity :  0.003   0.052   1674
  Dihedral  :  6.811  29.730   1350
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 25.21 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -4.25 (0.17), residues: 1152
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.13), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  28 
 HIS   0.002   0.001   HIS I  78 
 PHE   0.011   0.002   PHE D   3 
 TYR   0.014   0.001   TYR B 124 
 ARG   0.014   0.000   ARG H  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06053 (   96)
  hydrogen bonds       : angle       5.51315 (  288)
  SS BOND              : bond        0.00311 (   36)
  SS BOND              : angle       0.52226 (   72)
  covalent geometry    : bond        0.00278 ( 9405)
  covalent geometry    : angle       0.68083 (12708)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6999.91 seconds
wall clock time: 122 minutes 42.55 seconds (7362.55 seconds total)