Starting phenix.real_space_refine
on Thu Feb 22 12:19:25 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ev9_31325/02_2024/7ev9_31325_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ev9_31325/02_2024/7ev9_31325.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ev9_31325/02_2024/7ev9_31325.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ev9_31325/02_2024/7ev9_31325.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ev9_31325/02_2024/7ev9_31325_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ev9_31325/02_2024/7ev9_31325_neut_updated.pdb"
  }
  resolution = 2.6
  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=   0.001 sd=   0.067
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 17136 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Cu     24      5.60       5
     S      81      5.16       5
     C   11295      2.51       5
     N    2835      2.21       5
     O    2985      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   43": "NH1" <-> "NH2"
    Residue "A ARG   45": "NH1" <-> "NH2"
    Residue "A GLU   63": "OE1" <-> "OE2"
    Residue "A PHE   74": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  115": "NH1" <-> "NH2"
    Residue "A GLU  117": "OE1" <-> "OE2"
    Residue "A PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  131": "NH1" <-> "NH2"
    Residue "A ARG  132": "NH1" <-> "NH2"
    Residue "A ARG  167": "NH1" <-> "NH2"
    Residue "A TYR  183": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  190": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  209": "NH1" <-> "NH2"
    Residue "A PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  223": "NH1" <-> "NH2"
    Residue "A ARG  292": "NH1" <-> "NH2"
    Residue "A TYR  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  323": "NH1" <-> "NH2"
    Residue "A TYR  336": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  360": "NH1" <-> "NH2"
    Residue "A TYR  374": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  375": "NH1" <-> "NH2"
    Residue "A PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  393": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  400": "NH1" <-> "NH2"
    Residue "B ARG    9": "NH1" <-> "NH2"
    Residue "B GLU   13": "OE1" <-> "OE2"
    Residue "B PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   58": "NH1" <-> "NH2"
    Residue "B PHE   71": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   82": "NH1" <-> "NH2"
    Residue "B ARG   84": "NH1" <-> "NH2"
    Residue "B GLU  100": "OE1" <-> "OE2"
    Residue "B ARG  104": "NH1" <-> "NH2"
    Residue "B PHE  120": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  132": "OD1" <-> "OD2"
    Residue "B TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  143": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  156": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  182": "OD1" <-> "OD2"
    Residue "B TYR  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  190": "NH1" <-> "NH2"
    Residue "B PHE  219": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  228": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  229": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  236": "NH1" <-> "NH2"
    Residue "B ARG  242": "NH1" <-> "NH2"
    Residue "B PHE  243": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  116": "OD1" <-> "OD2"
    Residue "C ARG  117": "NH1" <-> "NH2"
    Residue "C ARG  129": "NH1" <-> "NH2"
    Residue "C TYR  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  152": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  198": "NH1" <-> "NH2"
    Residue "C GLU  284": "OE1" <-> "OE2"
    Residue "E ARG   43": "NH1" <-> "NH2"
    Residue "E ARG   45": "NH1" <-> "NH2"
    Residue "E GLU   63": "OE1" <-> "OE2"
    Residue "E PHE   74": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  115": "NH1" <-> "NH2"
    Residue "E GLU  117": "OE1" <-> "OE2"
    Residue "E PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  131": "NH1" <-> "NH2"
    Residue "E ARG  132": "NH1" <-> "NH2"
    Residue "E ARG  167": "NH1" <-> "NH2"
    Residue "E TYR  183": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  190": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  209": "NH1" <-> "NH2"
    Residue "E PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  223": "NH1" <-> "NH2"
    Residue "E ARG  292": "NH1" <-> "NH2"
    Residue "E TYR  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  323": "NH1" <-> "NH2"
    Residue "E TYR  336": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  360": "NH1" <-> "NH2"
    Residue "E TYR  374": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  375": "NH1" <-> "NH2"
    Residue "E PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  393": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  400": "NH1" <-> "NH2"
    Residue "F ARG    9": "NH1" <-> "NH2"
    Residue "F GLU   13": "OE1" <-> "OE2"
    Residue "F PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG   58": "NH1" <-> "NH2"
    Residue "F PHE   71": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG   82": "NH1" <-> "NH2"
    Residue "F ARG   84": "NH1" <-> "NH2"
    Residue "F GLU  100": "OE1" <-> "OE2"
    Residue "F ARG  104": "NH1" <-> "NH2"
    Residue "F PHE  120": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  132": "OD1" <-> "OD2"
    Residue "F TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  143": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  156": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  182": "OD1" <-> "OD2"
    Residue "F TYR  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  190": "NH1" <-> "NH2"
    Residue "F PHE  219": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  228": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  229": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG  236": "NH1" <-> "NH2"
    Residue "F ARG  242": "NH1" <-> "NH2"
    Residue "F PHE  243": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP  116": "OD1" <-> "OD2"
    Residue "G ARG  117": "NH1" <-> "NH2"
    Residue "G ARG  129": "NH1" <-> "NH2"
    Residue "G TYR  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  152": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG  198": "NH1" <-> "NH2"
    Residue "G GLU  284": "OE1" <-> "OE2"
    Residue "I ARG   43": "NH1" <-> "NH2"
    Residue "I ARG   45": "NH1" <-> "NH2"
    Residue "I GLU   63": "OE1" <-> "OE2"
    Residue "I PHE   74": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  115": "NH1" <-> "NH2"
    Residue "I GLU  117": "OE1" <-> "OE2"
    Residue "I PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  131": "NH1" <-> "NH2"
    Residue "I ARG  132": "NH1" <-> "NH2"
    Residue "I ARG  167": "NH1" <-> "NH2"
    Residue "I TYR  183": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  190": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  196": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  209": "NH1" <-> "NH2"
    Residue "I PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  223": "NH1" <-> "NH2"
    Residue "I ARG  292": "NH1" <-> "NH2"
    Residue "I TYR  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  323": "NH1" <-> "NH2"
    Residue "I TYR  336": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  360": "NH1" <-> "NH2"
    Residue "I TYR  374": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  375": "NH1" <-> "NH2"
    Residue "I PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  393": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG  400": "NH1" <-> "NH2"
    Residue "J ARG    9": "NH1" <-> "NH2"
    Residue "J GLU   13": "OE1" <-> "OE2"
    Residue "J PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG   58": "NH1" <-> "NH2"
    Residue "J PHE   71": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG   82": "NH1" <-> "NH2"
    Residue "J ARG   84": "NH1" <-> "NH2"
    Residue "J GLU  100": "OE1" <-> "OE2"
    Residue "J ARG  104": "NH1" <-> "NH2"
    Residue "J PHE  120": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ASP  132": "OD1" <-> "OD2"
    Residue "J TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  143": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  156": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ASP  182": "OD1" <-> "OD2"
    Residue "J TYR  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG  190": "NH1" <-> "NH2"
    Residue "J PHE  219": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR  228": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  229": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG  236": "NH1" <-> "NH2"
    Residue "J ARG  242": "NH1" <-> "NH2"
    Residue "J PHE  243": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K ASP  116": "OD1" <-> "OD2"
    Residue "K ARG  117": "NH1" <-> "NH2"
    Residue "K ARG  129": "NH1" <-> "NH2"
    Residue "K TYR  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE  152": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K ARG  198": "NH1" <-> "NH2"
    Residue "K GLU  284": "OE1" <-> "OE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 17220
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "A"
      Number of atoms: 3017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3017
          Classifications: {'peptide': 382}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 357}
    Chain: "B"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1811
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 11, 'TRANS': 208}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 904
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 3, 'TRANS': 108}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 3017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3017
          Classifications: {'peptide': 382}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 357}
    Chain: "F"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1811
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 11, 'TRANS': 208}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "G"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 904
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 3, 'TRANS': 108}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "I"
      Number of atoms: 3017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3017
          Classifications: {'peptide': 382}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 357}
    Chain: "J"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1811
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 11, 'TRANS': 208}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "K"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 904
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 3, 'TRANS': 108}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Unusual residues: {'CU1': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'CU1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Unusual residues: {'CU1': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "F"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'CU1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "I"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Unusual residues: {'CU1': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "J"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'CU1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 9.90, per 1000 atoms: 0.57
  Number of scatterers: 17220
  At special positions: 0
  Unit cell: (107.682, 107.682, 120.834, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cu     24     28.99
     S      81     16.00
     O    2985      8.00
     N    2835      7.00
     C   11295      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 7.05
  Conformation dependent library (CDL) restraints added in 3.1 seconds
  

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3942

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      75 helices and 24 sheets defined
      42.3% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 44
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 185 through 206
      removed outlier: 3.881A  pdb=" N   TRP A 195 " --> pdb=" O   TRP A 191 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   TRP A 206 " --> pdb=" O   TRP A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 220
      removed outlier: 3.648A  pdb=" N   ASP A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 257
      removed outlier: 3.696A  pdb=" N   ILE A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ILE A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 340
      No H-bonds generated for 'chain 'A' and resid 338 through 340'
    Processing helix  chain 'A' and resid 369 through 373
      removed outlier: 3.793A  pdb=" N   VAL A 373 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 381
      removed outlier: 3.638A  pdb=" N   ILE A 379 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE A 380 " --> pdb=" O   SER A 377 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR A 381 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 376 through 381'
    Processing helix  chain 'B' and resid 12 through 33
      removed outlier: 3.587A  pdb=" N   THR B  20 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU B  26 " --> pdb=" O   ASP B  22 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   PHE B  27 " --> pdb=" O   TRP B  23 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL B  32 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 45
    Processing helix  chain 'B' and resid 52 through 54
      No H-bonds generated for 'chain 'B' and resid 52 through 54'
    Processing helix  chain 'B' and resid 59 through 83
      Proline residue:  B  65  - end of helix
      removed outlier: 3.581A  pdb=" N   VAL B  69 " --> pdb=" O   PRO B  65 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   THR B  70 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   PHE B  71 " --> pdb=" O   VAL B  67 " (cutoff:3.500A)
      Proline residue:  B  72  - end of helix
      removed outlier: 3.736A  pdb=" N   SER B  77 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR B  78 " --> pdb=" O   ALA B  74 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 106
      removed outlier: 3.790A  pdb=" N   CYS B  92 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 137
    Processing helix  chain 'B' and resid 141 through 154
      removed outlier: 4.451A  pdb=" N   ALA B 149 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLY B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 168
      Proline residue:  B 162  - end of helix
      Proline residue:  B 166  - end of helix
    Processing helix  chain 'B' and resid 180 through 187
    Processing helix  chain 'B' and resid 212 through 237
      removed outlier: 3.642A  pdb=" N   ILE B 225 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU B 226 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE B 233 " --> pdb=" O   PHE B 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 112
      No H-bonds generated for 'chain 'C' and resid 109 through 112'
    Processing helix  chain 'C' and resid 124 through 149
    Processing helix  chain 'C' and resid 152 through 155
      No H-bonds generated for 'chain 'C' and resid 152 through 155'
    Processing helix  chain 'C' and resid 185 through 198
    Processing helix  chain 'C' and resid 208 through 215
      removed outlier: 3.863A  pdb=" N   VAL C 214 " --> pdb=" O   TYR C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 269
    Processing helix  chain 'C' and resid 281 through 283
      No H-bonds generated for 'chain 'C' and resid 281 through 283'
    Processing helix  chain 'E' and resid 40 through 44
    Processing helix  chain 'E' and resid 163 through 165
      No H-bonds generated for 'chain 'E' and resid 163 through 165'
    Processing helix  chain 'E' and resid 185 through 206
      removed outlier: 3.881A  pdb=" N   TRP E 195 " --> pdb=" O   TRP E 191 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   TRP E 206 " --> pdb=" O   TRP E 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 215 through 220
      removed outlier: 3.648A  pdb=" N   ASP E 220 " --> pdb=" O   LEU E 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 230 through 257
      removed outlier: 3.696A  pdb=" N   ILE E 244 " --> pdb=" O   LEU E 240 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ILE E 246 " --> pdb=" O   ALA E 242 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 338 through 340
      No H-bonds generated for 'chain 'E' and resid 338 through 340'
    Processing helix  chain 'E' and resid 369 through 373
      removed outlier: 3.793A  pdb=" N   VAL E 373 " --> pdb=" O   ALA E 370 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 376 through 381
      removed outlier: 3.638A  pdb=" N   ILE E 379 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE E 380 " --> pdb=" O   SER E 377 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR E 381 " --> pdb=" O   ASP E 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 376 through 381'
    Processing helix  chain 'F' and resid 12 through 33
      removed outlier: 3.588A  pdb=" N   THR F  20 " --> pdb=" O   GLN F  16 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU F  26 " --> pdb=" O   ASP F  22 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   PHE F  27 " --> pdb=" O   TRP F  23 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE F  30 " --> pdb=" O   LEU F  26 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL F  32 " --> pdb=" O   VAL F  28 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 45
    Processing helix  chain 'F' and resid 52 through 54
      No H-bonds generated for 'chain 'F' and resid 52 through 54'
    Processing helix  chain 'F' and resid 59 through 83
      Proline residue:  F  65  - end of helix
      removed outlier: 3.580A  pdb=" N   VAL F  69 " --> pdb=" O   PRO F  65 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   THR F  70 " --> pdb=" O   ILE F  66 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   PHE F  71 " --> pdb=" O   VAL F  67 " (cutoff:3.500A)
      Proline residue:  F  72  - end of helix
      removed outlier: 3.736A  pdb=" N   SER F  77 " --> pdb=" O   ALA F  73 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR F  78 " --> pdb=" O   ALA F  74 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU F  81 " --> pdb=" O   SER F  77 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 88 through 106
      removed outlier: 3.790A  pdb=" N   CYS F  92 " --> pdb=" O   GLY F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 125 through 137
    Processing helix  chain 'F' and resid 141 through 154
      removed outlier: 4.451A  pdb=" N   ALA F 149 " --> pdb=" O   ALA F 145 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLY F 153 " --> pdb=" O   ALA F 149 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 168
      Proline residue:  F 162  - end of helix
      Proline residue:  F 166  - end of helix
    Processing helix  chain 'F' and resid 180 through 187
    Processing helix  chain 'F' and resid 212 through 237
      removed outlier: 3.643A  pdb=" N   ILE F 225 " --> pdb=" O   ALA F 221 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU F 226 " --> pdb=" O   PHE F 222 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE F 233 " --> pdb=" O   PHE F 229 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 109 through 112
      No H-bonds generated for 'chain 'G' and resid 109 through 112'
    Processing helix  chain 'G' and resid 124 through 149
    Processing helix  chain 'G' and resid 152 through 155
      No H-bonds generated for 'chain 'G' and resid 152 through 155'
    Processing helix  chain 'G' and resid 185 through 198
    Processing helix  chain 'G' and resid 208 through 215
      removed outlier: 3.863A  pdb=" N   VAL G 214 " --> pdb=" O   TYR G 210 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 259 through 269
    Processing helix  chain 'G' and resid 281 through 283
      No H-bonds generated for 'chain 'G' and resid 281 through 283'
    Processing helix  chain 'I' and resid 40 through 44
    Processing helix  chain 'I' and resid 163 through 165
      No H-bonds generated for 'chain 'I' and resid 163 through 165'
    Processing helix  chain 'I' and resid 185 through 206
      removed outlier: 3.881A  pdb=" N   TRP I 195 " --> pdb=" O   TRP I 191 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   TRP I 206 " --> pdb=" O   TRP I 202 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 215 through 220
      removed outlier: 3.648A  pdb=" N   ASP I 220 " --> pdb=" O   LEU I 216 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 230 through 257
      removed outlier: 3.697A  pdb=" N   ILE I 244 " --> pdb=" O   LEU I 240 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ILE I 246 " --> pdb=" O   ALA I 242 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 338 through 340
      No H-bonds generated for 'chain 'I' and resid 338 through 340'
    Processing helix  chain 'I' and resid 369 through 373
      removed outlier: 3.794A  pdb=" N   VAL I 373 " --> pdb=" O   ALA I 370 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 376 through 381
      removed outlier: 3.639A  pdb=" N   ILE I 379 " --> pdb=" O   LEU I 376 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE I 380 " --> pdb=" O   SER I 377 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TYR I 381 " --> pdb=" O   ASP I 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 376 through 381'
    Processing helix  chain 'J' and resid 12 through 33
      removed outlier: 3.589A  pdb=" N   THR J  20 " --> pdb=" O   GLN J  16 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU J  26 " --> pdb=" O   ASP J  22 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   PHE J  27 " --> pdb=" O   TRP J  23 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE J  30 " --> pdb=" O   LEU J  26 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL J  32 " --> pdb=" O   VAL J  28 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 35 through 45
    Processing helix  chain 'J' and resid 52 through 54
      No H-bonds generated for 'chain 'J' and resid 52 through 54'
    Processing helix  chain 'J' and resid 59 through 83
      Proline residue:  J  65  - end of helix
      removed outlier: 3.580A  pdb=" N   VAL J  69 " --> pdb=" O   PRO J  65 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   THR J  70 " --> pdb=" O   ILE J  66 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   PHE J  71 " --> pdb=" O   VAL J  67 " (cutoff:3.500A)
      Proline residue:  J  72  - end of helix
      removed outlier: 3.735A  pdb=" N   SER J  77 " --> pdb=" O   ALA J  73 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TYR J  78 " --> pdb=" O   ALA J  74 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU J  81 " --> pdb=" O   SER J  77 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 88 through 106
      removed outlier: 3.789A  pdb=" N   CYS J  92 " --> pdb=" O   GLY J  88 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 125 through 137
    Processing helix  chain 'J' and resid 141 through 154
      removed outlier: 4.452A  pdb=" N   ALA J 149 " --> pdb=" O   ALA J 145 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLY J 153 " --> pdb=" O   ALA J 149 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 156 through 168
      Proline residue:  J 162  - end of helix
      Proline residue:  J 166  - end of helix
    Processing helix  chain 'J' and resid 180 through 187
    Processing helix  chain 'J' and resid 212 through 237
      removed outlier: 3.642A  pdb=" N   ILE J 225 " --> pdb=" O   ALA J 221 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU J 226 " --> pdb=" O   PHE J 222 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE J 233 " --> pdb=" O   PHE J 229 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 109 through 112
      No H-bonds generated for 'chain 'K' and resid 109 through 112'
    Processing helix  chain 'K' and resid 124 through 149
    Processing helix  chain 'K' and resid 152 through 155
      No H-bonds generated for 'chain 'K' and resid 152 through 155'
    Processing helix  chain 'K' and resid 185 through 198
    Processing helix  chain 'K' and resid 208 through 215
      removed outlier: 3.863A  pdb=" N   VAL K 214 " --> pdb=" O   TYR K 210 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 259 through 269
    Processing helix  chain 'K' and resid 281 through 283
      No H-bonds generated for 'chain 'K' and resid 281 through 283'
    Processing sheet with id=  A, first strand: chain 'A' and resid 47 through 50
      removed outlier: 6.413A  pdb=" N   LYS A 129 " --> pdb=" O   ARG A 100 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   ARG A 100 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 58 through 60
      removed outlier: 8.467A  pdb=" N   VAL A  59 " --> pdb=" O   TRP A 156 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   THR A 158 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 141 through 144
    Processing sheet with id=  D, first strand: chain 'A' and resid 169 through 171
    Processing sheet with id=  E, first strand: chain 'A' and resid 282 through 286
    Processing sheet with id=  F, first strand: chain 'A' and resid 298 through 300
    Processing sheet with id=  G, first strand: chain 'A' and resid 323 through 325
      removed outlier: 6.674A  pdb=" N   PHE A 392 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   PHE A 317 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU A 390 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 170 through 173
    Processing sheet with id=  I, first strand: chain 'E' and resid 47 through 50
      removed outlier: 6.413A  pdb=" N   LYS E 129 " --> pdb=" O   ARG E 100 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   ARG E 100 " --> pdb=" O   LYS E 129 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'E' and resid 58 through 60
      removed outlier: 8.467A  pdb=" N   VAL E  59 " --> pdb=" O   TRP E 156 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   THR E 158 " --> pdb=" O   VAL E  59 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'E' and resid 141 through 144
    Processing sheet with id=  L, first strand: chain 'E' and resid 169 through 171
    Processing sheet with id=  M, first strand: chain 'E' and resid 282 through 286
    Processing sheet with id=  N, first strand: chain 'E' and resid 298 through 300
    Processing sheet with id=  O, first strand: chain 'E' and resid 323 through 325
      removed outlier: 6.674A  pdb=" N   PHE E 392 " --> pdb=" O   GLY E 315 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   PHE E 317 " --> pdb=" O   LEU E 390 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU E 390 " --> pdb=" O   PHE E 317 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'F' and resid 170 through 173
    Processing sheet with id=  Q, first strand: chain 'I' and resid 47 through 50
      removed outlier: 6.412A  pdb=" N   LYS I 129 " --> pdb=" O   ARG I 100 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   ARG I 100 " --> pdb=" O   LYS I 129 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'I' and resid 58 through 60
      removed outlier: 8.466A  pdb=" N   VAL I  59 " --> pdb=" O   TRP I 156 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   THR I 158 " --> pdb=" O   VAL I  59 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'I' and resid 141 through 144
    Processing sheet with id=  T, first strand: chain 'I' and resid 169 through 171
    Processing sheet with id=  U, first strand: chain 'I' and resid 282 through 286
    Processing sheet with id=  V, first strand: chain 'I' and resid 298 through 300
    Processing sheet with id=  W, first strand: chain 'I' and resid 323 through 325
      removed outlier: 6.673A  pdb=" N   PHE I 392 " --> pdb=" O   GLY I 315 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   PHE I 317 " --> pdb=" O   LEU I 390 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU I 390 " --> pdb=" O   PHE I 317 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'J' and resid 170 through 173

    717 hydrogen bonds defined for protein.
    2115 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: 6.24

  Time building geometry restraints manager: 7.65 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2640
        1.32 -     1.44: 5417
        1.44 -     1.56: 9526
        1.56 -     1.69: 0
        1.69 -     1.81: 156
  Bond restraints: 17739
  Sorted by residual:
  bond pdb=" C   ILE B 102 "
       pdb=" N   ASN B 103 "
    ideal  model  delta    sigma   weight residual
    1.335  1.408 -0.073 1.31e-02 5.83e+03 3.13e+01
  bond pdb=" C   ILE F 102 "
       pdb=" N   ASN F 103 "
    ideal  model  delta    sigma   weight residual
    1.335  1.408 -0.073 1.31e-02 5.83e+03 3.13e+01
  bond pdb=" C   ILE J 102 "
       pdb=" N   ASN J 103 "
    ideal  model  delta    sigma   weight residual
    1.335  1.408 -0.073 1.31e-02 5.83e+03 3.10e+01
  bond pdb=" C   ASN F 103 "
       pdb=" N   ARG F 104 "
    ideal  model  delta    sigma   weight residual
    1.335  1.410 -0.075 1.36e-02 5.41e+03 3.08e+01
  bond pdb=" C   ASN J 103 "
       pdb=" N   ARG J 104 "
    ideal  model  delta    sigma   weight residual
    1.335  1.410 -0.075 1.36e-02 5.41e+03 3.08e+01
  ... (remaining 17734 not shown)

  Histogram of bond angle deviations from ideal:
       99.17 -   106.26: 570
      106.26 -   113.34: 9310
      113.34 -   120.43: 7302
      120.43 -   127.51: 6695
      127.51 -   134.60: 309
  Bond angle restraints: 24186
  Sorted by residual:
  angle pdb=" C   PHE I 212 "
        pdb=" N   ILE I 213 "
        pdb=" CA  ILE I 213 "
      ideal   model   delta    sigma   weight residual
     122.13  134.60  -12.47 1.85e+00 2.92e-01 4.54e+01
  angle pdb=" C   PHE A 212 "
        pdb=" N   ILE A 213 "
        pdb=" CA  ILE A 213 "
      ideal   model   delta    sigma   weight residual
     122.13  134.56  -12.43 1.85e+00 2.92e-01 4.51e+01
  angle pdb=" C   PHE E 212 "
        pdb=" N   ILE E 213 "
        pdb=" CA  ILE E 213 "
      ideal   model   delta    sigma   weight residual
     122.13  134.52  -12.39 1.85e+00 2.92e-01 4.49e+01
  angle pdb=" N   ILE I 213 "
        pdb=" CA  ILE I 213 "
        pdb=" C   ILE I 213 "
      ideal   model   delta    sigma   weight residual
     108.88  119.22  -10.34 2.16e+00 2.14e-01 2.29e+01
  angle pdb=" N   ILE E 213 "
        pdb=" CA  ILE E 213 "
        pdb=" C   ILE E 213 "
      ideal   model   delta    sigma   weight residual
     108.88  119.21  -10.33 2.16e+00 2.14e-01 2.29e+01
  ... (remaining 24181 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.63: 8680
       14.63 -    29.25: 1124
       29.25 -    43.88: 247
       43.88 -    58.51: 53
       58.51 -    73.14: 12
  Dihedral angle restraints: 10116
    sinusoidal: 3954
      harmonic: 6162
  Sorted by residual:
  dihedral pdb=" CA  ILE I 213 "
           pdb=" C   ILE I 213 "
           pdb=" N   PRO I 214 "
           pdb=" CA  PRO I 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.61   52.39     0      5.00e+00 4.00e-02 1.10e+02
  dihedral pdb=" CA  ILE E 213 "
           pdb=" C   ILE E 213 "
           pdb=" N   PRO E 214 "
           pdb=" CA  PRO E 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.62   52.38     0      5.00e+00 4.00e-02 1.10e+02
  dihedral pdb=" CA  ILE A 213 "
           pdb=" C   ILE A 213 "
           pdb=" N   PRO A 214 "
           pdb=" CA  PRO A 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.64   52.36     0      5.00e+00 4.00e-02 1.10e+02
  ... (remaining 10113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1692
       0.048 -    0.095: 650
       0.095 -    0.143: 224
       0.143 -    0.191: 28
       0.191 -    0.239: 19
  Chirality restraints: 2613
  Sorted by residual:
  chirality pdb=" CB  VAL E  59 "
            pdb=" CA  VAL E  59 "
            pdb=" CG1 VAL E  59 "
            pdb=" CG2 VAL E  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  VAL A  59 "
            pdb=" CA  VAL A  59 "
            pdb=" CG1 VAL A  59 "
            pdb=" CG2 VAL A  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  VAL I  59 "
            pdb=" CA  VAL I  59 "
            pdb=" CG1 VAL I  59 "
            pdb=" CG2 VAL I  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 2610 not shown)

  Planarity restraints: 3021
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE I 213 "    0.076 5.00e-02 4.00e+02   1.14e-01 2.07e+01
        pdb=" N   PRO I 214 "   -0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO I 214 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO I 214 "    0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 213 "    0.076 5.00e-02 4.00e+02   1.14e-01 2.07e+01
        pdb=" N   PRO E 214 "   -0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO E 214 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO E 214 "    0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 213 "    0.075 5.00e-02 4.00e+02   1.14e-01 2.06e+01
        pdb=" N   PRO A 214 "   -0.196 5.00e-02 4.00e+02
        pdb=" CA  PRO A 214 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO A 214 "    0.062 5.00e-02 4.00e+02
  ... (remaining 3018 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.25: 45
        2.25 -     2.92: 6803
        2.92 -     3.58: 23442
        3.58 -     4.24: 43986
        4.24 -     4.90: 74115
  Nonbonded interactions: 148391
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS I  33 "
            pdb="CU   CU1 I 502 "
     model   vdw
     1.593 3.060
  nonbonded pdb=" ND1 HIS A  33 "
            pdb="CU   CU1 A 502 "
     model   vdw
     1.594 3.060
  nonbonded pdb=" ND1 HIS E  33 "
            pdb="CU   CU1 E 502 "
     model   vdw
     1.595 3.060
  nonbonded pdb=" ND1 HIS E 137 "
            pdb="CU   CU1 E 503 "
     model   vdw
     1.611 3.060
  nonbonded pdb=" ND1 HIS I 137 "
            pdb="CU   CU1 I 503 "
     model   vdw
     1.612 3.060
  ... (remaining 148386 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
  selection = chain 'K'
}

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:             6.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.200
  Construct map_model_manager:             0.010
  Extract box with map and model:          19.690
  Check model and map are aligned:         0.290
  Set scattering table:                    0.140
  Process input model:                     51.920
  Find NCS groups from input model:        0.940
  Set up NCS constraints:                  0.120
  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:             0.010
  Load rotamer database and sin/cos tables:12.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   91.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
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      :  0.007   0.075  17739  Z= 0.422
  Angle     :  0.883  12.466  24186  Z= 0.506
  Chirality :  0.058   0.239   2613
  Planarity :  0.009   0.114   3021
  Dihedral  : 13.746  73.136   6174
  Min Nonbonded Distance : 1.593

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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: -3.14 (0.15), residues: 2106
  helix: -2.75 (0.12), residues: 930
  sheet: -0.38 (0.24), residues: 387
  loop : -1.85 (0.20), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP J 152 
 HIS   0.005   0.001   HIS J 232 
 PHE   0.021   0.002   PHE E  71 
 TYR   0.051   0.003   TYR G 210 
 ARG   0.006   0.001   ARG G 117 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.947 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.7610 (mtm110) cc_final: 0.5799 (mmp-170)
REVERT: A  237 MET cc_start: 0.6876 (ptp) cc_final: 0.6275 (ptt)
REVERT: A  343 GLU cc_start: 0.7584 (pm20) cc_final: 0.7368 (pm20)
REVERT: C  259 MET cc_start: 0.6332 (mtm) cc_final: 0.5924 (mtm)
REVERT: E  163 MET cc_start: 0.7942 (ttt) cc_final: 0.7720 (ttt)
REVERT: E  208 ARG cc_start: 0.7441 (mtm110) cc_final: 0.5531 (mmp-170)
REVERT: E  237 MET cc_start: 0.6873 (ptp) cc_final: 0.6285 (ptt)
REVERT: E  343 GLU cc_start: 0.7602 (pm20) cc_final: 0.7348 (pm20)
REVERT: F   24 MET cc_start: 0.7559 (mtm) cc_final: 0.7309 (mtt)
REVERT: F  100 GLU cc_start: 0.7520 (pt0) cc_final: 0.7234 (pt0)
REVERT: G  259 MET cc_start: 0.6487 (mtm) cc_final: 0.5845 (mtm)
REVERT: I  208 ARG cc_start: 0.7519 (mtm110) cc_final: 0.5796 (mmp-170)
REVERT: I  237 MET cc_start: 0.6945 (ptp) cc_final: 0.6335 (ptt)
REVERT: I  343 GLU cc_start: 0.7545 (pm20) cc_final: 0.7344 (pm20)
REVERT: J  100 GLU cc_start: 0.7632 (pt0) cc_final: 0.7349 (pt0)
REVERT: J  111 TRP cc_start: 0.6447 (m100) cc_final: 0.6206 (m-10)
REVERT: K  259 MET cc_start: 0.6462 (mtm) cc_final: 0.6244 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 1.4392
  time to fit residues: 409.8283
Evaluate side-chains
  189 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 179 optimal weight:    0.9980
   chunk 161 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0170
   chunk 55 optimal weight:    0.6980
   chunk 108 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 166 optimal weight:    0.0000
   chunk 64 optimal weight:    2.9990
   chunk 101 optimal weight:    0.3980
   chunk 124 optimal weight:    0.7980
   chunk 193 optimal weight:    4.9990
   overall best weight:    0.3622

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

Flipped N/Q/H residues before XYZ refinement:
A 137 HIS
A 187 ASN
A 192 HIS
A 265 GLN
A 401 GLN
B 103 ASN
B 107 ASN
B 187 ASN
B 240 ASN
C 134 HIS
C 264 GLN
E 187 ASN
E 192 HIS
E 265 GLN
E 399 ASN
E 401 GLN
** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 187 ASN
F 240 ASN
G 134 HIS
G 264 GLN
I 137 HIS
I 187 ASN
I 192 HIS
I 265 GLN
I 399 ASN
I 401 GLN
** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 187 ASN
J 240 ASN
K 134 HIS
K 264 GLN

Total number of N/Q/H flips: 30

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  17739  Z= 0.137
  Angle     :  0.526   8.733  24186  Z= 0.276
  Chirality :  0.042   0.140   2613
  Planarity :  0.006   0.099   3021
  Dihedral  :  5.452  49.456   2340
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 10.06 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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: -1.37 (0.17), residues: 2106
  helix: -0.94 (0.16), residues: 915
  sheet:  0.43 (0.25), residues: 378
  loop : -1.36 (0.20), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 152 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.012   0.001   PHE B  31 
 TYR   0.010   0.001   TYR B 188 
 ARG   0.005   0.000   ARG J 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 232
  time to evaluate  : 2.059 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
REVERT: A  208 ARG cc_start: 0.7534 (mtm110) cc_final: 0.5789 (mmp-170)
REVERT: A  404 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7618 (tm-30)
REVERT: B   43 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8139 (mp)
REVERT: B   84 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7032 (mmt90)
REVERT: C  198 ARG cc_start: 0.6615 (mpt180) cc_final: 0.6255 (mpp80)
REVERT: C  259 MET cc_start: 0.6475 (mtm) cc_final: 0.6232 (mtm)
REVERT: E  141 MET cc_start: 0.8595 (ptp) cc_final: 0.8377 (ptm)
REVERT: E  208 ARG cc_start: 0.7471 (mtm110) cc_final: 0.5603 (mmp-170)
REVERT: F   43 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8215 (mp)
REVERT: F   82 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6359 (mpt90)
REVERT: F   84 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7016 (mmt90)
REVERT: G  198 ARG cc_start: 0.6603 (mpt180) cc_final: 0.6361 (mpp80)
REVERT: G  259 MET cc_start: 0.6359 (mtm) cc_final: 0.5893 (mtm)
REVERT: I  208 ARG cc_start: 0.7504 (mtm110) cc_final: 0.5808 (mmp-170)
REVERT: I  237 MET cc_start: 0.6637 (ptp) cc_final: 0.6237 (ptt)
REVERT: I  404 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7761 (tt0)
  outliers start: 40
  outliers final: 7
  residues processed: 250
  average time/residue: 1.3350
  time to fit residues: 371.3337
Evaluate side-chains
  217 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 203
  time to evaluate  : 2.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   84 ARG
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  251 MET
Chi-restraints excluded: chain E residue  292 ARG
Chi-restraints excluded: chain F residue   43 LEU
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain G residue  268 SER
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 60 optimal weight:    9.9990
   chunk 160 optimal weight:    0.7980
   chunk 131 optimal weight:   10.0000
   chunk 53 optimal weight:    0.3980
   chunk 193 optimal weight:    5.9990
   chunk 209 optimal weight:    6.9990
   chunk 172 optimal weight:    3.9990
   chunk 192 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 155 optimal weight:    2.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A 137 HIS
A 399 ASN
B 240 ASN
E 399 ASN
F 103 ASN
F 107 ASN
F 240 ASN
I  72 HIS
I 137 HIS
I 399 ASN
J 103 ASN
J 107 ASN
J 240 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  17739  Z= 0.380
  Angle     :  0.620   8.878  24186  Z= 0.322
  Chirality :  0.046   0.144   2613
  Planarity :  0.006   0.104   3021
  Dihedral  :  5.652  50.649   2340
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.80 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 11.89 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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: -0.92 (0.17), residues: 2106
  helix: -0.53 (0.16), residues: 939
  sheet:  0.37 (0.25), residues: 384
  loop : -1.04 (0.21), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 152 
 HIS   0.005   0.001   HIS A 137 
 PHE   0.014   0.002   PHE B  27 
 TYR   0.022   0.002   TYR B 188 
 ARG   0.006   0.000   ARG J 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 207
  time to evaluate  : 1.770 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU G 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it.
REVERT: A  176 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7074 (mt0)
REVERT: A  208 ARG cc_start: 0.7569 (mtm110) cc_final: 0.5733 (mmp-170)
REVERT: A  299 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7350 (ttp-170)
REVERT: A  339 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7108 (p0)
REVERT: A  404 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7755 (tt0)
REVERT: B   84 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7015 (mmt90)
REVERT: B  150 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7298 (ttm)
REVERT: C  259 MET cc_start: 0.6627 (mtm) cc_final: 0.6414 (mtm)
REVERT: E  208 ARG cc_start: 0.7524 (mtm110) cc_final: 0.5623 (mmp-170)
REVERT: E  404 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7775 (tm-30)
REVERT: F   82 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6419 (mpt90)
REVERT: F   84 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6985 (mmt90)
REVERT: I  135 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7887 (t70)
REVERT: I  208 ARG cc_start: 0.7444 (mtm110) cc_final: 0.5684 (mmp-170)
REVERT: I  237 MET cc_start: 0.6810 (ptp) cc_final: 0.6227 (ptt)
REVERT: I  299 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7166 (ttp80)
REVERT: I  339 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7170 (p0)
REVERT: I  404 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7795 (tt0)
REVERT: J   22 ASP cc_start: 0.6317 (m-30) cc_final: 0.5979 (m-30)
REVERT: J   59 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8351 (mt)
REVERT: J  236 ARG cc_start: 0.6825 (mmt90) cc_final: 0.6543 (mmt90)
  outliers start: 67
  outliers final: 23
  residues processed: 246
  average time/residue: 1.4040
  time to fit residues: 382.5210
Evaluate side-chains
  231 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 194
  time to evaluate  : 1.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  299 ARG
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain B residue   84 ARG
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  283 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  404 GLN
Chi-restraints excluded: chain E residue  406 ASP
Chi-restraints excluded: chain F residue   43 LEU
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain F residue  150 MET
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain G residue  268 SER
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue  135 ASP
Chi-restraints excluded: chain I residue  283 SER
Chi-restraints excluded: chain I residue  299 ARG
Chi-restraints excluded: chain I residue  339 ASP
Chi-restraints excluded: chain I residue  352 SER
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain I residue  406 ASP
Chi-restraints excluded: chain J residue   48 TRP
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue  150 MET
Chi-restraints excluded: chain J residue  191 THR
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 191 optimal weight:    3.9990
   chunk 145 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 130 optimal weight:    0.8980
   chunk 194 optimal weight:    0.7980
   chunk 205 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   chunk 184 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 399 ASN
B 240 ASN
E  72 HIS
E 399 ASN
F 240 ASN
I 399 ASN
J 240 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17739  Z= 0.199
  Angle     :  0.533   8.519  24186  Z= 0.278
  Chirality :  0.043   0.141   2613
  Planarity :  0.005   0.100   3021
  Dihedral  :  5.287  49.368   2340
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.00 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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: -0.38 (0.18), residues: 2106
  helix: -0.09 (0.17), residues: 939
  sheet:  0.66 (0.26), residues: 378
  loop : -0.75 (0.21), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 152 
 HIS   0.004   0.001   HIS E 139 
 PHE   0.014   0.001   PHE B 219 
 TYR   0.016   0.001   TYR B 188 
 ARG   0.006   0.000   ARG F 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 208
  time to evaluate  : 2.057 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU G 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it.
REVERT: A  208 ARG cc_start: 0.7563 (mtm110) cc_final: 0.5815 (mmp-170)
REVERT: A  226 GLU cc_start: 0.7186 (pp20) cc_final: 0.6858 (pp20)
REVERT: A  404 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7721 (tm-30)
REVERT: C  198 ARG cc_start: 0.7215 (mpp80) cc_final: 0.6672 (mpp80)
REVERT: C  259 MET cc_start: 0.6642 (mtm) cc_final: 0.6407 (mtm)
REVERT: E  208 ARG cc_start: 0.7483 (mtm110) cc_final: 0.5634 (mmp-170)
REVERT: E  226 GLU cc_start: 0.7338 (pp20) cc_final: 0.6983 (pp20)
REVERT: F   82 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6290 (mpt90)
REVERT: F   84 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7007 (mmt90)
REVERT: G  198 ARG cc_start: 0.7064 (mpp80) cc_final: 0.6779 (mpp80)
REVERT: I  208 ARG cc_start: 0.7401 (mtm110) cc_final: 0.5658 (mmp-170)
REVERT: I  237 MET cc_start: 0.6672 (ptp) cc_final: 0.6218 (ptt)
REVERT: I  339 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7129 (p0)
REVERT: I  404 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7782 (tt0)
REVERT: J   22 ASP cc_start: 0.6202 (m-30) cc_final: 0.5832 (m-30)
REVERT: J   59 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8284 (mt)
REVERT: J  236 ARG cc_start: 0.6774 (mmt90) cc_final: 0.6453 (mmt90)
  outliers start: 46
  outliers final: 12
  residues processed: 233
  average time/residue: 1.3511
  time to fit residues: 350.1453
Evaluate side-chains
  216 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 198
  time to evaluate  : 1.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue   48 TRP
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  406 ASP
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain G residue  268 SER
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue  339 ASP
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 171 optimal weight:    3.9990
   chunk 116 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 153 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 175 optimal weight:    4.9990
   chunk 142 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 105 optimal weight:    0.2980
   chunk 184 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 240 ASN
E 399 ASN
F 240 ASN
I 399 ASN
J 240 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  17739  Z= 0.282
  Angle     :  0.566   8.561  24186  Z= 0.295
  Chirality :  0.044   0.145   2613
  Planarity :  0.005   0.103   3021
  Dihedral  :  5.353  49.423   2340
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 13.56 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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: -0.29 (0.18), residues: 2106
  helix:  0.03 (0.17), residues: 939
  sheet:  0.61 (0.26), residues: 384
  loop : -0.70 (0.21), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 152 
 HIS   0.005   0.001   HIS E 139 
 PHE   0.012   0.001   PHE E  71 
 TYR   0.020   0.001   TYR B 188 
 ARG   0.006   0.000   ARG F 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 200
  time to evaluate  : 1.971 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU G 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it.
REVERT: A  208 ARG cc_start: 0.7598 (mtm110) cc_final: 0.5962 (mmp-170)
REVERT: A  299 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7348 (ttp-170)
REVERT: A  339 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7116 (p0)
REVERT: A  404 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7729 (tm-30)
REVERT: C  259 MET cc_start: 0.6767 (mtm) cc_final: 0.6547 (mtm)
REVERT: E  208 ARG cc_start: 0.7513 (mtm110) cc_final: 0.5647 (mmp-170)
REVERT: F   82 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6329 (mpt90)
REVERT: F   84 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6959 (mmt90)
REVERT: I  208 ARG cc_start: 0.7425 (mtm110) cc_final: 0.5682 (mmp-170)
REVERT: I  237 MET cc_start: 0.6780 (ptp) cc_final: 0.6235 (ptt)
REVERT: I  299 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7218 (ttp80)
REVERT: I  339 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7168 (p0)
REVERT: I  404 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7787 (tt0)
REVERT: J   22 ASP cc_start: 0.6255 (m-30) cc_final: 0.5870 (m-30)
REVERT: J   59 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8320 (mt)
REVERT: J  236 ARG cc_start: 0.6754 (mmt90) cc_final: 0.6444 (mmt90)
  outliers start: 63
  outliers final: 27
  residues processed: 236
  average time/residue: 1.3654
  time to fit residues: 358.1022
Evaluate side-chains
  233 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 197
  time to evaluate  : 1.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  299 ARG
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue   48 TRP
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  283 SER
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  406 ASP
Chi-restraints excluded: chain F residue   48 TRP
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain G residue  268 SER
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue  283 SER
Chi-restraints excluded: chain I residue  299 ARG
Chi-restraints excluded: chain I residue  334 THR
Chi-restraints excluded: chain I residue  339 ASP
Chi-restraints excluded: chain I residue  352 SER
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain I residue  406 ASP
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   48 TRP
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue  150 MET
Chi-restraints excluded: chain J residue  191 THR
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 185 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 120 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 206 optimal weight:    8.9990
   chunk 171 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9980
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 240 ASN
E 176 GLN
E 399 ASN
F 240 ASN
I 399 ASN
J 240 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  17739  Z= 0.448
  Angle     :  0.639   8.747  24186  Z= 0.331
  Chirality :  0.048   0.147   2613
  Planarity :  0.006   0.108   3021
  Dihedral  :  5.591  49.489   2340
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.85 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 13.61 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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: -0.42 (0.18), residues: 2106
  helix: -0.11 (0.17), residues: 945
  sheet:  0.54 (0.25), residues: 384
  loop : -0.74 (0.22), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP J 152 
 HIS   0.005   0.001   HIS E 139 
 PHE   0.013   0.002   PHE F  27 
 TYR   0.023   0.002   TYR B 188 
 ARG   0.006   0.000   ARG F 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 198
  time to evaluate  : 1.864 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU G 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it.
REVERT: A  208 ARG cc_start: 0.7587 (mtm110) cc_final: 0.5918 (mmp-170)
REVERT: A  299 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7354 (ttp-170)
REVERT: A  339 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7150 (p0)
REVERT: A  404 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7701 (tt0)
REVERT: B   84 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7116 (mmt90)
REVERT: E  208 ARG cc_start: 0.7505 (mtm110) cc_final: 0.5660 (mmp-170)
REVERT: E  404 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7694 (tm-30)
REVERT: F   82 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6370 (mpt90)
REVERT: F   84 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7000 (mmt90)
REVERT: I  208 ARG cc_start: 0.7436 (mtm110) cc_final: 0.5782 (mmp-170)
REVERT: I  237 MET cc_start: 0.6985 (ptp) cc_final: 0.6319 (ptt)
REVERT: I  299 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7155 (ttp80)
REVERT: I  339 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7166 (p0)
REVERT: I  404 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7746 (tt0)
REVERT: J   22 ASP cc_start: 0.6224 (m-30) cc_final: 0.5848 (m-30)
REVERT: J   59 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8363 (mt)
REVERT: J  236 ARG cc_start: 0.6789 (mmt90) cc_final: 0.6504 (mmt90)
  outliers start: 73
  outliers final: 43
  residues processed: 236
  average time/residue: 1.4415
  time to fit residues: 377.3693
Evaluate side-chains
  244 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 190
  time to evaluate  : 2.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  299 ARG
Chi-restraints excluded: chain A residue  309 ASN
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   48 TRP
Chi-restraints excluded: chain B residue   84 ARG
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  165 GLU
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  178 VAL
Chi-restraints excluded: chain E residue  251 MET
Chi-restraints excluded: chain E residue  283 SER
Chi-restraints excluded: chain E residue  333 THR
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  404 GLN
Chi-restraints excluded: chain E residue  406 ASP
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   48 TRP
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain F residue  116 ILE
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain G residue  210 TYR
Chi-restraints excluded: chain G residue  268 SER
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue   82 ASP
Chi-restraints excluded: chain I residue  165 GLU
Chi-restraints excluded: chain I residue  269 MET
Chi-restraints excluded: chain I residue  283 SER
Chi-restraints excluded: chain I residue  299 ARG
Chi-restraints excluded: chain I residue  334 THR
Chi-restraints excluded: chain I residue  339 ASP
Chi-restraints excluded: chain I residue  352 SER
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain I residue  406 ASP
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue   48 TRP
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue  112 THR
Chi-restraints excluded: chain J residue  150 MET
Chi-restraints excluded: chain J residue  191 THR
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 198 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 117 optimal weight:    0.5980
   chunk 150 optimal weight:    0.5980
   chunk 116 optimal weight:    0.6980
   chunk 173 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 205 optimal weight:    4.9990
   chunk 128 optimal weight:    2.9990
   chunk 125 optimal weight:    0.6980
   chunk 94 optimal weight:    0.1980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 240 ASN
C 276 GLN
E 176 GLN
E 399 ASN
F 240 ASN
G 276 GLN
I 399 ASN
J 240 ASN
K 276 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  17739  Z= 0.167
  Angle     :  0.516   8.562  24186  Z= 0.269
  Chirality :  0.043   0.143   2613
  Planarity :  0.005   0.102   3021
  Dihedral  :  5.114  48.404   2340
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.17 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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:  0.03 (0.18), residues: 2106
  helix:  0.37 (0.17), residues: 921
  sheet:  0.81 (0.26), residues: 378
  loop : -0.65 (0.21), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 231 
 HIS   0.003   0.001   HIS E  72 
 PHE   0.012   0.001   PHE E  71 
 TYR   0.012   0.001   TYR F 188 
 ARG   0.006   0.000   ARG F 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 198
  time to evaluate  : 1.918 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU G 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it.
REVERT: A  208 ARG cc_start: 0.7576 (mtm110) cc_final: 0.5958 (mmp-170)
REVERT: A  299 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7307 (ttp-170)
REVERT: A  339 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7114 (p0)
REVERT: A  404 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7620 (tm-30)
REVERT: B   84 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7095 (mmt90)
REVERT: E  165 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7417 (pt0)
REVERT: E  208 ARG cc_start: 0.7490 (mtm110) cc_final: 0.5649 (mmp-170)
REVERT: F   22 ASP cc_start: 0.5928 (m-30) cc_final: 0.5619 (m-30)
REVERT: F   82 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6373 (mpt90)
REVERT: F   84 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7014 (mmt90)
REVERT: F  150 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6943 (ttm)
REVERT: I   53 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8175 (p)
REVERT: I  208 ARG cc_start: 0.7476 (mtm110) cc_final: 0.5850 (mmp-170)
REVERT: I  237 MET cc_start: 0.6686 (ptp) cc_final: 0.6269 (ptt)
REVERT: I  299 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7207 (ttp80)
REVERT: I  404 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7738 (tt0)
REVERT: J  236 ARG cc_start: 0.6695 (mmt90) cc_final: 0.6373 (mmt90)
  outliers start: 48
  outliers final: 22
  residues processed: 226
  average time/residue: 1.3862
  time to fit residues: 347.0534
Evaluate side-chains
  228 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 196
  time to evaluate  : 1.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  299 ARG
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   84 ARG
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  251 MET
Chi-restraints excluded: chain E residue  283 SER
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  406 ASP
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain F residue  150 MET
Chi-restraints excluded: chain G residue  210 TYR
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue  165 GLU
Chi-restraints excluded: chain I residue  299 ARG
Chi-restraints excluded: chain I residue  334 THR
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue  116 ILE
Chi-restraints excluded: chain J residue  150 MET
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 122 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0020
   chunk 40 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 139 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 161 optimal weight:    0.1980
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
B 240 ASN
E 176 GLN
E 399 ASN
F 240 ASN
I 399 ASN
J 240 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  17739  Z= 0.170
  Angle     :  0.513   8.390  24186  Z= 0.267
  Chirality :  0.042   0.142   2613
  Planarity :  0.005   0.106   3021
  Dihedral  :  4.999  47.870   2340
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.94 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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:  0.25 (0.18), residues: 2106
  helix:  0.54 (0.17), residues: 921
  sheet:  0.94 (0.26), residues: 378
  loop : -0.52 (0.21), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 231 
 HIS   0.003   0.001   HIS A 139 
 PHE   0.012   0.001   PHE E  71 
 TYR   0.015   0.001   TYR B 188 
 ARG   0.005   0.000   ARG F 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 199
  time to evaluate  : 2.046 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU G 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it.
REVERT: A  208 ARG cc_start: 0.7582 (mtm110) cc_final: 0.5973 (mmp-170)
REVERT: A  226 GLU cc_start: 0.7174 (pp20) cc_final: 0.6791 (pp20)
REVERT: A  299 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7338 (ttp-170)
REVERT: A  339 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7146 (p0)
REVERT: A  404 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7653 (tm-30)
REVERT: B   84 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7030 (mmt90)
REVERT: E  165 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7446 (pt0)
REVERT: E  208 ARG cc_start: 0.7517 (mtm110) cc_final: 0.5696 (mmp-170)
REVERT: F   82 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6297 (mpt90)
REVERT: F   84 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6958 (mmt90)
REVERT: F  150 MET cc_start: 0.7278 (ttm) cc_final: 0.6901 (ttt)
REVERT: I   53 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8222 (p)
REVERT: I  208 ARG cc_start: 0.7422 (mtm110) cc_final: 0.5790 (mmp-170)
REVERT: I  237 MET cc_start: 0.6599 (ptp) cc_final: 0.6202 (ptt)
REVERT: I  299 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7193 (ttp80)
REVERT: I  404 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7800 (tt0)
  outliers start: 40
  outliers final: 22
  residues processed: 226
  average time/residue: 1.4025
  time to fit residues: 351.4198
Evaluate side-chains
  222 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 191
  time to evaluate  : 1.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  299 ARG
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   84 ARG
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  283 SER
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  406 ASP
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain G residue  268 SER
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue  165 GLU
Chi-restraints excluded: chain I residue  283 SER
Chi-restraints excluded: chain I residue  299 ARG
Chi-restraints excluded: chain I residue  334 THR
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue  116 ILE
Chi-restraints excluded: chain J residue  150 MET
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 186 optimal weight:    1.9990
   chunk 196 optimal weight:    0.9990
   chunk 179 optimal weight:    0.8980
   chunk 191 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 150 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 172 optimal weight:    2.9990
   chunk 180 optimal weight:    6.9990
   chunk 190 optimal weight:    1.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
B 240 ASN
E 176 GLN
F 240 ASN
G 276 GLN
I 399 ASN
J 240 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  17739  Z= 0.231
  Angle     :  0.540   8.421  24186  Z= 0.281
  Chirality :  0.043   0.144   2613
  Planarity :  0.005   0.105   3021
  Dihedral  :  5.108  48.478   2340
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.13 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.11 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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:  0.24 (0.18), residues: 2106
  helix:  0.55 (0.17), residues: 918
  sheet:  0.91 (0.26), residues: 378
  loop : -0.54 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J 152 
 HIS   0.004   0.001   HIS E 139 
 PHE   0.012   0.001   PHE E  71 
 TYR   0.018   0.001   TYR B 188 
 ARG   0.007   0.000   ARG J 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 190
  time to evaluate  : 1.850 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU G 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it.
REVERT: A  208 ARG cc_start: 0.7607 (mtm110) cc_final: 0.5977 (mmp-170)
REVERT: A  299 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7308 (ttp-170)
REVERT: A  339 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7150 (p0)
REVERT: A  404 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7683 (tm-30)
REVERT: B   84 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7054 (mmt90)
REVERT: B  150 MET cc_start: 0.7449 (ttm) cc_final: 0.6994 (tpp)
REVERT: E  165 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7445 (pt0)
REVERT: E  208 ARG cc_start: 0.7533 (mtm110) cc_final: 0.5700 (mmp-170)
REVERT: F   82 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6296 (mpt90)
REVERT: F   84 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7008 (mmt90)
REVERT: F  150 MET cc_start: 0.7324 (ttm) cc_final: 0.6976 (ttt)
REVERT: I  163 MET cc_start: 0.7859 (ttt) cc_final: 0.7568 (tpp)
REVERT: I  208 ARG cc_start: 0.7485 (mtm110) cc_final: 0.5874 (mmp-170)
REVERT: I  237 MET cc_start: 0.6629 (ptp) cc_final: 0.6208 (ptt)
REVERT: I  299 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7196 (ttp80)
REVERT: I  404 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7806 (tt0)
  outliers start: 43
  outliers final: 27
  residues processed: 218
  average time/residue: 1.4170
  time to fit residues: 341.6868
Evaluate side-chains
  224 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 189
  time to evaluate  : 1.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  299 ARG
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   48 TRP
Chi-restraints excluded: chain B residue   84 ARG
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  170 VAL
Chi-restraints excluded: chain E residue  251 MET
Chi-restraints excluded: chain E residue  283 SER
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  406 ASP
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain G residue  268 SER
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue  165 GLU
Chi-restraints excluded: chain I residue  283 SER
Chi-restraints excluded: chain I residue  299 ARG
Chi-restraints excluded: chain I residue  334 THR
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain I residue  406 ASP
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue  116 ILE
Chi-restraints excluded: chain J residue  150 MET
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 125 optimal weight:    0.5980
   chunk 202 optimal weight:    0.9990
   chunk 123 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0670
   chunk 140 optimal weight:    0.9990
   chunk 212 optimal weight:    6.9990
   chunk 195 optimal weight:    0.6980
   chunk 168 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 130 optimal weight:    0.0060
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.4734

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
B 240 ASN
C 276 GLN
E 176 GLN
E 399 ASN
F 240 ASN
I 399 ASN
J 240 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  17739  Z= 0.151
  Angle     :  0.501   8.318  24186  Z= 0.261
  Chirality :  0.042   0.140   2613
  Planarity :  0.005   0.103   3021
  Dihedral  :  4.897  47.678   2340
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.56 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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:  0.47 (0.18), residues: 2106
  helix:  0.79 (0.18), residues: 900
  sheet:  0.84 (0.25), residues: 393
  loop : -0.38 (0.22), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 231 
 HIS   0.003   0.001   HIS I 139 
 PHE   0.012   0.001   PHE F  27 
 TYR   0.012   0.001   TYR B 188 
 ARG   0.007   0.000   ARG J 236 

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

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

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4212 Ramachandran restraints generated.
    2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 193
  time to evaluate  : 1.884 
Fit side-chains
TARDY: cannot create tardy model for: "LEU C 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU G 286 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU K 286 " (corrupted residue). Skipping it.
REVERT: A  208 ARG cc_start: 0.7592 (mtm110) cc_final: 0.5970 (mmp-170)
REVERT: A  226 GLU cc_start: 0.7179 (pp20) cc_final: 0.6824 (pp20)
REVERT: A  299 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7191 (ttp80)
REVERT: A  339 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7227 (p0)
REVERT: A  404 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7702 (tm-30)
REVERT: B   84 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6988 (mmt90)
REVERT: B  150 MET cc_start: 0.7330 (ttm) cc_final: 0.7002 (tpp)
REVERT: E  141 MET cc_start: 0.8641 (ptp) cc_final: 0.8417 (ptm)
REVERT: E  165 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7465 (pt0)
REVERT: E  208 ARG cc_start: 0.7494 (mtm110) cc_final: 0.5801 (mmp-170)
REVERT: F   82 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6281 (mpt90)
REVERT: F   84 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6965 (mmt90)
REVERT: F  150 MET cc_start: 0.7315 (ttm) cc_final: 0.7034 (ttm)
REVERT: I   53 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8210 (p)
REVERT: I  208 ARG cc_start: 0.7426 (mtm110) cc_final: 0.5792 (mmp-170)
REVERT: I  237 MET cc_start: 0.6549 (ptp) cc_final: 0.6173 (ptt)
REVERT: I  299 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7218 (ttp80)
REVERT: I  404 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7815 (tt0)
REVERT: J  150 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6621 (ptt)
REVERT: J  236 ARG cc_start: 0.6881 (mmt90) cc_final: 0.6505 (mmt90)
  outliers start: 33
  outliers final: 19
  residues processed: 216
  average time/residue: 1.4578
  time to fit residues: 347.8343
Evaluate side-chains
  222 residues out of total 1800 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 2.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  283 SER
Chi-restraints excluded: chain A residue  299 ARG
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   84 ARG
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain E residue  135 ASP
Chi-restraints excluded: chain E residue  251 MET
Chi-restraints excluded: chain E residue  283 SER
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  406 ASP
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   82 ARG
Chi-restraints excluded: chain F residue   84 ARG
Chi-restraints excluded: chain G residue  268 SER
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue  165 GLU
Chi-restraints excluded: chain I residue  299 ARG
Chi-restraints excluded: chain I residue  334 THR
Chi-restraints excluded: chain I residue  404 GLN
Chi-restraints excluded: chain J residue   29 VAL
Chi-restraints excluded: chain J residue  116 ILE
Chi-restraints excluded: chain J residue  150 MET
Chi-restraints excluded: chain K residue  268 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 134 optimal weight:    0.9990
   chunk 180 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 155 optimal weight:    0.0170
   chunk 24 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 169 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 173 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.0026

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

Flipped N/Q/H residues before XYZ refinement:
A 176 GLN
B 240 ASN
E 176 GLN
F 240 ASN
I 399 ASN
J 240 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.140274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.099916 restraints weight = 16919.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.74
r_work: 0.3149 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  17739  Z= 0.412
  Angle     :  0.622   8.697  24186  Z= 0.322
  Chirality :  0.047   0.149   2613
  Planarity :  0.006   0.112   3021
  Dihedral  :  5.376  48.995   2340
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.42 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.17 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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:  0.08 (0.18), residues: 2106
  helix:  0.37 (0.17), residues: 921
  sheet:  0.81 (0.25), residues: 384
  loop : -0.56 (0.21), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F  48 
 HIS   0.005   0.001   HIS A 139 
 PHE   0.012   0.002   PHE J  27 
 TYR   0.021   0.002   TYR B 188 
 ARG   0.007   0.000   ARG J 236 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6381.69 seconds
wall clock time: 114 minutes 10.16 seconds (6850.16 seconds total)