Starting phenix.real_space_refine
on Mon Feb 19 21:44:25 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wru_21888/02_2024/6wru_21888_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wru_21888/02_2024/6wru_21888.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wru_21888/02_2024/6wru_21888.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wru_21888/02_2024/6wru_21888.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wru_21888/02_2024/6wru_21888_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wru_21888/02_2024/6wru_21888_trim_updated.pdb"
  }
  resolution = 3.1
  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=   0.013 sd=   0.292
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P    2771      5.49       5
     S      59      5.16       5
     C   40429      2.51       5
     N   15151      2.21       5
     O   23282      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   22": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   23": "NH1" <-> "NH2"
    Residue "A ARG   29": "NH1" <-> "NH2"
    Residue "A GLU   36": "OE1" <-> "OE2"
    Residue "A ARG   41": "NH1" <-> "NH2"
    Residue "A GLU   46": "OE1" <-> "OE2"
    Residue "A ARG   53": "NH1" <-> "NH2"
    Residue "A ARG   64": "NH1" <-> "NH2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A GLU   87": "OE1" <-> "OE2"
    Residue "A ARG   91": "NH1" <-> "NH2"
    Residue "A ARG  103": "NH1" <-> "NH2"
    Residue "A ARG  111": "NH1" <-> "NH2"
    Residue "B GLU   23": "OE1" <-> "OE2"
    Residue "B TYR   83": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  117": "OE1" <-> "OE2"
    Residue "B GLU  145": "OE1" <-> "OE2"
    Residue "B GLU  180": "OE1" <-> "OE2"
    Residue "B ARG  261": "NH1" <-> "NH2"
    Residue "C ARG    3": "NH1" <-> "NH2"
    Residue "C ARG   13": "NH1" <-> "NH2"
    Residue "C ARG   48": "NH1" <-> "NH2"
    Residue "C ARG   70": "NH1" <-> "NH2"
    Residue "C GLU  103": "OE1" <-> "OE2"
    Residue "D GLU   15": "OE1" <-> "OE2"
    Residue "D GLU   54": "OE1" <-> "OE2"
    Residue "D ARG   67": "NH1" <-> "NH2"
    Residue "D ARG   78": "NH1" <-> "NH2"
    Residue "D ARG   84": "NH1" <-> "NH2"
    Residue "E TYR   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG   84": "NH1" <-> "NH2"
    Residue "E ARG   88": "NH1" <-> "NH2"
    Residue "F GLU   18": "OE1" <-> "OE2"
    Residue "F ARG   32": "NH1" <-> "NH2"
    Residue "F PHE   46": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG   64": "NH1" <-> "NH2"
    Residue "F ARG   76": "NH1" <-> "NH2"
    Residue "F GLU   84": "OE1" <-> "OE2"
    Residue "G GLU   36": "OE1" <-> "OE2"
    Residue "H GLU   45": "OE1" <-> "OE2"
    Residue "H GLU   47": "OE1" <-> "OE2"
    Residue "J ARG   18": "NH1" <-> "NH2"
    Residue "J ARG   37": "NH1" <-> "NH2"
    Residue "K GLU    5": "OE1" <-> "OE2"
    Residue "K GLU   13": "OE1" <-> "OE2"
    Residue "K GLU   15": "OE1" <-> "OE2"
    Residue "K ARG   29": "NH1" <-> "NH2"
    Residue "K ARG   47": "NH1" <-> "NH2"
    Residue "K ARG   52": "NH1" <-> "NH2"
    Residue "K ARG   60": "NH1" <-> "NH2"
    Residue "K GLU   61": "OE1" <-> "OE2"
    Residue "L GLU   21": "OE1" <-> "OE2"
    Residue "L GLU   32": "OE1" <-> "OE2"
    Residue "L GLU   42": "OE1" <-> "OE2"
    Residue "L ARG   86": "NH1" <-> "NH2"
    Residue "L ARG   92": "NH1" <-> "NH2"
    Residue "L PHE  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ARG  138": "NH1" <-> "NH2"
    Residue "L ASP  159": "OD1" <-> "OD2"
    Residue "M ARG   10": "NH1" <-> "NH2"
    Residue "M GLU   24": "OE1" <-> "OE2"
    Residue "M ARG   44": "NH1" <-> "NH2"
    Residue "N ARG    6": "NH1" <-> "NH2"
    Residue "N ARG    7": "NH1" <-> "NH2"
    Residue "N GLU   29": "OE1" <-> "OE2"
    Residue "O GLU   11": "OE1" <-> "OE2"
    Residue "O GLU   28": "OE1" <-> "OE2"
    Residue "P ARG    4": "NH1" <-> "NH2"
    Residue "P ARG   20": "NH1" <-> "NH2"
    Residue "P ARG   22": "NH1" <-> "NH2"
    Residue "P ARG   34": "NH1" <-> "NH2"
    Residue "Q ARG   13": "NH1" <-> "NH2"
    Residue "Q ARG   42": "NH1" <-> "NH2"
    Residue "Q ARG   57": "NH1" <-> "NH2"
    Residue "S GLU   35": "OE1" <-> "OE2"
    Residue "S ARG   54": "NH1" <-> "NH2"
    Residue "S ARG   62": "NH1" <-> "NH2"
    Residue "S ARG  107": "NH1" <-> "NH2"
    Residue "S GLU  120": "OE1" <-> "OE2"
    Residue "S GLU  159": "OE1" <-> "OE2"
    Residue "S ARG  168": "NH1" <-> "NH2"
    Residue "U ARG    3": "NH1" <-> "NH2"
    Residue "U GLU   32": "OE1" <-> "OE2"
    Residue "U GLU   39": "OE1" <-> "OE2"
    Residue "U GLU   60": "OE1" <-> "OE2"
    Residue "U GLU   88": "OE1" <-> "OE2"
    Residue "U GLU  114": "OE1" <-> "OE2"
    Residue "U GLU  126": "OE1" <-> "OE2"
    Residue "U GLU  134": "OE1" <-> "OE2"
    Residue "U ARG  163": "NH1" <-> "NH2"
    Residue "U ARG  170": "NH1" <-> "NH2"
    Residue "V ARG    2": "NH1" <-> "NH2"
    Residue "V GLU   13": "OE1" <-> "OE2"
    Residue "V ARG   14": "NH1" <-> "NH2"
    Residue "V ARG   38": "NH1" <-> "NH2"
    Residue "V TYR   45": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V GLU   70": "OE1" <-> "OE2"
    Residue "V GLU  130": "OE1" <-> "OE2"
    Residue "V ARG  144": "NH1" <-> "NH2"
    Residue "W ASP   73": "OD1" <-> "OD2"
    Residue "W GLU  108": "OE1" <-> "OE2"
    Residue "X GLU    5": "OE1" <-> "OE2"
    Residue "X GLU   51": "OE1" <-> "OE2"
    Residue "X GLU   73": "OE1" <-> "OE2"
    Residue "X GLU   86": "OE1" <-> "OE2"
    Residue "X GLU  105": "OE1" <-> "OE2"
    Residue "X GLU  134": "OE1" <-> "OE2"
    Residue "Y ARG   10": "NH1" <-> "NH2"
    Residue "Y ARG   45": "NH1" <-> "NH2"
    Residue "Y GLU   48": "OE1" <-> "OE2"
    Residue "Y ARG   51": "NH1" <-> "NH2"
    Residue "Y ARG   56": "NH1" <-> "NH2"
    Residue "Y ARG   60": "NH1" <-> "NH2"
    Residue "Y PHE  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU  111": "OE1" <-> "OE2"
    Residue "Y ARG  115": "NH1" <-> "NH2"
    Residue "Y PHE  131": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y GLU  136": "OE1" <-> "OE2"
    Residue "Z GLU   34": "OE1" <-> "OE2"
    Residue "Z ARG   67": "NH1" <-> "NH2"
    Residue "Z GLU  115": "OE1" <-> "OE2"
    Residue "a GLU   71": "OE1" <-> "OE2"
    Residue "a GLU   91": "OE1" <-> "OE2"
    Residue "a GLU  114": "OE1" <-> "OE2"
    Residue "a GLU  118": "OE1" <-> "OE2"
    Residue "I ARG   22": "NH1" <-> "NH2"
    Residue "I ARG   28": "NH1" <-> "NH2"
    Residue "I ARG   49": "NH1" <-> "NH2"
    Residue "I ASP   64": "OD1" <-> "OD2"
    Residue "I PHE   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG   79": "NH1" <-> "NH2"
  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: 81693
  Number of models: 1
  Model: ""
    Number of chains: 29
    Chain: "A"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 915
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 4, 'TRANS': 108}
    Chain: "B"
      Number of atoms: 2103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2103
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 17, 'TRANS': 257}
    Chain: "C"
      Number of atoms: 943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 943
          Classifications: {'peptide': 116}
          Link IDs: {'TRANS': 115}
    Chain: "D"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 785
          Classifications: {'peptide': 100}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 97}
    Chain: "E"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 853
          Classifications: {'peptide': 111}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 711
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 2, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 689
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 727
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "J"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 463
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 1, 'TRANS': 57}
    Chain: "K"
      Number of atoms: 481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 481
          Classifications: {'peptide': 58}
          Link IDs: {'TRANS': 57}
    Chain: "L"
      Number of atoms: 1628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1628
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 8, 'TRANS': 206}
    Chain: "M"
      Number of atoms: 432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 432
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 2, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 397
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 3, 'TRANS': 46}
    Chain: "O"
      Number of atoms: 390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 390
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "P"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 372
          Classifications: {'peptide': 44}
          Link IDs: {'PTRANS': 1, 'TRANS': 42}
    Chain: "Q"
      Number of atoms: 521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 521
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "R"
      Number of atoms: 296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 296
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 3, 'TRANS': 33}
    Chain: "S"
      Number of atoms: 1472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1472
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 9, 'TRANS': 182}
    Chain: "U"
      Number of atoms: 1360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1360
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 7, 'TRANS': 166}
    Chain: "V"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1138
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 6, 'TRANS': 136}
    Chain: "W"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 911
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "X"
      Number of atoms: 1082
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1082
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 5, 'TRANS': 138}
    Chain: "Y"
      Number of atoms: 1089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1089
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 7, 'TRANS': 128}
    Chain: "Z"
      Number of atoms: 899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 899
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 1, 'TRANS': 112}
          Chain breaks: 1
    Chain: "a"
      Number of atoms: 899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 899
          Classifications: {'peptide': 116}
          Link IDs: {'PCIS': 1, 'TRANS': 114}
    Chain: "1"
      Number of atoms: 57132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2665, 57132
          Inner-chain residues flagged as termini: ['pdbres="  A 1 318 "', 'pdbres="  A 11459 "', 'pdbres="  U 11540 "', 'pdbres="  G 11556 "']
          Classifications: {'RNA': 2665}
          Modifications used: {'5*END': 5, 'rna2p_pur': 254, 'rna2p_pyr': 130, 'rna3p_pur': 1274, 'rna3p_pyr': 1007}
          Link IDs: {'rna2p': 384, 'rna3p': 2280}
          Chain breaks: 7
    Chain: "2"
      Number of atoms: 2381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 2381
          Classifications: {'RNA': 112}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 49}
          Link IDs: {'rna2p': 12, 'rna3p': 99}
    Chain: "I"
      Number of atoms: 597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 597
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "1"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'U7Y': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 32.30, per 1000 atoms: 0.40
  Number of scatterers: 81693
  At special positions: 0
  Unit cell: (226.98, 230.86, 182.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      59     16.00
     P    2771     15.00
     F       1      9.00
     O   23282      8.00
     N   15151      7.00
     C   40429      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  33 " - pdb=" SG  CYS N  43 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  14 " - pdb=" SG  CYS R  27 " distance=2.04

  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: 32.06
  Conformation dependent library (CDL) restraints added in 4.2 seconds
  

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5148

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      62 helices and 41 sheets defined
      20.4% alpha, 17.6% beta
      784 base pairs and 1475 stacking pairs defined.
    Time for finding SS restraints: 37.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 14
      No H-bonds generated for 'chain 'A' and resid 12 through 14'
    Processing helix  chain 'A' and resid 101 through 103
      No H-bonds generated for 'chain 'A' and resid 101 through 103'
    Processing helix  chain 'B' and resid 132 through 134
      No H-bonds generated for 'chain 'B' and resid 132 through 134'
    Processing helix  chain 'B' and resid 198 through 202
      removed outlier: 4.254A  pdb=" N   GLU B 201 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 224
      No H-bonds generated for 'chain 'B' and resid 222 through 224'
    Processing helix  chain 'C' and resid 9 through 18
      removed outlier: 3.642A  pdb=" N   ARG C  13 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS C  16 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   THR C  17 " --> pdb=" O   ARG C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 29
    Processing helix  chain 'C' and resid 32 through 72
      removed outlier: 4.115A  pdb=" N   GLN C  37 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ARG C  51 " --> pdb=" O   PHE C  47 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   LYS C  54 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ARG C  55 " --> pdb=" O   ARG C  51 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG C  58 " --> pdb=" O   LYS C  54 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLN C  71 " --> pdb=" O   ALA C  67 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   HIS C  72 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 86
    Processing helix  chain 'C' and resid 92 through 101
    Processing helix  chain 'C' and resid 103 through 115
      removed outlier: 3.964A  pdb=" N   GLN C 108 " --> pdb=" O   LYS C 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 14 through 24
      removed outlier: 4.437A  pdb=" N   LEU E  19 " --> pdb=" O   ARG E  15 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   VAL E  20 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASP E  22 " --> pdb=" O   ARG E  18 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LEU E  23 " --> pdb=" O   LEU E  19 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ILE E  24 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 37
    Processing helix  chain 'E' and resid 44 through 60
      removed outlier: 3.699A  pdb=" N   ALA E  58 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLU E  59 " --> pdb=" O   LEU E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 91
      No H-bonds generated for 'chain 'E' and resid 89 through 91'
    Processing helix  chain 'F' and resid 35 through 45
      removed outlier: 3.637A  pdb=" N   GLU F  43 " --> pdb=" O   LYS F  39 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 65 through 67
      No H-bonds generated for 'chain 'G' and resid 65 through 67'
    Processing helix  chain 'H' and resid 15 through 22
    Processing helix  chain 'H' and resid 45 through 55
      removed outlier: 3.550A  pdb=" N   ILE H  49 " --> pdb=" O   GLU H  45 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU H  54 " --> pdb=" O   LYS H  50 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 51 through 54
      No H-bonds generated for 'chain 'J' and resid 51 through 54'
    Processing helix  chain 'K' and resid 10 through 34
      removed outlier: 3.989A  pdb=" N   LYS K  22 " --> pdb=" O   ILE K  18 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLU K  24 " --> pdb=" O   SER K  20 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   LEU K  25 " --> pdb=" O   SER K  21 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA K  33 " --> pdb=" O   ARG K  29 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 40 through 60
      removed outlier: 3.910A  pdb=" N   ARG K  44 " --> pdb=" O   ALA K  41 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ARG K  47 " --> pdb=" O   ARG K  44 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   LEU K  53 " --> pdb=" O   ILE K  50 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   VAL K  56 " --> pdb=" O   LEU K  53 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 71 through 80
      removed outlier: 3.520A  pdb=" N   LYS L  78 " --> pdb=" O   GLU L  74 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS L  79 " --> pdb=" O   GLY L  75 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA L  80 " --> pdb=" O   HIS L  76 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 107 through 110
    Processing helix  chain 'L' and resid 130 through 133
      No H-bonds generated for 'chain 'L' and resid 130 through 133'
    Processing helix  chain 'M' and resid 17 through 25
    Processing helix  chain 'M' and resid 41 through 49
      removed outlier: 3.685A  pdb=" N   GLY M  45 " --> pdb=" O   PRO M  41 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLN M  46 " --> pdb=" O   ALA M  42 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 12 through 16
    Processing helix  chain 'P' and resid 10 through 17
    Processing helix  chain 'P' and resid 19 through 22
      No H-bonds generated for 'chain 'P' and resid 19 through 22'
    Processing helix  chain 'P' and resid 26 through 38
      removed outlier: 3.558A  pdb=" N   LYS P  30 " --> pdb=" O   LYS P  26 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL P  31 " --> pdb=" O   ASN P  27 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG P  37 " --> pdb=" O   ALA P  33 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS P  38 " --> pdb=" O   ARG P  34 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 52 through 57
    Processing helix  chain 'R' and resid 30 through 32
      No H-bonds generated for 'chain 'R' and resid 30 through 32'
    Processing helix  chain 'S' and resid 30 through 44
      removed outlier: 3.762A  pdb=" N   GLU S  35 " --> pdb=" O   SER S  31 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU S  44 " --> pdb=" O   GLN S  40 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 103 through 119
    Processing helix  chain 'S' and resid 136 through 146
    Processing helix  chain 'S' and resid 184 through 188
    Processing helix  chain 'S' and resid 198 through 205
    Processing helix  chain 'U' and resid 62 through 80
      removed outlier: 3.626A  pdb=" N   ALA U  70 " --> pdb=" O   GLY U  66 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   VAL U  79 " --> pdb=" O   MET U  75 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 138 through 151
      removed outlier: 4.375A  pdb=" N   VAL U 151 " --> pdb=" O   ASN U 147 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 26 through 38
      removed outlier: 3.861A  pdb=" N   GLU V  32 " --> pdb=" O   ARG V  28 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 60 through 62
      No H-bonds generated for 'chain 'V' and resid 60 through 62'
    Processing helix  chain 'V' and resid 92 through 109
      Proline residue:  V  98  - end of helix
      removed outlier: 3.520A  pdb=" N   LEU V 101 " --> pdb=" O   ASN V  97 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   MET V 109 " --> pdb=" O   SER V 105 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 114 through 118
      removed outlier: 3.563A  pdb=" N   LYS V 118 " --> pdb=" O   ARG V 114 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'V' and resid 114 through 118'
    Processing helix  chain 'V' and resid 120 through 122
      No H-bonds generated for 'chain 'V' and resid 120 through 122'
    Processing helix  chain 'W' and resid 114 through 117
      No H-bonds generated for 'chain 'W' and resid 114 through 117'
    Processing helix  chain 'X' and resid 38 through 40
      No H-bonds generated for 'chain 'X' and resid 38 through 40'
    Processing helix  chain 'X' and resid 57 through 59
      No H-bonds generated for 'chain 'X' and resid 57 through 59'
    Processing helix  chain 'X' and resid 80 through 84
      removed outlier: 3.801A  pdb=" N   LYS X  84 " --> pdb=" O   GLN X  81 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 95 through 99
    Processing helix  chain 'X' and resid 133 through 138
    Processing helix  chain 'Y' and resid 44 through 58
    Processing helix  chain 'Y' and resid 111 through 121
    Processing helix  chain 'Z' and resid 10 through 27
    Processing helix  chain 'Z' and resid 34 through 53
      removed outlier: 3.824A  pdb=" N   GLU Z  39 " --> pdb=" O   ALA Z  35 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   SER Z  42 " --> pdb=" O   LYS Z  38 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL Z  43 " --> pdb=" O   GLU Z  39 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU Z  45 " --> pdb=" O   ARG Z  41 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   LYS Z  46 " --> pdb=" O   SER Z  42 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU Z  47 " --> pdb=" O   VAL Z  43 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU Z  50 " --> pdb=" O   LYS Z  46 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 56 through 62
    Processing helix  chain 'Z' and resid 81 through 84
      No H-bonds generated for 'chain 'Z' and resid 81 through 84'
    Processing helix  chain 'Z' and resid 88 through 92
    Processing helix  chain 'a' and resid 9 through 18
      removed outlier: 3.677A  pdb=" N   LYS a  13 " --> pdb=" O   LYS a   9 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG a  14 " --> pdb=" O   VAL a  10 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 70 through 86
      removed outlier: 3.517A  pdb=" N   ASP a  86 " --> pdb=" O   LYS a  82 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 104 through 110
    Processing helix  chain 'a' and resid 113 through 115
      No H-bonds generated for 'chain 'a' and resid 113 through 115'
    Processing sheet with id=  A, first strand: chain 'A' and resid 85 through 90
      removed outlier: 4.025A  pdb=" N   LYS A  85 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   THR A  27 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLU A  36 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
      removed outlier: 9.084A  pdb=" N   GLU A  46 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE A  66 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   THR A  62 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 3 through 5
    Processing sheet with id=  C, first strand: chain 'B' and resid 34 through 36
    Processing sheet with id=  D, first strand: chain 'B' and resid 101 through 105
      removed outlier: 3.606A  pdb=" N   SER B  80 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL B  95 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   VAL B  78 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 129 through 131
    Processing sheet with id=  F, first strand: chain 'B' and resid 171 through 175
    Processing sheet with id=  G, first strand: chain 'D' and resid 11 through 14
      removed outlier: 4.008A  pdb=" N   PHE D  40 " --> pdb=" O   ILE D   4 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   GLU D   6 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   VAL D  38 " --> pdb=" O   GLU D   6 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'D' and resid 19 through 22
    Processing sheet with id=  I, first strand: chain 'D' and resid 32 through 35
      removed outlier: 6.747A  pdb=" N   THR D  61 " --> pdb=" O   ILE D  97 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   ILE D  97 " --> pdb=" O   THR D  61 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'D' and resid 71 through 77
      removed outlier: 4.236A  pdb=" N   SER D  82 " --> pdb=" O   LYS D  77 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'E' and resid 2 through 7
      removed outlier: 6.448A  pdb=" N   SER E 108 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   VAL E  71 " --> pdb=" O   SER E 108 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'E' and resid 82 through 87
    Processing sheet with id=  M, first strand: chain 'F' and resid 52 through 58
      removed outlier: 4.476A  pdb=" N   ARG F  76 " --> pdb=" O   VAL F  29 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'G' and resid 20 through 22
    Processing sheet with id=  O, first strand: chain 'G' and resid 40 through 43
    Processing sheet with id=  P, first strand: chain 'G' and resid 81 through 84
    Processing sheet with id=  Q, first strand: chain 'G' and resid 23 through 27
      removed outlier: 6.608A  pdb=" N   VAL G  34 " --> pdb=" O   ILE G  24 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   THR G  26 " --> pdb=" O   ARG G  32 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ARG G  32 " --> pdb=" O   THR G  26 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'H' and resid 41 through 44
      removed outlier: 6.226A  pdb=" N   ILE H  89 " --> pdb=" O   VAL H  30 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   TYR H  32 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   PHE H  91 " --> pdb=" O   TYR H  32 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   HIS H  88 " --> pdb=" O   GLN H  78 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP H  76 " --> pdb=" O   ASP H  90 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   LEU H  92 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   VAL H  74 " --> pdb=" O   LEU H  92 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'J' and resid 13 through 18
    Processing sheet with id=  T, first strand: chain 'J' and resid 33 through 40
      removed outlier: 4.054A  pdb=" N   VAL J  40 " --> pdb=" O   LYS J  43 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'L' and resid 178 through 180
      removed outlier: 6.704A  pdb=" N   VAL L  27 " --> pdb=" O   ILE L  10 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   MET L  12 " --> pdb=" O   VAL L  25 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   VAL L  25 " --> pdb=" O   MET L  12 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   GLN L  14 " --> pdb=" O   ILE L  23 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE L  23 " --> pdb=" O   GLN L  14 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN L 187 " --> pdb=" O   LEU L 196 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   LYS L 198 " --> pdb=" O   VAL L 185 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL L 185 " --> pdb=" O   LYS L 198 " (cutoff:3.500A)
    Processing sheet with id=  V, first strand: chain 'L' and resid 89 through 91
      removed outlier: 3.677A  pdb=" N   GLN L  37 " --> pdb=" O   GLN L  50 " (cutoff:3.500A)
    Processing sheet with id=  W, first strand: chain 'M' and resid 54 through 57
      removed outlier: 3.605A  pdb=" N   LYS M   3 " --> pdb=" O   VAL M  37 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   GLN M   5 " --> pdb=" O   VAL M  35 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL M  35 " --> pdb=" O   GLN M   5 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'N' and resid 27 through 29
    Processing sheet with id=  Y, first strand: chain 'O' and resid 2 through 7
    Processing sheet with id=  Z, first strand: chain 'O' and resid 32 through 36
    Processing sheet with id= AA, first strand: chain 'R' and resid 15 through 19
    Processing sheet with id= AB, first strand: chain 'S' and resid 123 through 125
      removed outlier: 6.335A  pdb=" N   LEU S 192 " --> pdb=" O   THR S 124 " (cutoff:3.500A)
    Processing sheet with id= AC, first strand: chain 'U' and resid 16 through 20
      removed outlier: 3.666A  pdb=" N   VAL U  24 " --> pdb=" O   THR U  36 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   SER U  34 " --> pdb=" O   VAL U  26 " (cutoff:3.500A)
    Processing sheet with id= AD, first strand: chain 'U' and resid 161 through 163
    Processing sheet with id= AE, first strand: chain 'U' and resid 95 through 99
    Processing sheet with id= AF, first strand: chain 'V' and resid 16 through 20
      removed outlier: 6.507A  pdb=" N   TYR V  54 " --> pdb=" O   TYR V  17 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   ILE V  19 " --> pdb=" O   TYR V  54 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ILE V  56 " --> pdb=" O   ILE V  19 " (cutoff:3.500A)
    Processing sheet with id= AG, first strand: chain 'V' and resid 74 through 78
    Processing sheet with id= AH, first strand: chain 'W' and resid 7 through 9
      removed outlier: 6.674A  pdb=" N   VAL W  40 " --> pdb=" O   ILE W  22 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   VAL W  24 " --> pdb=" O   VAL W  38 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   VAL W  38 " --> pdb=" O   VAL W  24 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ALA W  83 " --> pdb=" O   VAL W  63 " (cutoff:3.500A)
    Processing sheet with id= AI, first strand: chain 'X' and resid 75 through 78
    Processing sheet with id= AJ, first strand: chain 'Y' and resid 129 through 133
      removed outlier: 3.853A  pdb=" N   PHE Y 104 " --> pdb=" O   LEU Y  34 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ALA Y  36 " --> pdb=" O   ILE Y 102 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE Y 102 " --> pdb=" O   ALA Y  36 " (cutoff:3.500A)
    Processing sheet with id= AK, first strand: chain 'Y' and resid 40 through 43
      removed outlier: 7.013A  pdb=" N   TYR Y  74 " --> pdb=" O   GLU Y  91 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   TRP Y  93 " --> pdb=" O   THR Y  72 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR Y  72 " --> pdb=" O   TRP Y  93 " (cutoff:3.500A)
    Processing sheet with id= AL, first strand: chain 'Z' and resid 29 through 33
      removed outlier: 3.637A  pdb=" N   GLY Z 107 " --> pdb=" O   SER Z 116 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ILE Z 118 " --> pdb=" O   LYS Z 105 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   LYS Z 105 " --> pdb=" O   ILE Z 118 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   GLU Z 120 " --> pdb=" O   ILE Z 103 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   ILE Z 103 " --> pdb=" O   GLU Z 120 " (cutoff:3.500A)
    Processing sheet with id= AM, first strand: chain 'a' and resid 30 through 35
    Processing sheet with id= AN, first strand: chain 'I' and resid 53 through 55
      removed outlier: 7.209A  pdb=" N   LYS I  85 " --> pdb=" O   TYR I  54 " (cutoff:3.500A)
    Processing sheet with id= AO, first strand: chain 'I' and resid 59 through 61
      removed outlier: 3.508A  pdb=" N   TYR I  46 " --> pdb=" O   LEU I  67 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ALA I  69 " --> pdb=" O   ILE I  44 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ILE I  44 " --> pdb=" O   ALA I  69 " (cutoff:3.500A)

    568 hydrogen bonds defined for protein.
    1533 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1976 hydrogen bonds
      3174 hydrogen bond angles
      0 basepair planarities
      784 basepair parallelities
      1475 stacking parallelities
  Total time for adding SS restraints: 124.26

  Time building geometry restraints manager: 34.87 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 7732
        1.31 -     1.44: 39831
        1.44 -     1.57: 35900
        1.57 -     1.69: 5535
        1.69 -     1.82: 104
  Bond restraints: 89102
  Sorted by residual:
  bond pdb=" N3  U7Y 13001 "
       pdb=" N4  U7Y 13001 "
    ideal  model  delta    sigma   weight residual
    1.324  1.546 -0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" C16 U7Y 13001 "
       pdb=" O3  U7Y 13001 "
    ideal  model  delta    sigma   weight residual
    1.402  1.186  0.216 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" C2  U7Y 13001 "
       pdb=" N5  U7Y 13001 "
    ideal  model  delta    sigma   weight residual
    1.327  1.480 -0.153 2.00e-02 2.50e+03 5.83e+01
  bond pdb=" C12 U7Y 13001 "
       pdb=" C7  U7Y 13001 "
    ideal  model  delta    sigma   weight residual
    1.378  1.524 -0.146 2.00e-02 2.50e+03 5.32e+01
  bond pdb=" C5  U7Y 13001 "
       pdb=" C6  U7Y 13001 "
    ideal  model  delta    sigma   weight residual
    1.396  1.523 -0.127 2.00e-02 2.50e+03 4.03e+01
  ... (remaining 89097 not shown)

  Histogram of bond angle deviations from ideal:
       90.28 -    99.07: 22
       99.07 -   107.86: 24979
      107.86 -   116.65: 55305
      116.65 -   125.44: 43347
      125.44 -   134.23: 10305
  Bond angle restraints: 133958
  Sorted by residual:
  angle pdb=" O2'   C 1 831 "
        pdb=" C2'   C 1 831 "
        pdb=" C1'   C 1 831 "
      ideal   model   delta    sigma   weight residual
     108.40   90.28   18.12 1.50e+00 4.44e-01 1.46e+02
  angle pdb=" C4'   G 11522 "
        pdb=" C3'   G 11522 "
        pdb=" O3'   G 11522 "
      ideal   model   delta    sigma   weight residual
     113.00  128.25  -15.25 1.50e+00 4.44e-01 1.03e+02
  angle pdb=" O3'   A 11275 "
        pdb=" C3'   A 11275 "
        pdb=" C2'   A 11275 "
      ideal   model   delta    sigma   weight residual
     109.50   95.08   14.42 1.50e+00 4.44e-01 9.24e+01
  angle pdb=" O2'   C 1  31 "
        pdb=" C2'   C 1  31 "
        pdb=" C1'   C 1  31 "
      ideal   model   delta    sigma   weight residual
     108.40   94.01   14.39 1.50e+00 4.44e-01 9.20e+01
  angle pdb=" C   THR X  30 "
        pdb=" CA  THR X  30 "
        pdb=" CB  THR X  30 "
      ideal   model   delta    sigma   weight residual
     109.83  119.30   -9.47 9.90e-01 1.02e+00 9.16e+01
  ... (remaining 133953 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 50006
       35.97 -    71.94: 6268
       71.94 -   107.91: 617
      107.91 -   143.89: 24
      143.89 -   179.86: 37
  Dihedral angle restraints: 56952
    sinusoidal: 48936
      harmonic: 8016
  Sorted by residual:
  dihedral pdb=" O4'   C 11781 "
           pdb=" C1'   C 11781 "
           pdb=" N1    C 11781 "
           pdb=" C2    C 11781 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   20.14  179.86     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   C 1 402 "
           pdb=" C1'   C 1 402 "
           pdb=" N1    C 1 402 "
           pdb=" C2    C 1 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   22.56  177.44     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U 11216 "
           pdb=" C1'   U 11216 "
           pdb=" N1    U 11216 "
           pdb=" C2    U 11216 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   22.94  177.06     1      1.50e+01 4.44e-03 8.53e+01
  ... (remaining 56949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.172: 16744
       0.172 -    0.343: 457
       0.343 -    0.515: 32
       0.515 -    0.686: 2
       0.686 -    0.858: 1
  Chirality restraints: 17236
  Sorted by residual:
  chirality pdb=" CA  PHE L  53 "
            pdb=" N   PHE L  53 "
            pdb=" C   PHE L  53 "
            pdb=" CB  PHE L  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.65    0.86 2.00e-01 2.50e+01 1.84e+01
  chirality pdb=" C3'   G 12745 "
            pdb=" C4'   G 12745 "
            pdb=" O3'   G 12745 "
            pdb=" C2'   G 12745 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.91   -0.57 2.00e-01 2.50e+01 8.05e+00
  chirality pdb=" C3'   U 11493 "
            pdb=" C4'   U 11493 "
            pdb=" O3'   U 11493 "
            pdb=" C2'   U 11493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.94   -0.54 2.00e-01 2.50e+01 7.31e+00
  ... (remaining 17233 not shown)

  Planarity restraints: 6634
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G 1 675 "   -0.064 2.00e-02 2.50e+03   3.05e-02 2.79e+01
        pdb=" N9    G 1 675 "    0.081 2.00e-02 2.50e+03
        pdb=" C8    G 1 675 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    G 1 675 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    G 1 675 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G 1 675 "   -0.014 2.00e-02 2.50e+03
        pdb=" O6    G 1 675 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G 1 675 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2    G 1 675 "    0.003 2.00e-02 2.50e+03
        pdb=" N2    G 1 675 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    G 1 675 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    G 1 675 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G 12056 "    0.059 2.00e-02 2.50e+03   2.74e-02 2.25e+01
        pdb=" N9    G 12056 "   -0.072 2.00e-02 2.50e+03
        pdb=" C8    G 12056 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G 12056 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    G 12056 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G 12056 "    0.011 2.00e-02 2.50e+03
        pdb=" O6    G 12056 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    G 12056 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G 12056 "   -0.005 2.00e-02 2.50e+03
        pdb=" N2    G 12056 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G 12056 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4    G 12056 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 12902 "    0.049 2.00e-02 2.50e+03   2.75e-02 2.09e+01
        pdb=" N9    A 12902 "   -0.076 2.00e-02 2.50e+03
        pdb=" C8    A 12902 "    0.010 2.00e-02 2.50e+03
        pdb=" N7    A 12902 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A 12902 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    A 12902 "    0.006 2.00e-02 2.50e+03
        pdb=" N6    A 12902 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A 12902 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A 12902 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A 12902 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A 12902 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 6631 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 1337
        2.59 -     3.17: 60460
        3.17 -     3.74: 148095
        3.74 -     4.32: 222314
        4.32 -     4.90: 303334
  Nonbonded interactions: 735540
  Sorted by model distance:
  nonbonded pdb=" O2'   U 1 286 "
            pdb=" O4'   G 1 287 "
     model   vdw
     2.010 2.440
  nonbonded pdb=" OP2   G 11169 "
            pdb=" O2'   A 11170 "
     model   vdw
     2.030 2.440
  nonbonded pdb=" O2'   U 12318 "
            pdb=" O2    C 12401 "
     model   vdw
     2.057 2.440
  nonbonded pdb=" OD2 ASP Z 112 "
            pdb=" O2'   G 11693 "
     model   vdw
     2.060 2.440
  nonbonded pdb=" O2    U 11540 "
            pdb=" O2'   C 11624 "
     model   vdw
     2.068 2.440
  ... (remaining 735535 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             5.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.090
  Extract box with map and model:          18.180
  Check model and map are aligned:         0.900
  Set scattering table:                    0.560
  Process input model:                     281.230
  Find NCS groups from input model:        1.340
  Set up NCS constraints:                  0.220
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  310.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
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      :  0.008   0.222  89102  Z= 0.506
  Angle     :  1.067  18.124 133958  Z= 0.710
  Chirality :  0.065   0.858  17236
  Planarity :  0.006   0.046   6634
  Dihedral  : 24.406 179.858  51798
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.52 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.13), residues: 2776
  helix: -2.38 (0.17), residues: 664
  sheet: -2.25 (0.19), residues: 602
  loop : -2.70 (0.13), residues: 1510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP B 213 
 HIS   0.009   0.002   HIS C  29 
 PHE   0.041   0.002   PHE K  30 
 TYR   0.018   0.002   TYR S  99 
 ARG   0.010   0.001   ARG E  15 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  471 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 438
  time to evaluate  : 3.329 
Fit side-chains
   revert: symmetry clash
REVERT: L  140 PRO cc_start: 0.7219 (Cg_endo) cc_final: 0.6811 (Cg_exo)
REVERT: L  189 ASP cc_start: 0.7969 (t0) cc_final: 0.7736 (t0)
REVERT: M    5 GLN cc_start: 0.8430 (tt0) cc_final: 0.8005 (tt0)
REVERT: S  106 ARG cc_start: 0.6289 (mtp85) cc_final: 0.5449 (mtt180)
REVERT: S  201 LYS cc_start: 0.8519 (tppp) cc_final: 0.8167 (tptt)
REVERT: V   62 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8082 (mptt)
REVERT: X   39 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8906 (mtmm)
REVERT: Z   84 LYS cc_start: 0.8712 (tttm) cc_final: 0.8509 (tttp)
  outliers start: 33
  outliers final: 10
  residues processed: 459
  average time/residue: 0.9084
  time to fit residues: 669.9191
Evaluate side-chains
  374 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 364
  time to evaluate  : 3.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain C residue    9 VAL
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain W residue   73 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 462 optimal weight:    7.9990
   chunk 415 optimal weight:    4.9990
   chunk 230 optimal weight:    3.9990
   chunk 141 optimal weight:    0.9990
   chunk 280 optimal weight:    9.9990
   chunk 221 optimal weight:    0.9990
   chunk 429 optimal weight:    4.9990
   chunk 166 optimal weight:    0.9980
   chunk 261 optimal weight:    7.9990
   chunk 319 optimal weight:    4.9990
   chunk 497 optimal weight:    5.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 ASN
B  58 HIS
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN
C  38 GLN
** C  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  61 ASN
E 102 HIS
H  88 HIS
J  30 ASN
J  34 GLN
K  17 GLN
K  27 ASN
L  33 ASN
L  47 ASN
L 146 HIS
L 176 ASN
M  19 GLN
M  46 GLN
M  52 HIS
** N  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O   4 ASN
O  45 HIS
P   7 GLN
P  13 HIS
Q   7 HIS
Q  31 HIS
Q  35 ASN
R  34 GLN
S  40 GLN
S  46 GLN
S  67 GLN
S 121 ASN
** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 188 ASN
U  45 GLN
U  65 HIS
U  77 GLN
U  81 GLN
V  11 ASN
V  48 HIS
V 136 GLN
X  27 ASN
Y  71 HIS
Z  79 GLN
Z 106 GLN

Total number of N/Q/H flips: 43

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  89102  Z= 0.259
  Angle     :  0.652  11.601 133958  Z= 0.339
  Chirality :  0.041   0.316  17236
  Planarity :  0.005   0.057   6634
  Dihedral  : 23.371 179.482  46099
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.62 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.14), residues: 2776
  helix: -1.51 (0.19), residues: 659
  sheet: -1.75 (0.19), residues: 625
  loop : -2.36 (0.13), residues: 1492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 213 
 HIS   0.008   0.001   HIS M  52 
 PHE   0.021   0.002   PHE K  30 
 TYR   0.011   0.002   TYR S  99 
 ARG   0.006   0.000   ARG a  19 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  433 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 385
  time to evaluate  : 3.421 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.6522 (tt0) cc_final: 0.6268 (tt0)
REVERT: A  106 ARG cc_start: 0.7262 (mmp80) cc_final: 0.6851 (mmm160)
REVERT: B   23 GLU cc_start: 0.8012 (pt0) cc_final: 0.7584 (pt0)
REVERT: L   66 ASN cc_start: 0.8652 (t0) cc_final: 0.8291 (t0)
REVERT: L  189 ASP cc_start: 0.8052 (t0) cc_final: 0.7763 (t0)
REVERT: M    5 GLN cc_start: 0.8272 (tt0) cc_final: 0.7821 (tt0)
REVERT: S  201 LYS cc_start: 0.8497 (tppp) cc_final: 0.8287 (tptt)
REVERT: V   62 LYS cc_start: 0.8491 (mmtm) cc_final: 0.8205 (mptt)
REVERT: Z   29 ARG cc_start: 0.8126 (ptm-80) cc_final: 0.7751 (ttp80)
REVERT: Z   84 LYS cc_start: 0.8648 (tttm) cc_final: 0.8423 (tttp)
  outliers start: 48
  outliers final: 39
  residues processed: 415
  average time/residue: 0.8600
  time to fit residues: 586.5701
Evaluate side-chains
  404 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 365
  time to evaluate  : 4.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue    4 LYS
Chi-restraints excluded: chain E residue   40 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue    6 ILE
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain J residue   36 VAL
Chi-restraints excluded: chain K residue   17 GLN
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   32 ASN
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  192 LEU
Chi-restraints excluded: chain U residue   16 THR
Chi-restraints excluded: chain U residue  113 VAL
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   85 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  112 SER
Chi-restraints excluded: chain W residue   42 THR
Chi-restraints excluded: chain X residue   73 GLU
Chi-restraints excluded: chain Y residue   28 THR
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Z residue   25 ILE
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain Z residue  118 ILE
Chi-restraints excluded: chain a residue   22 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 276 optimal weight:    6.9990
   chunk 154 optimal weight:    1.9990
   chunk 414 optimal weight:    6.9990
   chunk 338 optimal weight:    9.9990
   chunk 137 optimal weight:    8.9990
   chunk 498 optimal weight:    6.9990
   chunk 538 optimal weight:    7.9990
   chunk 443 optimal weight:    9.9990
   chunk 494 optimal weight:    8.9990
   chunk 169 optimal weight:    7.9990
   chunk 399 optimal weight:    8.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN
B 153 GLN
** C  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  69 GLN
G   2 HIS
** L  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P   9 ASN
S  67 GLN
** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  23 HIS
U  81 GLN
** U  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V  59 ASN
** a  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 102 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.092  89102  Z= 0.610
  Angle     :  0.905  14.163 133958  Z= 0.453
  Chirality :  0.054   0.421  17236
  Planarity :  0.007   0.097   6634
  Dihedral  : 23.482 179.979  46092
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 18.20 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.08 (0.14), residues: 2776
  helix: -1.67 (0.18), residues: 677
  sheet: -1.63 (0.20), residues: 616
  loop : -2.44 (0.13), residues: 1483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B 213 
 HIS   0.007   0.002   HIS L 143 
 PHE   0.025   0.003   PHE K  30 
 TYR   0.019   0.003   TYR S  99 
 ARG   0.011   0.001   ARG B  13 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  455 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 92
    poor density    : 363
  time to evaluate  : 3.332 
Fit side-chains
REVERT: E   27 LYS cc_start: 0.8937 (mttp) cc_final: 0.8566 (mttp)
REVERT: F   22 GLU cc_start: 0.5131 (OUTLIER) cc_final: 0.4029 (pm20)
REVERT: F   40 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7842 (mtp)
REVERT: L   66 ASN cc_start: 0.8646 (t0) cc_final: 0.8350 (t0)
REVERT: L  189 ASP cc_start: 0.7934 (t0) cc_final: 0.7653 (t0)
REVERT: P   29 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7917 (mtt-85)
REVERT: S  106 ARG cc_start: 0.6496 (mtp85) cc_final: 0.5857 (mtt180)
REVERT: S  201 LYS cc_start: 0.8575 (tppp) cc_final: 0.8272 (tptt)
REVERT: V   62 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8220 (mptt)
REVERT: V  117 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7747 (mp0)
REVERT: X   71 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8670 (ttt90)
REVERT: Y    1 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7381 (mtt)
REVERT: Z   84 LYS cc_start: 0.8804 (tttm) cc_final: 0.8570 (tttp)
  outliers start: 92
  outliers final: 68
  residues processed: 428
  average time/residue: 0.8976
  time to fit residues: 636.8185
Evaluate side-chains
  430 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 357
  time to evaluate  : 3.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue    4 LYS
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   40 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue    6 ILE
Chi-restraints excluded: chain F residue   22 GLU
Chi-restraints excluded: chain F residue   40 MET
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain J residue    3 LYS
Chi-restraints excluded: chain J residue   36 VAL
Chi-restraints excluded: chain L residue   25 VAL
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   27 MET
Chi-restraints excluded: chain N residue   32 ASN
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   31 GLU
Chi-restraints excluded: chain Q residue   37 SER
Chi-restraints excluded: chain Q residue   53 SER
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  192 LEU
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain U residue   16 THR
Chi-restraints excluded: chain U residue   53 VAL
Chi-restraints excluded: chain U residue  113 VAL
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   85 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  112 SER
Chi-restraints excluded: chain V residue  117 GLU
Chi-restraints excluded: chain W residue   18 GLU
Chi-restraints excluded: chain W residue   42 THR
Chi-restraints excluded: chain W residue   51 VAL
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain W residue  110 ASN
Chi-restraints excluded: chain X residue   29 LYS
Chi-restraints excluded: chain X residue   71 ARG
Chi-restraints excluded: chain Y residue    1 MET
Chi-restraints excluded: chain Y residue   28 THR
Chi-restraints excluded: chain Y residue   46 GLN
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   72 THR
Chi-restraints excluded: chain Z residue   25 ILE
Chi-restraints excluded: chain Z residue   42 SER
Chi-restraints excluded: chain Z residue   65 THR
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain Z residue  118 ILE
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   33 VAL
Chi-restraints excluded: chain a residue   86 ASP
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 492 optimal weight:    2.9990
   chunk 374 optimal weight:    5.9990
   chunk 258 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 237 optimal weight:    1.9990
   chunk 334 optimal weight:    1.9990
   chunk 500 optimal weight:    2.9990
   chunk 529 optimal weight:    7.9990
   chunk 261 optimal weight:    6.9990
   chunk 474 optimal weight:    5.9990
   chunk 142 optimal weight:    0.6980
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 GLN
** C  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  61 ASN
G   2 HIS
** L  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  89102  Z= 0.213
  Angle     :  0.584  11.191 133958  Z= 0.304
  Chirality :  0.037   0.324  17236
  Planarity :  0.004   0.045   6634
  Dihedral  : 23.155 179.481  46092
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 20.14 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.15), residues: 2776
  helix: -0.98 (0.20), residues: 670
  sheet: -1.27 (0.20), residues: 615
  loop : -2.20 (0.14), residues: 1491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 213 
 HIS   0.005   0.001   HIS C  29 
 PHE   0.011   0.001   PHE L  53 
 TYR   0.011   0.001   TYR S  99 
 ARG   0.006   0.000   ARG V  14 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 369
  time to evaluate  : 3.302 
Fit side-chains
REVERT: A   96 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.6527 (mtt180)
REVERT: B   23 GLU cc_start: 0.8060 (pt0) cc_final: 0.7639 (pt0)
REVERT: B  213 TRP cc_start: 0.7875 (p90) cc_final: 0.7416 (p90)
REVERT: C   88 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8000 (mt)
REVERT: L   66 ASN cc_start: 0.8515 (t0) cc_final: 0.8257 (t0)
REVERT: L  189 ASP cc_start: 0.8057 (t0) cc_final: 0.7785 (t0)
REVERT: V   62 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8152 (mptt)
REVERT: V  117 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7756 (mp0)
REVERT: Y    1 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7396 (mtt)
REVERT: Z   28 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7459 (mt-10)
REVERT: I   19 LYS cc_start: 0.8298 (mtpp) cc_final: 0.8065 (mtpp)
  outliers start: 76
  outliers final: 50
  residues processed: 414
  average time/residue: 0.8640
  time to fit residues: 589.3134
Evaluate side-chains
  418 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 364
  time to evaluate  : 3.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue    4 LYS
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue    6 ILE
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain G residue    4 LYS
Chi-restraints excluded: chain L residue   25 VAL
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   64 LYS
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   50 ASN
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain Q residue   53 SER
Chi-restraints excluded: chain S residue   66 LYS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  192 LEU
Chi-restraints excluded: chain U residue   20 ASP
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  112 SER
Chi-restraints excluded: chain V residue  117 GLU
Chi-restraints excluded: chain W residue   18 GLU
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain X residue   96 LEU
Chi-restraints excluded: chain Y residue    1 MET
Chi-restraints excluded: chain Y residue   28 THR
Chi-restraints excluded: chain Y residue   44 SER
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   72 THR
Chi-restraints excluded: chain Z residue   42 SER
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   33 VAL
Chi-restraints excluded: chain a residue   68 THR
Chi-restraints excluded: chain a residue  105 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 441 optimal weight:    8.9990
   chunk 300 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 394 optimal weight:    6.9990
   chunk 218 optimal weight:    0.9990
   chunk 452 optimal weight:    5.9990
   chunk 366 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 270 optimal weight:   10.0000
   chunk 475 optimal weight:   10.0000
   chunk 133 optimal weight:    0.8980
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  61 ASN
G   2 HIS
** G  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS
** L  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  43 GLN
S  82 GLN
U  97 GLN
X   4 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  89102  Z= 0.365
  Angle     :  0.695  12.243 133958  Z= 0.356
  Chirality :  0.043   0.345  17236
  Planarity :  0.005   0.062   6634
  Dihedral  : 23.198 179.516  46090
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 20.78 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.15), residues: 2776
  helix: -1.06 (0.20), residues: 676
  sheet: -1.28 (0.20), residues: 628
  loop : -2.15 (0.14), residues: 1472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 213 
 HIS   0.005   0.001   HIS C  29 
 PHE   0.015   0.002   PHE S  90 
 TYR   0.015   0.002   TYR Y  74 
 ARG   0.008   0.001   ARG a  19 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  472 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 111
    poor density    : 361
  time to evaluate  : 4.731 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6510 (mmt180)
REVERT: B   23 GLU cc_start: 0.8039 (pt0) cc_final: 0.7607 (pt0)
REVERT: B   62 TYR cc_start: 0.8839 (t80) cc_final: 0.8605 (t80)
REVERT: B  213 TRP cc_start: 0.7854 (p90) cc_final: 0.7322 (p90)
REVERT: C   88 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7903 (mt)
REVERT: D   11 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8320 (mt0)
REVERT: F   22 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.3050 (mp0)
REVERT: L   66 ASN cc_start: 0.8531 (t0) cc_final: 0.8292 (t0)
REVERT: L  189 ASP cc_start: 0.8010 (t0) cc_final: 0.7754 (t0)
REVERT: S  106 ARG cc_start: 0.6270 (mtp85) cc_final: 0.5724 (mtt180)
REVERT: U   97 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5305 (mp-120)
REVERT: U  163 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7060 (ptm160)
REVERT: V   62 LYS cc_start: 0.8529 (mmtm) cc_final: 0.8277 (mptt)
REVERT: V  117 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7836 (mp0)
REVERT: X   71 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8492 (ttt90)
REVERT: Y    1 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7458 (mtt)
  outliers start: 111
  outliers final: 82
  residues processed: 441
  average time/residue: 0.8904
  time to fit residues: 651.2042
Evaluate side-chains
  443 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 91
    poor density    : 352
  time to evaluate  : 3.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   17 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   11 GLN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   40 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue    6 ILE
Chi-restraints excluded: chain F residue   22 GLU
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain G residue    4 LYS
Chi-restraints excluded: chain G residue   66 SER
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain J residue   36 VAL
Chi-restraints excluded: chain J residue   60 THR
Chi-restraints excluded: chain L residue   25 VAL
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   61 LYS
Chi-restraints excluded: chain L residue   64 LYS
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   42 VAL
Chi-restraints excluded: chain N residue   50 ASN
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain P residue   44 SER
Chi-restraints excluded: chain Q residue   37 SER
Chi-restraints excluded: chain Q residue   53 SER
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain S residue   66 LYS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  118 VAL
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  192 LEU
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain U residue   16 THR
Chi-restraints excluded: chain U residue   20 ASP
Chi-restraints excluded: chain U residue   84 VAL
Chi-restraints excluded: chain U residue   97 GLN
Chi-restraints excluded: chain U residue  113 VAL
Chi-restraints excluded: chain U residue  163 ARG
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   65 PHE
Chi-restraints excluded: chain V residue   85 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  112 SER
Chi-restraints excluded: chain V residue  117 GLU
Chi-restraints excluded: chain W residue   18 GLU
Chi-restraints excluded: chain W residue   42 THR
Chi-restraints excluded: chain W residue   51 VAL
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain W residue  110 ASN
Chi-restraints excluded: chain X residue   71 ARG
Chi-restraints excluded: chain X residue   96 LEU
Chi-restraints excluded: chain Y residue    1 MET
Chi-restraints excluded: chain Y residue   28 THR
Chi-restraints excluded: chain Y residue   44 SER
Chi-restraints excluded: chain Y residue   46 GLN
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   72 THR
Chi-restraints excluded: chain Z residue    4 ARG
Chi-restraints excluded: chain Z residue   42 SER
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain Z residue  118 ILE
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   33 VAL
Chi-restraints excluded: chain a residue   65 THR
Chi-restraints excluded: chain a residue   68 THR
Chi-restraints excluded: chain a residue  105 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 178 optimal weight:    5.9990
   chunk 477 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 310 optimal weight:    8.9990
   chunk 130 optimal weight:    1.9990
   chunk 530 optimal weight:   10.0000
   chunk 440 optimal weight:    9.9990
   chunk 245 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 175 optimal weight:    8.9990
   chunk 278 optimal weight:    8.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   2 HIS
** L  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  46 GLN
** U  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  89102  Z= 0.293
  Angle     :  0.647  11.796 133958  Z= 0.336
  Chirality :  0.041   0.324  17236
  Planarity :  0.005   0.058   6634
  Dihedral  : 23.190 179.405  46090
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 20.94 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.15), residues: 2776
  helix: -0.95 (0.20), residues: 676
  sheet: -1.22 (0.20), residues: 627
  loop : -2.07 (0.14), residues: 1473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 213 
 HIS   0.005   0.001   HIS C  29 
 PHE   0.012   0.002   PHE K  26 
 TYR   0.014   0.002   TYR S  99 
 ARG   0.008   0.000   ARG a  19 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  468 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 115
    poor density    : 353
  time to evaluate  : 3.368 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.6497 (mmt180)
REVERT: B   23 GLU cc_start: 0.8069 (pt0) cc_final: 0.7645 (pt0)
REVERT: B   62 TYR cc_start: 0.8846 (t80) cc_final: 0.8568 (t80)
REVERT: B  213 TRP cc_start: 0.7859 (p90) cc_final: 0.7376 (p90)
REVERT: C   88 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7900 (mt)
REVERT: D   11 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8275 (mt0)
REVERT: F   22 GLU cc_start: 0.4455 (OUTLIER) cc_final: 0.3021 (mp0)
REVERT: L   66 ASN cc_start: 0.8511 (t0) cc_final: 0.8243 (t0)
REVERT: L  189 ASP cc_start: 0.8001 (t0) cc_final: 0.7751 (t0)
REVERT: U  163 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7040 (ptm160)
REVERT: V   62 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8273 (mptt)
REVERT: V  117 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7836 (mp0)
REVERT: W  113 LYS cc_start: 0.8332 (tptp) cc_final: 0.8087 (tppt)
REVERT: X   71 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8510 (ttt90)
REVERT: Y    1 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7449 (mtt)
  outliers start: 115
  outliers final: 86
  residues processed: 436
  average time/residue: 0.8595
  time to fit residues: 626.3823
Evaluate side-chains
  442 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 94
    poor density    : 348
  time to evaluate  : 3.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   17 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   11 GLN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue    4 LYS
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   40 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue   22 GLU
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain G residue    4 LYS
Chi-restraints excluded: chain G residue   66 SER
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain J residue   36 VAL
Chi-restraints excluded: chain J residue   60 THR
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue   25 VAL
Chi-restraints excluded: chain L residue   29 GLU
Chi-restraints excluded: chain L residue   42 GLU
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   61 LYS
Chi-restraints excluded: chain L residue   64 LYS
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain M residue   11 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue   32 ASN
Chi-restraints excluded: chain N residue   42 VAL
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain P residue   44 SER
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain Q residue   37 SER
Chi-restraints excluded: chain Q residue   53 SER
Chi-restraints excluded: chain S residue   66 LYS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  118 VAL
Chi-restraints excluded: chain S residue  127 ASP
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  192 LEU
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain U residue   16 THR
Chi-restraints excluded: chain U residue   20 ASP
Chi-restraints excluded: chain U residue   84 VAL
Chi-restraints excluded: chain U residue  163 ARG
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   65 PHE
Chi-restraints excluded: chain V residue   85 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  112 SER
Chi-restraints excluded: chain V residue  117 GLU
Chi-restraints excluded: chain W residue   18 GLU
Chi-restraints excluded: chain W residue   42 THR
Chi-restraints excluded: chain W residue   51 VAL
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain W residue  110 ASN
Chi-restraints excluded: chain X residue   71 ARG
Chi-restraints excluded: chain X residue   96 LEU
Chi-restraints excluded: chain Y residue    1 MET
Chi-restraints excluded: chain Y residue   28 THR
Chi-restraints excluded: chain Y residue   44 SER
Chi-restraints excluded: chain Y residue   46 GLN
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   72 THR
Chi-restraints excluded: chain Z residue    4 ARG
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain Z residue  118 ILE
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   33 VAL
Chi-restraints excluded: chain a residue   49 LYS
Chi-restraints excluded: chain a residue   65 THR
Chi-restraints excluded: chain a residue   68 THR
Chi-restraints excluded: chain a residue  105 VAL
Chi-restraints excluded: chain I residue   18 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 511 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 302 optimal weight:   10.0000
   chunk 387 optimal weight:    6.9990
   chunk 299 optimal weight:    8.9990
   chunk 446 optimal weight:    7.9990
   chunk 296 optimal weight:   10.0000
   chunk 528 optimal weight:    7.9990
   chunk 330 optimal weight:    6.9990
   chunk 322 optimal weight:    7.9990
   chunk 243 optimal weight:    4.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 GLN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   2 HIS
** H  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  46 GLN
S 182 ASN
** U  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.090  89102  Z= 0.632
  Angle     :  0.920  13.826 133958  Z= 0.459
  Chirality :  0.055   0.429  17236
  Planarity :  0.007   0.093   6634
  Dihedral  : 23.431 179.996  46090
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 20.44 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -2.72 (0.14), residues: 2776
  helix: -1.36 (0.19), residues: 680
  sheet: -1.41 (0.20), residues: 610
  loop : -2.20 (0.14), residues: 1486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B 213 
 HIS   0.007   0.002   HIS B 230 
 PHE   0.019   0.003   PHE S  90 
 TYR   0.020   0.003   TYR S  99 
 ARG   0.008   0.001   ARG V  14 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  496 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 136
    poor density    : 360
  time to evaluate  : 3.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.6516 (mmt180)
REVERT: B   39 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8489 (mttm)
REVERT: C   88 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7993 (mt)
REVERT: D   11 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8365 (mt0)
REVERT: F   22 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.3693 (pm20)
REVERT: L   66 ASN cc_start: 0.8560 (t0) cc_final: 0.8313 (t0)
REVERT: L  189 ASP cc_start: 0.7927 (t0) cc_final: 0.7674 (t0)
REVERT: L  210 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7181 (mt-10)
REVERT: Q   49 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8728 (mt)
REVERT: S  106 ARG cc_start: 0.6419 (mtp180) cc_final: 0.5720 (mtt180)
REVERT: S  174 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7492 (tp40)
REVERT: U  163 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7114 (ptm160)
REVERT: V   62 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8294 (mptt)
REVERT: V  117 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7849 (mp0)
REVERT: Y    1 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7407 (mtt)
  outliers start: 136
  outliers final: 107
  residues processed: 457
  average time/residue: 0.8550
  time to fit residues: 645.5347
Evaluate side-chains
  476 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 118
    poor density    : 358
  time to evaluate  : 3.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   17 THR
Chi-restraints excluded: chain B residue   39 LYS
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   11 GLN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue    4 LYS
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   40 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue    6 ILE
Chi-restraints excluded: chain F residue   22 GLU
Chi-restraints excluded: chain F residue   35 LYS
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain F residue   69 GLN
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue   89 LEU
Chi-restraints excluded: chain G residue    4 LYS
Chi-restraints excluded: chain G residue   20 GLU
Chi-restraints excluded: chain G residue   66 SER
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain J residue   36 VAL
Chi-restraints excluded: chain J residue   60 THR
Chi-restraints excluded: chain L residue   25 VAL
Chi-restraints excluded: chain L residue   42 GLU
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   61 LYS
Chi-restraints excluded: chain L residue   64 LYS
Chi-restraints excluded: chain L residue  106 SER
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain L residue  210 GLU
Chi-restraints excluded: chain L residue  215 ILE
Chi-restraints excluded: chain M residue   11 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue    3 VAL
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   32 ASN
Chi-restraints excluded: chain N residue   42 VAL
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain P residue   44 SER
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain Q residue   37 SER
Chi-restraints excluded: chain Q residue   49 LEU
Chi-restraints excluded: chain Q residue   53 SER
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain S residue   66 LYS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  118 VAL
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  192 LEU
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain U residue   16 THR
Chi-restraints excluded: chain U residue   20 ASP
Chi-restraints excluded: chain U residue   23 HIS
Chi-restraints excluded: chain U residue   53 VAL
Chi-restraints excluded: chain U residue   84 VAL
Chi-restraints excluded: chain U residue  113 VAL
Chi-restraints excluded: chain U residue  163 ARG
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   65 PHE
Chi-restraints excluded: chain V residue   85 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  112 SER
Chi-restraints excluded: chain V residue  117 GLU
Chi-restraints excluded: chain W residue   18 GLU
Chi-restraints excluded: chain W residue   42 THR
Chi-restraints excluded: chain W residue   51 VAL
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain W residue  110 ASN
Chi-restraints excluded: chain X residue   96 LEU
Chi-restraints excluded: chain X residue  123 VAL
Chi-restraints excluded: chain Y residue    1 MET
Chi-restraints excluded: chain Y residue   28 THR
Chi-restraints excluded: chain Y residue   44 SER
Chi-restraints excluded: chain Y residue   46 GLN
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   72 THR
Chi-restraints excluded: chain Y residue  122 SER
Chi-restraints excluded: chain Z residue    4 ARG
Chi-restraints excluded: chain Z residue   42 SER
Chi-restraints excluded: chain Z residue   65 THR
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain Z residue  118 ILE
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   33 VAL
Chi-restraints excluded: chain a residue   65 THR
Chi-restraints excluded: chain a residue   68 THR
Chi-restraints excluded: chain a residue   86 ASP
Chi-restraints excluded: chain a residue  105 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 326 optimal weight:    0.6980
   chunk 210 optimal weight:    0.5980
   chunk 315 optimal weight:    4.9990
   chunk 159 optimal weight:    0.6980
   chunk 103 optimal weight:    6.9990
   chunk 102 optimal weight:    0.8980
   chunk 335 optimal weight:    0.6980
   chunk 359 optimal weight:    2.9990
   chunk 261 optimal weight:    0.3980
   chunk 49 optimal weight:    2.9990
   chunk 415 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  14 GLN
B  44 ASN
B 163 GLN
E  61 ASN
G   2 HIS
N  45 ASN
S  46 GLN
S 182 ASN
** U  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  46 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056  89102  Z= 0.116
  Angle     :  0.536   9.371 133958  Z= 0.281
  Chirality :  0.034   0.355  17236
  Planarity :  0.004   0.047   6634
  Dihedral  : 23.114 179.276  46090
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 23.81 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.15), residues: 2776
  helix: -0.48 (0.21), residues: 661
  sheet: -1.04 (0.20), residues: 612
  loop : -1.95 (0.14), residues: 1503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP Y  65 
 HIS   0.004   0.001   HIS C  29 
 PHE   0.010   0.001   PHE A  76 
 TYR   0.009   0.001   TYR A 101 
 ARG   0.007   0.000   ARG K   7 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  436 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 367
  time to evaluate  : 3.288 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 GLU cc_start: 0.8005 (pt0) cc_final: 0.7589 (pt0)
REVERT: B  213 TRP cc_start: 0.7778 (p90) cc_final: 0.7209 (p90)
REVERT: C   88 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7832 (mt)
REVERT: D   11 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8206 (mt0)
REVERT: L   66 ASN cc_start: 0.8396 (t0) cc_final: 0.8160 (t0)
REVERT: L  189 ASP cc_start: 0.8084 (t0) cc_final: 0.7747 (t0)
REVERT: U  163 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6901 (ptm160)
REVERT: V   62 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8231 (mptt)
REVERT: V  117 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7727 (mp0)
REVERT: W  113 LYS cc_start: 0.8358 (tptp) cc_final: 0.8062 (tppt)
REVERT: X   71 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7277 (ttt90)
REVERT: a   43 GLN cc_start: 0.8207 (pt0) cc_final: 0.7907 (pt0)
  outliers start: 69
  outliers final: 50
  residues processed: 411
  average time/residue: 0.8476
  time to fit residues: 577.6320
Evaluate side-chains
  409 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 354
  time to evaluate  : 3.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   11 GLN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue    4 LYS
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   40 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue    6 ILE
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain G residue    4 LYS
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain J residue   60 THR
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue   25 VAL
Chi-restraints excluded: chain L residue   42 GLU
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   64 LYS
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue   19 THR
Chi-restraints excluded: chain S residue   66 LYS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  118 VAL
Chi-restraints excluded: chain S residue  127 ASP
Chi-restraints excluded: chain U residue   20 ASP
Chi-restraints excluded: chain U residue  163 ARG
Chi-restraints excluded: chain V residue   65 PHE
Chi-restraints excluded: chain V residue   85 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  117 GLU
Chi-restraints excluded: chain W residue   18 GLU
Chi-restraints excluded: chain W residue   51 VAL
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain X residue   71 ARG
Chi-restraints excluded: chain Y residue   44 SER
Chi-restraints excluded: chain Y residue   46 GLN
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Z residue    4 ARG
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   65 THR
Chi-restraints excluded: chain a residue   68 THR
Chi-restraints excluded: chain a residue  105 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   75 VAL
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 480 optimal weight:    7.9990
   chunk 506 optimal weight:   10.0000
   chunk 461 optimal weight:   10.0000
   chunk 492 optimal weight:    6.9990
   chunk 505 optimal weight:    6.9990
   chunk 296 optimal weight:   10.0000
   chunk 214 optimal weight:    0.9980
   chunk 386 optimal weight:    7.9990
   chunk 151 optimal weight:    5.9990
   chunk 444 optimal weight:    9.9990
   chunk 465 optimal weight:    7.9990
   overall best weight:    5.7988

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  61 ASN
G   2 HIS
K  36 GLN
M  48 ASN
S  46 GLN
S  82 GLN
U  97 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.086  89102  Z= 0.577
  Angle     :  0.866  12.801 133958  Z= 0.433
  Chirality :  0.053   0.411  17236
  Planarity :  0.007   0.086   6634
  Dihedral  : 23.301 179.891  46087
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 22.00 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.49 (0.15), residues: 2776
  helix: -1.14 (0.19), residues: 680
  sheet: -1.26 (0.20), residues: 617
  loop : -2.09 (0.14), residues: 1479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B 213 
 HIS   0.007   0.002   HIS G   2 
 PHE   0.019   0.003   PHE S  90 
 TYR   0.019   0.003   TYR S  99 
 ARG   0.009   0.001   ARG a  19 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  458 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 104
    poor density    : 354
  time to evaluate  : 3.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.6539 (mmt180)
REVERT: B   62 TYR cc_start: 0.8889 (t80) cc_final: 0.8599 (t80)
REVERT: B  213 TRP cc_start: 0.7907 (p90) cc_final: 0.7331 (p90)
REVERT: C   88 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7983 (mt)
REVERT: D   11 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8361 (mt0)
REVERT: L   66 ASN cc_start: 0.8537 (t0) cc_final: 0.8282 (t0)
REVERT: L  189 ASP cc_start: 0.7957 (t0) cc_final: 0.7681 (t0)
REVERT: L  190 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7396 (m)
REVERT: S  106 ARG cc_start: 0.6387 (mtp180) cc_final: 0.5717 (mtt180)
REVERT: U  163 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7090 (ptm160)
REVERT: V   62 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8282 (mptt)
REVERT: V  117 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7853 (mp0)
REVERT: W  113 LYS cc_start: 0.8456 (tptp) cc_final: 0.8172 (tppt)
  outliers start: 104
  outliers final: 80
  residues processed: 429
  average time/residue: 0.8676
  time to fit residues: 617.7172
Evaluate side-chains
  436 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 86
    poor density    : 350
  time to evaluate  : 3.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   11 GLN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue    4 LYS
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   40 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue    6 ILE
Chi-restraints excluded: chain F residue   35 LYS
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain G residue    4 LYS
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   20 GLU
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain J residue   60 THR
Chi-restraints excluded: chain L residue   25 VAL
Chi-restraints excluded: chain L residue   42 GLU
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   61 LYS
Chi-restraints excluded: chain L residue   64 LYS
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  190 THR
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  213 THR
Chi-restraints excluded: chain M residue   11 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue    5 VAL
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   19 THR
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain Q residue   19 SER
Chi-restraints excluded: chain Q residue   37 SER
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain S residue   66 LYS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  118 VAL
Chi-restraints excluded: chain S residue  127 ASP
Chi-restraints excluded: chain S residue  192 LEU
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain U residue   20 ASP
Chi-restraints excluded: chain U residue   23 HIS
Chi-restraints excluded: chain U residue   43 PHE
Chi-restraints excluded: chain U residue   76 VAL
Chi-restraints excluded: chain U residue   84 VAL
Chi-restraints excluded: chain U residue  163 ARG
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   65 PHE
Chi-restraints excluded: chain V residue   85 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  112 SER
Chi-restraints excluded: chain V residue  117 GLU
Chi-restraints excluded: chain W residue   18 GLU
Chi-restraints excluded: chain W residue   42 THR
Chi-restraints excluded: chain W residue   51 VAL
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain X residue   96 LEU
Chi-restraints excluded: chain Y residue   28 THR
Chi-restraints excluded: chain Y residue   44 SER
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Z residue    4 ARG
Chi-restraints excluded: chain Z residue   42 SER
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   33 VAL
Chi-restraints excluded: chain a residue   65 THR
Chi-restraints excluded: chain a residue   68 THR
Chi-restraints excluded: chain a residue   86 ASP
Chi-restraints excluded: chain a residue  105 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 490 optimal weight:    3.9990
   chunk 323 optimal weight:    1.9990
   chunk 520 optimal weight:    9.9990
   chunk 317 optimal weight:    5.9990
   chunk 246 optimal weight:    2.9990
   chunk 361 optimal weight:    3.9990
   chunk 545 optimal weight:    0.0570
   chunk 502 optimal weight:    2.9990
   chunk 434 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 335 optimal weight:    1.9990
   overall best weight:    1.8106

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

Flipped N/Q/H residues before XYZ refinement:
B  44 ASN
E  61 ASN
G   2 HIS
** H  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 182 ASN
M  48 ASN
S  46 GLN
S  82 GLN
Y  46 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  89102  Z= 0.215
  Angle     :  0.596  10.919 133958  Z= 0.310
  Chirality :  0.038   0.324  17236
  Planarity :  0.005   0.050   6634
  Dihedral  : 23.107 179.793  46087
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 23.05 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.15), residues: 2776
  helix: -0.73 (0.20), residues: 676
  sheet: -1.12 (0.20), residues: 623
  loop : -1.97 (0.15), residues: 1477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 213 
 HIS   0.006   0.001   HIS G   2 
 PHE   0.012   0.001   PHE L  53 
 TYR   0.012   0.001   TYR S  99 
 ARG   0.009   0.000   ARG a  19 

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

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

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5552 Ramachandran restraints generated.
    2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 85
    poor density    : 355
  time to evaluate  : 3.279 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.6516 (mmt180)
REVERT: B   23 GLU cc_start: 0.8012 (pt0) cc_final: 0.7590 (pt0)
REVERT: B   30 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7208 (tt0)
REVERT: B   62 TYR cc_start: 0.8838 (t80) cc_final: 0.8507 (t80)
REVERT: B  213 TRP cc_start: 0.7818 (p90) cc_final: 0.7249 (p90)
REVERT: C   88 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7851 (mt)
REVERT: D   11 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8305 (mt0)
REVERT: L   66 ASN cc_start: 0.8437 (t0) cc_final: 0.8187 (t0)
REVERT: L  189 ASP cc_start: 0.8096 (t0) cc_final: 0.7818 (t0)
REVERT: L  190 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7253 (m)
REVERT: U   23 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.4825 (m90)
REVERT: U  163 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6927 (ptm160)
REVERT: V   62 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8321 (mptt)
REVERT: V  117 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7806 (mp0)
REVERT: W  113 LYS cc_start: 0.8321 (tptp) cc_final: 0.8106 (tppt)
REVERT: Y    1 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7437 (mtt)
REVERT: a   82 LYS cc_start: 0.7690 (mptt) cc_final: 0.7443 (mmtm)
  outliers start: 85
  outliers final: 71
  residues processed: 412
  average time/residue: 0.8473
  time to fit residues: 580.8146
Evaluate side-chains
  432 residues out of total 2373 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 80
    poor density    : 352
  time to evaluate  : 3.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   30 GLU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain D residue   11 GLN
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue    4 LYS
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   40 ASN
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue    6 ILE
Chi-restraints excluded: chain F residue   35 LYS
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   68 TYR
Chi-restraints excluded: chain G residue    4 LYS
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain J residue   60 THR
Chi-restraints excluded: chain L residue   25 VAL
Chi-restraints excluded: chain L residue   42 GLU
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   54 GLU
Chi-restraints excluded: chain L residue   64 LYS
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  190 THR
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  197 VAL
Chi-restraints excluded: chain M residue   11 SER
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain O residue    1 MET
Chi-restraints excluded: chain O residue   10 THR
Chi-restraints excluded: chain O residue   19 THR
Chi-restraints excluded: chain P residue   25 THR
Chi-restraints excluded: chain Q residue   53 SER
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain S residue   51 VAL
Chi-restraints excluded: chain S residue   66 LYS
Chi-restraints excluded: chain S residue   77 THR
Chi-restraints excluded: chain S residue  118 VAL
Chi-restraints excluded: chain S residue  127 ASP
Chi-restraints excluded: chain S residue  177 THR
Chi-restraints excluded: chain S residue  192 LEU
Chi-restraints excluded: chain S residue  194 ILE
Chi-restraints excluded: chain U residue   20 ASP
Chi-restraints excluded: chain U residue   23 HIS
Chi-restraints excluded: chain U residue  163 ARG
Chi-restraints excluded: chain V residue   19 ILE
Chi-restraints excluded: chain V residue   65 PHE
Chi-restraints excluded: chain V residue   85 ILE
Chi-restraints excluded: chain V residue   99 GLU
Chi-restraints excluded: chain V residue  112 SER
Chi-restraints excluded: chain V residue  117 GLU
Chi-restraints excluded: chain W residue   18 GLU
Chi-restraints excluded: chain W residue   51 VAL
Chi-restraints excluded: chain W residue   54 LYS
Chi-restraints excluded: chain Y residue    1 MET
Chi-restraints excluded: chain Y residue   28 THR
Chi-restraints excluded: chain Y residue   44 SER
Chi-restraints excluded: chain Y residue   46 GLN
Chi-restraints excluded: chain Y residue   55 THR
Chi-restraints excluded: chain Y residue   72 THR
Chi-restraints excluded: chain Z residue    4 ARG
Chi-restraints excluded: chain Z residue   42 SER
Chi-restraints excluded: chain Z residue   95 GLU
Chi-restraints excluded: chain a residue   22 LEU
Chi-restraints excluded: chain a residue   23 SER
Chi-restraints excluded: chain a residue   49 LYS
Chi-restraints excluded: chain a residue   65 THR
Chi-restraints excluded: chain a residue   68 THR
Chi-restraints excluded: chain a residue   86 ASP
Chi-restraints excluded: chain a residue  105 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   88 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 548
   random chunks:
   chunk 266 optimal weight:    5.9990
   chunk 345 optimal weight:    6.9990
   chunk 463 optimal weight:    8.9990
   chunk 133 optimal weight:    5.9990
   chunk 400 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 120 optimal weight:    3.9990
   chunk 435 optimal weight:    7.9990
   chunk 182 optimal weight:    0.9990
   chunk 447 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  44 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  61 ASN
G   2 HIS
** H  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  17 GLN
S  46 GLN
S  82 GLN
Y  46 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.132224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.109659 restraints weight = 101097.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 0.96
r_work: 0.2796 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2683 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.141  89102  Z= 0.336
  Angle     :  0.651  59.189 133958  Z= 0.345
  Chirality :  0.041   0.449  17236
  Planarity :  0.005   0.051   6634
  Dihedral  : 23.107 179.740  46087
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 23.01 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.15), residues: 2776
  helix: -0.73 (0.20), residues: 676
  sheet: -1.09 (0.20), residues: 623
  loop : -1.97 (0.15), residues: 1477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 213 
 HIS   0.006   0.001   HIS C  29 
 PHE   0.012   0.002   PHE K  26 
 TYR   0.013   0.002   TYR S  99 
 ARG   0.009   0.001   ARG a  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12735.16 seconds
wall clock time: 229 minutes 12.53 seconds (13752.53 seconds total)