Starting phenix.real_space_refine
on Tue May 20 22:45:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k28_36831/05_2025/8k28_36831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k28_36831/05_2025/8k28_36831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k28_36831/05_2025/8k28_36831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k28_36831/05_2025/8k28_36831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k28_36831/05_2025/8k28_36831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k28_36831/05_2025/8k28_36831.cif"
  }
  resolution = 3.54
  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=   0.007 sd=   0.083
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: 5
    Type Number    sf(0)   Gaussians
     P     119      5.49       5
     S      70      5.16       5
     C   12674      2.51       5
     N    3523      2.21       5
     O    4354      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 20740
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 173, 1345
          Classifications: {'peptide': 173}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 165}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "B"
      Number of atoms: 1898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1898
          Classifications: {'peptide': 246}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 234}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 6
    Chain: "C"
      Number of atoms: 2291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2291
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 7, 'TRANS': 294}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 2289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2289
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 7, 'TRANS': 294}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "E"
      Number of atoms: 2297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2297
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 7, 'TRANS': 294}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "F"
      Number of atoms: 2297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2297
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 293}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "G"
      Number of atoms: 2285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2285
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 293}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "I"
      Number of atoms: 1291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1291
          Classifications: {'peptide': 166}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 162}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "Q"
      Number of atoms: 677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 677
          Classifications: {'DNA': 33}
          Link IDs: {'rna3p': 32}
    Chain: "R"
      Number of atoms: 556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 556
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "P"
      Number of atoms: 1237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 1237
          Classifications: {'RNA': 59}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 20, 'rna3p_pur': 13, 'rna3p_pyr': 15}
          Link IDs: {'rna2p': 31, 'rna3p': 27}
    Chain: "H"
      Number of atoms: 2277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2277
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 293}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 33
  Time building chain proxies: 12.52, per 1000 atoms: 0.60
  Number of scatterers: 20740
  At special positions: 0
  Unit cell: (116.6, 138.6, 183.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      70     16.00
     P     119     15.00
     O    4354      8.00
     N    3523      7.00
     C   12674      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.85
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4374

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 47 sheets defined
      25.4% alpha, 23.1% beta
      29 base pairs and 59 stacking pairs defined.
    Time for finding SS restraints: 7.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 12
    Processing helix  chain 'A' and resid 48 through 52
      removed outlier: 3.685A  pdb=" N   ALA A  52 " --> pdb=" O   PRO A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 68
      removed outlier: 4.003A  pdb=" N   VAL A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 77
      removed outlier: 3.673A  pdb=" N   ILE A  75 " --> pdb=" O   MET A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 90
      removed outlier: 4.008A  pdb=" N   LEU A  87 " --> pdb=" O   GLU A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 131
      removed outlier: 3.787A  pdb=" N   ILE A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 3.915A  pdb=" N   ASN A 151 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   CYS A 152 " --> pdb=" O   PRO A 149 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 148 through 152'
    Processing helix  chain 'A' and resid 153 through 159
      removed outlier: 3.776A  pdb=" N   MET A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 42
      removed outlier: 3.730A  pdb=" N   PHE B  32 " --> pdb=" O   PRO B  28 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLY B  36 " --> pdb=" O   PHE B  32 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU B  37 " --> pdb=" O   CYS B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 122
      removed outlier: 4.312A  pdb=" N   LEU B 113 " --> pdb=" O   CYS B 109 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ASP B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   PHE B 120 " --> pdb=" O   LYS B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 155
      removed outlier: 3.678A  pdb=" N   SER B 150 " --> pdb=" O   GLU B 146 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL B 151 " --> pdb=" O   GLU B 147 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA B 154 " --> pdb=" O   SER B 150 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   MET B 155 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 177
      removed outlier: 3.586A  pdb=" N   ASP B 173 " --> pdb=" O   ASN B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 223
      No H-bonds generated for 'chain 'B' and resid 221 through 223'
    Processing helix  chain 'C' and resid 98 through 105
    Processing helix  chain 'C' and resid 111 through 126
      removed outlier: 3.898A  pdb=" N   LEU C 115 " --> pdb=" O   ASP C 111 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY C 126 " --> pdb=" O   ASN C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 179
      removed outlier: 3.776A  pdb=" N   ALA C 167 " --> pdb=" O   ASP C 163 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   GLU C 168 " --> pdb=" O   VAL C 164 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   ILE C 169 " --> pdb=" O   ASP C 165 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   VAL C 176 " --> pdb=" O   MET C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 235
    Processing helix  chain 'C' and resid 269 through 279
      removed outlier: 3.774A  pdb=" N   ASP C 275 " --> pdb=" O   PHE C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 298
    Processing helix  chain 'D' and resid 100 through 107
    Processing helix  chain 'D' and resid 111 through 125
      removed outlier: 3.522A  pdb=" N   LEU D 115 " --> pdb=" O   ASP D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 178
    Processing helix  chain 'D' and resid 225 through 234
      removed outlier: 4.018A  pdb=" N   ARG D 234 " --> pdb=" O   GLY D 230 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 280
      removed outlier: 3.552A  pdb=" N   ASP D 275 " --> pdb=" O   PHE D 271 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLY D 276 " --> pdb=" O   THR D 272 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   ALA D 277 " --> pdb=" O   LEU D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 296
    Processing helix  chain 'E' and resid 53 through 58
      removed outlier: 4.173A  pdb=" N   ASP E  58 " --> pdb=" O   ASN E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 98 through 105
    Processing helix  chain 'E' and resid 111 through 125
      removed outlier: 3.749A  pdb=" N   ASN E 122 " --> pdb=" O   ARG E 118 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ILE E 123 " --> pdb=" O   TYR E 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 164 through 178
      removed outlier: 4.079A  pdb=" N   ILE E 169 " --> pdb=" O   ASP E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 225 through 234
    Processing helix  chain 'E' and resid 269 through 280
      removed outlier: 3.818A  pdb=" N   LEU E 273 " --> pdb=" O   ASP E 269 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ASP E 275 " --> pdb=" O   PHE E 271 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 286 through 298
    Processing helix  chain 'F' and resid 99 through 107
    Processing helix  chain 'F' and resid 112 through 125
      removed outlier: 3.606A  pdb=" N   TYR F 117 " --> pdb=" O   GLY F 113 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE F 123 " --> pdb=" O   TYR F 119 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 163 through 179
      removed outlier: 3.954A  pdb=" N   ALA F 167 " --> pdb=" O   ASP F 163 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   MET F 172 " --> pdb=" O   GLU F 168 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY F 179 " --> pdb=" O   GLY F 175 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 225 through 234
    Processing helix  chain 'F' and resid 269 through 280
      removed outlier: 3.962A  pdb=" N   LEU F 273 " --> pdb=" O   ASP F 269 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 286 through 298
    Processing helix  chain 'G' and resid 53 through 57
    Processing helix  chain 'G' and resid 99 through 107
    Processing helix  chain 'G' and resid 111 through 125
      removed outlier: 3.677A  pdb=" N   LEU G 115 " --> pdb=" O   ASP G 111 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE G 123 " --> pdb=" O   TYR G 119 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 164 through 179
      removed outlier: 3.760A  pdb=" N   ILE G 169 " --> pdb=" O   ASP G 165 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   MET G 172 " --> pdb=" O   GLU G 168 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY G 175 " --> pdb=" O   ASP G 171 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 225 through 234
      removed outlier: 3.547A  pdb=" N   ALA G 232 " --> pdb=" O   LYS G 228 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 269 through 280
      removed outlier: 3.745A  pdb=" N   LEU G 273 " --> pdb=" O   ASP G 269 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASP G 275 " --> pdb=" O   PHE G 271 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 284 through 296
      removed outlier: 3.758A  pdb=" N   GLN G 288 " --> pdb=" O   THR G 284 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE G 290 " --> pdb=" O   GLU G 286 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 16 through 30
    Processing helix  chain 'I' and resid 62 through 69
      removed outlier: 3.734A  pdb=" N   LEU I  66 " --> pdb=" O   ASP I  62 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   THR I  67 " --> pdb=" O   ARG I  63 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 98 through 109
      removed outlier: 3.523A  pdb=" N   LEU I 102 " --> pdb=" O   SER I  98 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ARG I 109 " --> pdb=" O   ARG I 105 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 115 through 121
      removed outlier: 3.749A  pdb=" N   TYR I 121 " --> pdb=" O   ALA I 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 107
    Processing helix  chain 'H' and resid 111 through 125
      removed outlier: 4.088A  pdb=" N   LEU H 115 " --> pdb=" O   ASP H 111 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE H 123 " --> pdb=" O   TYR H 119 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 164 through 177
      removed outlier: 3.736A  pdb=" N   ILE H 169 " --> pdb=" O   ASP H 165 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   MET H 172 " --> pdb=" O   GLU H 168 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLY H 175 " --> pdb=" O   ASP H 171 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL H 176 " --> pdb=" O   MET H 172 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 225 through 234
      removed outlier: 3.584A  pdb=" N   ALA H 232 " --> pdb=" O   LYS H 228 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 269 through 280
    Processing helix  chain 'H' and resid 284 through 298
      removed outlier: 3.650A  pdb=" N   GLN H 288 " --> pdb=" O   THR H 284 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   MET H 289 " --> pdb=" O   GLU H 285 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE H 290 " --> pdb=" O   GLU H 286 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG H 297 " --> pdb=" O   ALA H 293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17
      removed outlier: 3.559A  pdb=" N   PHE A  17 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP A  45 " --> pdb=" O   PHE A  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32
    Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 108
      removed outlier: 3.836A  pdb=" N   GLY A 111 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
      removed outlier: 9.630A  pdb=" N   TYR B 206 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ILE A 114 " --> pdb=" O   TYR B 206 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   ALA B 208 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   VAL A 116 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108
      removed outlier: 3.836A  pdb=" N   GLY A 111 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
      removed outlier: 9.630A  pdb=" N   TYR B 206 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ILE A 114 " --> pdb=" O   TYR B 206 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   ALA B 208 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   VAL A 116 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   ALA B 205 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   LYS B 191 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LEU B 207 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   THR B 213 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   VAL B 183 " --> pdb=" O   THR B 213 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE B 215 " --> pdb=" O   PRO B 181 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141
    Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.936A  pdb=" N   ALA B  49 " --> pdb=" O   GLU B 103 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ALA B  94 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY B  14 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   LEU B 100 " --> pdb=" O   LYS B   8 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   LYS B   8 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   PHE B 102 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   ILE B   6 " --> pdb=" O   PHE B 102 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   VAL B 104 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   PHE B   4 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 59
      removed outlier: 5.733A  pdb=" N   ALA B  94 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY B  14 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   LEU B 100 " --> pdb=" O   LYS B   8 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   LYS B   8 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   PHE B 102 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   ILE B   6 " --> pdb=" O   PHE B 102 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   VAL B 104 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   PHE B   4 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 233
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12
    Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18
    Processing sheet with id=AB2, first strand: chain 'C' and resid 16 through 18
      removed outlier: 3.822A  pdb=" N   SER C 138 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 40 through 47
      removed outlier: 3.560A  pdb=" N   GLY C  46 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 9.618A  pdb=" N   LEU C 211 " --> pdb=" O   ILE C  62 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   THR C  64 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LYS C 213 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 217 through 218
    Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 255
      removed outlier: 3.681A  pdb=" N   VAL C 255 " --> pdb=" O   VAL C 260 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL C 260 " --> pdb=" O   VAL C 255 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 12
      removed outlier: 3.689A  pdb=" N   GLY D 299 " --> pdb=" O   TYR D  12 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 16 through 18
    Processing sheet with id=AB8, first strand: chain 'D' and resid 16 through 18
    Processing sheet with id=AB9, first strand: chain 'D' and resid 40 through 44
      removed outlier: 7.002A  pdb=" N   THR D  64 " --> pdb=" O   LEU D 211 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   LYS D 213 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 217 through 218
    Processing sheet with id=AC2, first strand: chain 'D' and resid 254 through 255
      removed outlier: 3.745A  pdb=" N   VAL D 255 " --> pdb=" O   VAL D 260 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL D 260 " --> pdb=" O   VAL D 255 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 12
    Processing sheet with id=AC4, first strand: chain 'E' and resid 16 through 18
    Processing sheet with id=AC5, first strand: chain 'E' and resid 16 through 18
    Processing sheet with id=AC6, first strand: chain 'E' and resid 40 through 47
      removed outlier: 3.812A  pdb=" N   ASN E  61 " --> pdb=" O   GLY E  46 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   ALA E  68 " --> pdb=" O   VAL E 199 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 217 through 218
    Processing sheet with id=AC8, first strand: chain 'E' and resid 235 through 237
    Processing sheet with id=AC9, first strand: chain 'E' and resid 254 through 255
    Processing sheet with id=AD1, first strand: chain 'F' and resid 16 through 18
    Processing sheet with id=AD2, first strand: chain 'F' and resid 16 through 18
    Processing sheet with id=AD3, first strand: chain 'F' and resid 40 through 45
    Processing sheet with id=AD4, first strand: chain 'F' and resid 203 through 204
      removed outlier: 4.233A  pdb=" N   GLN F 214 " --> pdb=" O   GLU F 204 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'F' and resid 217 through 218
    Processing sheet with id=AD6, first strand: chain 'F' and resid 235 through 237
    Processing sheet with id=AD7, first strand: chain 'F' and resid 254 through 255
      removed outlier: 3.635A  pdb=" N   VAL F 260 " --> pdb=" O   VAL F 255 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'G' and resid 11 through 12
    Processing sheet with id=AD9, first strand: chain 'G' and resid 16 through 18
    Processing sheet with id=AE1, first strand: chain 'G' and resid 16 through 18
      removed outlier: 3.953A  pdb=" N   VAL G 145 " --> pdb=" O   GLN G 148 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'G' and resid 39 through 44
      removed outlier: 4.541A  pdb=" N   ALA G  68 " --> pdb=" O   VAL G 199 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'G' and resid 217 through 218
    Processing sheet with id=AE4, first strand: chain 'G' and resid 235 through 237
    Processing sheet with id=AE5, first strand: chain 'I' and resid 53 through 55
    Processing sheet with id=AE6, first strand: chain 'I' and resid 91 through 94
      removed outlier: 4.267A  pdb=" N   PHE I 148 " --> pdb=" O   VAL I  94 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AE8, first strand: chain 'H' and resid 16 through 18
    Processing sheet with id=AE9, first strand: chain 'H' and resid 16 through 18
      removed outlier: 3.767A  pdb=" N   VAL H 145 " --> pdb=" O   GLN H 148 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'H' and resid 40 through 43
    Processing sheet with id=AF2, first strand: chain 'H' and resid 235 through 237

    655 hydrogen bonds defined for protein.
    1788 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      73 hydrogen bonds
      142 hydrogen bond angles
      0 basepair planarities
      29 basepair parallelities
      59 stacking parallelities
  Total time for adding SS restraints: 8.19

  Time building geometry restraints manager: 5.69 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 3415
        1.31 -     1.44: 6236
        1.44 -     1.57: 11330
        1.57 -     1.70: 238
        1.70 -     1.83: 126
  Bond restraints: 21345
  Sorted by residual:
  bond pdb=" CA  ALA E 125 "
       pdb=" C   ALA E 125 "
    ideal  model  delta    sigma   weight residual
    1.523  1.423  0.100 1.34e-02 5.57e+03 5.54e+01
  bond pdb=" CA  GLU D  93 "
       pdb=" C   GLU D  93 "
    ideal  model  delta    sigma   weight residual
    1.523  1.429  0.094 1.34e-02 5.57e+03 4.91e+01
  bond pdb=" CA  ALA D   6 "
       pdb=" C   ALA D   6 "
    ideal  model  delta    sigma   weight residual
    1.528  1.446  0.082 1.18e-02 7.18e+03 4.82e+01
  bond pdb=" CA  ALA E  92 "
       pdb=" C   ALA E  92 "
    ideal  model  delta    sigma   weight residual
    1.528  1.439  0.089 1.33e-02 5.65e+03 4.44e+01
  bond pdb=" CA  TYR D  99 "
       pdb=" C   TYR D  99 "
    ideal  model  delta    sigma   weight residual
    1.523  1.434  0.089 1.34e-02 5.57e+03 4.42e+01
  ... (remaining 21340 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.56: 28920
        3.56 -     7.12: 460
        7.12 -    10.68: 91
       10.68 -    14.23: 13
       14.23 -    17.79: 6
  Bond angle restraints: 29490
  Sorted by residual:
  angle pdb=" N   ALA F  57 "
        pdb=" CA  ALA F  57 "
        pdb=" C   ALA F  57 "
      ideal   model   delta    sigma   weight residual
     114.56   96.77   17.79 1.27e+00 6.20e-01 1.96e+02
  angle pdb=" N   PHE F 112 "
        pdb=" CA  PHE F 112 "
        pdb=" C   PHE F 112 "
      ideal   model   delta    sigma   weight residual
     112.59   95.87   16.72 1.22e+00 6.72e-01 1.88e+02
  angle pdb=" N   ASP F  58 "
        pdb=" CA  ASP F  58 "
        pdb=" C   ASP F  58 "
      ideal   model   delta    sigma   weight residual
     111.14   98.83   12.31 1.08e+00 8.57e-01 1.30e+02
  angle pdb=" N   SER D 100 "
        pdb=" CA  SER D 100 "
        pdb=" C   SER D 100 "
      ideal   model   delta    sigma   weight residual
     114.04  101.36   12.68 1.24e+00 6.50e-01 1.05e+02
  angle pdb=" C   ALA D   6 "
        pdb=" N   PRO D   7 "
        pdb=" CA  PRO D   7 "
      ideal   model   delta    sigma   weight residual
     119.76  110.87    8.89 1.00e+00 1.00e+00 7.90e+01
  ... (remaining 29485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.29: 11665
       35.29 -    70.59: 790
       70.59 -   105.88: 55
      105.88 -   141.17: 2
      141.17 -   176.47: 5
  Dihedral angle restraints: 12517
    sinusoidal: 5672
      harmonic: 6845
  Sorted by residual:
  dihedral pdb=" O4'   U P  34 "
           pdb=" C1'   U P  34 "
           pdb=" N1    U P  34 "
           pdb=" C2    U P  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   49.50  150.50     1      1.50e+01 4.44e-03 7.98e+01
  dihedral pdb=" N   PRO F  54 "
           pdb=" C   PRO F  54 "
           pdb=" CA  PRO F  54 "
           pdb=" CB  PRO F  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  131.79  -16.69     0      2.50e+00 1.60e-01 4.46e+01
  dihedral pdb=" O4'   U P  35 "
           pdb=" C1'   U P  35 "
           pdb=" N1    U P  35 "
           pdb=" C2    U P  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -80.46  -79.54     1      1.50e+01 4.44e-03 3.49e+01
  ... (remaining 12514 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.145: 3289
       0.145 -    0.290: 132
       0.290 -    0.435: 12
       0.435 -    0.579: 4
       0.579 -    0.724: 1
  Chirality restraints: 3438
  Sorted by residual:
  chirality pdb=" CA  PRO F  54 "
            pdb=" N   PRO F  54 "
            pdb=" C   PRO F  54 "
            pdb=" CB  PRO F  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.99    0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" C3'   U P  34 "
            pdb=" C4'   U P  34 "
            pdb=" O3'   U P  34 "
            pdb=" C2'   U P  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.92   -0.56 2.00e-01 2.50e+01 7.72e+00
  chirality pdb=" CG  LEU D 270 "
            pdb=" CB  LEU D 270 "
            pdb=" CD1 LEU D 270 "
            pdb=" CD2 LEU D 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 7.07e+00
  ... (remaining 3435 not shown)

  Planarity restraints: 3410
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G  45 "    0.022 2.00e-02 2.50e+03   4.32e-02 1.86e+01
        pdb=" C   ALA G  45 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   ALA G  45 "    0.028 2.00e-02 2.50e+03
        pdb=" N   GLY G  46 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 124 "   -0.021 2.00e-02 2.50e+03   4.23e-02 1.79e+01
        pdb=" C   ALA E 124 "    0.073 2.00e-02 2.50e+03
        pdb=" O   ALA E 124 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ALA E 125 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR H 245 "    0.066 5.00e-02 4.00e+02   1.00e-01 1.60e+01
        pdb=" N   PRO H 246 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO H 246 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO H 246 "    0.054 5.00e-02 4.00e+02
  ... (remaining 3407 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 1064
        2.70 -     3.25: 19175
        3.25 -     3.80: 36665
        3.80 -     4.35: 45318
        4.35 -     4.90: 73134
  Nonbonded interactions: 175356
  Sorted by model distance:
  nonbonded pdb=" N   TYR D  99 "
            pdb=" N   SER D 100 "
     model   vdw
     2.151 2.560
  nonbonded pdb=" N   ALA F  57 "
            pdb=" N   ASP F  58 "
     model   vdw
     2.229 2.560
  nonbonded pdb=" N   VAL F  50 "
            pdb=" O   VAL F  50 "
     model   vdw
     2.241 2.496
  nonbonded pdb=" N   PHE F 112 "
            pdb=" N   GLY F 113 "
     model   vdw
     2.262 2.560
  nonbonded pdb=" O   GLY A  39 "
            pdb=" OG1 THR A  42 "
     model   vdw
     2.268 3.040
  ... (remaining 175351 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 2 through 37 or (resid 38 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 39 through 58 or (resid 59 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 60 through 97 or (resid 98 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 99 through 107 or (r \ 
esid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 t \ 
hrough 129 or (resid 130 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 131 through 132 or (resid 133 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 205 through 209 or (resid 210 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 211 through 256 or (r \ 
esid 257 and (name N or name CA or name C or name O or name CB )) or resid 258 t \ 
hrough 266 or (resid 267 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 268 through 303))
  selection = (chain 'D' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 7 through 37 or (resid 38 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 39 through 58 or (resid 59 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 60 through 106 or (resid 107 throu \ 
gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ 
ough 129 or (resid 130 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 131 through 132 or (resid 133 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 205 through 209 or (resid 210 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 211 through 256 or (res \ 
id 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thr \ 
ough 303))
  selection = (chain 'E' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 7 through 37 or (resid 38 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 39 through 58 or (resid 59 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 60 through 106 or (resid 107 throu \ 
gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ 
ough 129 or (resid 130 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 131 through 132 or (resid 133 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 205 through 209 or (resid 210 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 211 through 256 or (res \ 
id 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thr \ 
ough 266 or (resid 267 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 268 through 303))
  selection = (chain 'F' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 7 through 37 or (resid 38 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 39 through 97 or (resid 98 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 99 through 106 or (resid 107 throu \ 
gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ 
ough 129 or (resid 130 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 131 through 132 or (resid 133 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 205 through 209 or (resid 210 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 211 through 256 or (res \ 
id 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thr \ 
ough 266 or (resid 267 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 268 through 303))
  selection = (chain 'G' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 7 through 37 or (resid 38 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 39 through 97 or (resid 98 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 99 through 106 or (resid 107 throu \ 
gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ 
ough 129 or (resid 130 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 131 through 132 or (resid 133 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 205 through 256 or (resid 257 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 258 through 303))
  selection = (chain 'H' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 7 through 58 or (resid 59 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 60 through 97 or (resid 98 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 99 through 106 or (resid 107 throu \ 
gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ 
ough 209 or (resid 210 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 211 through 266 or (resid 267 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 268 through 303))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.680
  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:             0.020
  Extract box with map and model:          0.790
  Check model and map are aligned:         0.160
  Set scattering table:                    0.190
  Process input model:                     52.160
  Find NCS groups from input model:        0.800
  Set up NCS constraints:                  0.080
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.100  21345  Z= 0.455
  Angle     :  1.177  17.793  29490  Z= 0.686
  Chirality :  0.069   0.724   3438
  Planarity :  0.007   0.100   3410
  Dihedral  : 21.076 176.466   8143
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  7.48 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 26.88 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -3.27 (0.15), residues: 2379
  helix: -2.68 (0.15), residues: 612
  sheet: -0.75 (0.25), residues: 444
  loop : -2.48 (0.15), residues: 1323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP H  28 
 HIS   0.021   0.002   HIS A 122 
 PHE   0.054   0.003   PHE D 150 
 TYR   0.050   0.003   TYR D  81 
 ARG   0.012   0.001   ARG I 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16943 (  707)
  hydrogen bonds       : angle       7.79720 ( 1930)
  covalent geometry    : bond        0.00736 (21345)
  covalent geometry    : angle       1.17731 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  372 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 291
  time to evaluate  : 1.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.8382 (tpt170) cc_final: 0.8158 (tpt170)
REVERT: E  147 ASP cc_start: 0.6461 (m-30) cc_final: 0.5997 (t0)
REVERT: F  267 LYS cc_start: 0.7547 (tttp) cc_final: 0.7336 (mtpp)
REVERT: G   48 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8039 (tm-30)
REVERT: G  268 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7346 (p)
REVERT: H  104 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7724 (pt0)
REVERT: H  224 MET cc_start: 0.8152 (ptp) cc_final: 0.7714 (ptp)
  outliers start: 81
  outliers final: 17
  residues processed: 339
  average time/residue: 0.2964
  time to fit residues: 161.8524
Evaluate side-chains
  243 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 224
  time to evaluate  : 2.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain F residue   55 ASN
Chi-restraints excluded: chain G residue   48 GLN
Chi-restraints excluded: chain G residue   55 ASN
Chi-restraints excluded: chain G residue  191 MET
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  268 THR
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   56 PHE
Chi-restraints excluded: chain H residue  278 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 208 optimal weight:    4.9990
   chunk 187 optimal weight:    8.9990
   chunk 103 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 193 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 117 optimal weight:    0.9990
   chunk 144 optimal weight:    3.9990
   chunk 224 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 ASN
B  74 GLN
D  82 ASN
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 266 ASN
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.153060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.110518 restraints weight = 47071.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.111856 restraints weight = 29773.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.112709 restraints weight = 19773.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  21345  Z= 0.175
  Angle     :  0.641   8.777  29490  Z= 0.346
  Chirality :  0.043   0.206   3438
  Planarity :  0.005   0.073   3410
  Dihedral  : 20.704 177.492   4146
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.56 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 23.46 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -2.49 (0.16), residues: 2379
  helix: -1.39 (0.19), residues: 628
  sheet: -0.72 (0.23), residues: 494
  loop : -2.22 (0.15), residues: 1257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G 130 
 HIS   0.007   0.001   HIS A 122 
 PHE   0.024   0.002   PHE A   9 
 TYR   0.023   0.002   TYR F  12 
 ARG   0.004   0.000   ARG D 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  707)
  hydrogen bonds       : angle       5.72225 ( 1930)
  covalent geometry    : bond        0.00380 (21345)
  covalent geometry    : angle       0.64093 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 245
  time to evaluate  : 1.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.7164 (mp0) cc_final: 0.6670 (tm-30)
REVERT: A  129 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8002 (mm-30)
REVERT: A  133 GLU cc_start: 0.7087 (mp0) cc_final: 0.6819 (pm20)
REVERT: B  158 CYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5483 (m)
REVERT: B  179 LEU cc_start: 0.7173 (tp) cc_final: 0.6964 (tt)
REVERT: B  226 PHE cc_start: 0.5752 (OUTLIER) cc_final: 0.5303 (m-80)
REVERT: C   12 TYR cc_start: 0.7187 (m-10) cc_final: 0.6805 (m-10)
REVERT: C  120 VAL cc_start: 0.8345 (m) cc_final: 0.8116 (m)
REVERT: D   88 ASP cc_start: 0.6639 (t70) cc_final: 0.6419 (t0)
REVERT: E  143 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7811 (mt)
REVERT: E  147 ASP cc_start: 0.6602 (m-30) cc_final: 0.6180 (t0)
REVERT: G   48 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7681 (tm-30)
REVERT: G  119 TYR cc_start: 0.8962 (m-80) cc_final: 0.8703 (m-80)
REVERT: G  268 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7575 (p)
REVERT: I  121 TYR cc_start: 0.0586 (OUTLIER) cc_final: -0.0926 (t80)
REVERT: I  130 LYS cc_start: 0.7961 (pttm) cc_final: 0.7458 (pttp)
REVERT: H  274 MET cc_start: 0.8489 (ttm) cc_final: 0.8109 (ttm)
  outliers start: 101
  outliers final: 55
  residues processed: 324
  average time/residue: 0.2650
  time to fit residues: 140.9332
Evaluate side-chains
  271 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 210
  time to evaluate  : 1.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue  158 CYS
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  197 HIS
Chi-restraints excluded: chain B residue  226 PHE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  244 THR
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  284 THR
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  143 ILE
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  235 THR
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain F residue   55 ASN
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  156 LEU
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  247 ILE
Chi-restraints excluded: chain F residue  284 THR
Chi-restraints excluded: chain F residue  291 VAL
Chi-restraints excluded: chain G residue   48 GLN
Chi-restraints excluded: chain G residue   91 LYS
Chi-restraints excluded: chain G residue  183 VAL
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  268 THR
Chi-restraints excluded: chain I residue    6 SER
Chi-restraints excluded: chain I residue   56 PHE
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 182 optimal weight:    1.9990
   chunk 153 optimal weight:    0.7980
   chunk 210 optimal weight:   30.0000
   chunk 154 optimal weight:    0.9990
   chunk 168 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   chunk 39 optimal weight:   30.0000
   chunk 137 optimal weight:    0.4980
   chunk 92 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 138 optimal weight:    0.3980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A  67 ASN
A  70 ASN
B  74 GLN
B  78 ASN
C 227 GLN
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 ASN
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  78 HIS
H  33 ASN
H  61 ASN
** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.151294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.108094 restraints weight = 46899.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.111276 restraints weight = 24433.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.113311 restraints weight = 16384.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  21345  Z= 0.130
  Angle     :  0.593  10.164  29490  Z= 0.318
  Chirality :  0.042   0.270   3438
  Planarity :  0.004   0.062   3410
  Dihedral  : 20.514 178.676   4137
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.39 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 22.99 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -2.11 (0.16), residues: 2379
  helix: -0.89 (0.20), residues: 619
  sheet: -0.48 (0.24), residues: 477
  loop : -2.06 (0.16), residues: 1283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 130 
 HIS   0.007   0.001   HIS A 122 
 PHE   0.020   0.001   PHE I 145 
 TYR   0.022   0.001   TYR F  12 
 ARG   0.005   0.000   ARG H 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  707)
  hydrogen bonds       : angle       5.29580 ( 1930)
  covalent geometry    : bond        0.00284 (21345)
  covalent geometry    : angle       0.59319 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 243
  time to evaluate  : 2.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 TYR cc_start: 0.6131 (t80) cc_final: 0.5697 (t80)
REVERT: A   57 GLU cc_start: 0.7185 (mp0) cc_final: 0.6688 (tm-30)
REVERT: A   83 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6486 (tp30)
REVERT: A  165 GLN cc_start: 0.7190 (mp10) cc_final: 0.6869 (mp10)
REVERT: B  179 LEU cc_start: 0.7261 (tp) cc_final: 0.7059 (tt)
REVERT: B  226 PHE cc_start: 0.5881 (OUTLIER) cc_final: 0.5449 (m-80)
REVERT: C   12 TYR cc_start: 0.7119 (m-10) cc_final: 0.6895 (m-10)
REVERT: C  129 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7464 (mt)
REVERT: C  168 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7557 (pm20)
REVERT: D   88 ASP cc_start: 0.6560 (t70) cc_final: 0.6244 (t0)
REVERT: E  147 ASP cc_start: 0.6551 (m-30) cc_final: 0.6184 (t0)
REVERT: E  156 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8212 (pp)
REVERT: E  273 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6955 (pp)
REVERT: F  111 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7294 (t0)
REVERT: G   48 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7593 (tm-30)
REVERT: G  119 TYR cc_start: 0.8955 (m-80) cc_final: 0.8668 (m-80)
REVERT: G  268 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7915 (p)
REVERT: G  270 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7907 (tp)
REVERT: I  121 TYR cc_start: 0.0711 (OUTLIER) cc_final: -0.0788 (t80)
REVERT: I  130 LYS cc_start: 0.7964 (pttm) cc_final: 0.7593 (pttm)
REVERT: H  274 MET cc_start: 0.8275 (ttm) cc_final: 0.7967 (ttm)
  outliers start: 107
  outliers final: 68
  residues processed: 329
  average time/residue: 0.2735
  time to fit residues: 148.9489
Evaluate side-chains
  296 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 217
  time to evaluate  : 2.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  197 HIS
Chi-restraints excluded: chain B residue  226 PHE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue  129 LEU
Chi-restraints excluded: chain C residue  168 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  227 GLN
Chi-restraints excluded: chain C residue  244 THR
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  129 LEU
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  284 THR
Chi-restraints excluded: chain D residue  295 LEU
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain F residue   55 ASN
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain F residue  111 ASP
Chi-restraints excluded: chain F residue  132 ASN
Chi-restraints excluded: chain F residue  145 VAL
Chi-restraints excluded: chain F residue  156 LEU
Chi-restraints excluded: chain F residue  166 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  247 ILE
Chi-restraints excluded: chain F residue  284 THR
Chi-restraints excluded: chain F residue  291 VAL
Chi-restraints excluded: chain G residue   20 ASN
Chi-restraints excluded: chain G residue   48 GLN
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  183 VAL
Chi-restraints excluded: chain G residue  191 MET
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  268 THR
Chi-restraints excluded: chain G residue  270 LEU
Chi-restraints excluded: chain G residue  273 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain I residue    6 SER
Chi-restraints excluded: chain I residue   78 HIS
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   61 ASN
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  142 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 144 optimal weight:    4.9990
   chunk 41 optimal weight:    0.3980
   chunk 75 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 57 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 27 optimal weight:   30.0000
   chunk 108 optimal weight:    0.9990
   chunk 186 optimal weight:   10.0000
   chunk 176 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
B  74 GLN
** B  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 227 GLN
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 109 ASN
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  78 HIS
H  33 ASN
** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.151660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.109117 restraints weight = 47349.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.110701 restraints weight = 27591.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.111875 restraints weight = 18300.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  21345  Z= 0.176
  Angle     :  0.595  10.228  29490  Z= 0.320
  Chirality :  0.042   0.187   3438
  Planarity :  0.004   0.054   3410
  Dihedral  : 20.366 177.904   4132
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.64 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 22.42 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -1.97 (0.16), residues: 2379
  helix: -0.66 (0.20), residues: 626
  sheet: -0.48 (0.24), residues: 474
  loop : -2.01 (0.16), residues: 1279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 239 
 HIS   0.006   0.001   HIS A 122 
 PHE   0.039   0.001   PHE E 205 
 TYR   0.026   0.002   TYR F  12 
 ARG   0.006   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  707)
  hydrogen bonds       : angle       5.18317 ( 1930)
  covalent geometry    : bond        0.00390 (21345)
  covalent geometry    : angle       0.59492 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 117
    poor density    : 232
  time to evaluate  : 2.108 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 TYR cc_start: 0.6387 (t80) cc_final: 0.5958 (t80)
REVERT: A   57 GLU cc_start: 0.7334 (mp0) cc_final: 0.6894 (tm-30)
REVERT: A   70 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7904 (t0)
REVERT: A   83 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6457 (tp30)
REVERT: A  165 GLN cc_start: 0.7186 (mp10) cc_final: 0.6760 (mp10)
REVERT: B  179 LEU cc_start: 0.7155 (tp) cc_final: 0.6953 (tt)
REVERT: B  226 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5684 (m-80)
REVERT: C  168 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7530 (pm20)
REVERT: D   56 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7120 (p0)
REVERT: D   88 ASP cc_start: 0.6626 (t70) cc_final: 0.6368 (t0)
REVERT: E  147 ASP cc_start: 0.6542 (m-30) cc_final: 0.6292 (t0)
REVERT: E  156 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8305 (pp)
REVERT: E  180 GLU cc_start: 0.6149 (mm-30) cc_final: 0.5930 (mm-30)
REVERT: E  273 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7107 (pp)
REVERT: F  111 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7357 (t0)
REVERT: G   48 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7541 (tm-30)
REVERT: G  119 TYR cc_start: 0.8988 (m-80) cc_final: 0.8757 (m-80)
REVERT: G  185 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8350 (pp)
REVERT: G  268 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8006 (p)
REVERT: G  270 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8053 (tp)
REVERT: I  121 TYR cc_start: 0.0335 (OUTLIER) cc_final: -0.1199 (t80)
REVERT: H  104 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8173 (mm-40)
REVERT: H  274 MET cc_start: 0.8418 (ttm) cc_final: 0.8008 (ttm)
  outliers start: 117
  outliers final: 76
  residues processed: 327
  average time/residue: 0.2617
  time to fit residues: 141.4983
Evaluate side-chains
  308 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 219
  time to evaluate  : 2.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  226 PHE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  168 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  244 THR
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   56 ASP
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  284 THR
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain F residue   33 ASN
Chi-restraints excluded: chain F residue   55 ASN
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain F residue  111 ASP
Chi-restraints excluded: chain F residue  132 ASN
Chi-restraints excluded: chain F residue  145 VAL
Chi-restraints excluded: chain F residue  166 VAL
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  247 ILE
Chi-restraints excluded: chain F residue  250 GLU
Chi-restraints excluded: chain F residue  291 VAL
Chi-restraints excluded: chain G residue   20 ASN
Chi-restraints excluded: chain G residue   48 GLN
Chi-restraints excluded: chain G residue   91 LYS
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  185 LEU
Chi-restraints excluded: chain G residue  191 MET
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  229 ILE
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  268 THR
Chi-restraints excluded: chain G residue  270 LEU
Chi-restraints excluded: chain G residue  273 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   78 HIS
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  147 MET
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   16 ILE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   35 THR
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  132 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  233 ILE
Chi-restraints excluded: chain H residue  300 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 208 optimal weight:    6.9990
   chunk 142 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 123 optimal weight:    0.8980
   chunk 205 optimal weight:   40.0000
   chunk 52 optimal weight:    7.9990
   chunk 27 optimal weight:   20.0000
   chunk 183 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    2.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
A 165 GLN
B  74 GLN
B  78 ASN
C  72 HIS
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  78 HIS
H  33 ASN
** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.150329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.109490 restraints weight = 48761.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.110316 restraints weight = 27373.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.111335 restraints weight = 18588.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  21345  Z= 0.247
  Angle     :  0.649   7.590  29490  Z= 0.348
  Chirality :  0.044   0.208   3438
  Planarity :  0.004   0.053   3410
  Dihedral  : 20.328 177.942   4131
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.15 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  7.01 %
    Allowed  : 22.78 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -1.97 (0.16), residues: 2379
  helix: -0.63 (0.20), residues: 628
  sheet: -0.58 (0.24), residues: 482
  loop : -1.99 (0.16), residues: 1269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP G 239 
 HIS   0.007   0.001   HIS A 122 
 PHE   0.025   0.002   PHE E 205 
 TYR   0.023   0.002   TYR F  12 
 ARG   0.005   0.001   ARG D 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03879 (  707)
  hydrogen bonds       : angle       5.26077 ( 1930)
  covalent geometry    : bond        0.00543 (21345)
  covalent geometry    : angle       0.64923 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 135
    poor density    : 220
  time to evaluate  : 2.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 TYR cc_start: 0.6541 (t80) cc_final: 0.6157 (t80)
REVERT: A   57 GLU cc_start: 0.7347 (mp0) cc_final: 0.6934 (tm-30)
REVERT: A   83 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6257 (tp30)
REVERT: B  226 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5769 (m-80)
REVERT: C  168 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7610 (pm20)
REVERT: D   56 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.6985 (p0)
REVERT: D   88 ASP cc_start: 0.6939 (t70) cc_final: 0.6522 (t0)
REVERT: E  133 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8037 (ttm-80)
REVERT: E  156 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8352 (pp)
REVERT: E  273 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7319 (pp)
REVERT: F   55 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7365 (p0)
REVERT: F  111 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7246 (t0)
REVERT: G   48 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7632 (tm-30)
REVERT: G  185 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8434 (pp)
REVERT: G  268 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8345 (p)
REVERT: G  270 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7994 (tp)
REVERT: I  121 TYR cc_start: 0.0399 (OUTLIER) cc_final: -0.1276 (t80)
  outliers start: 135
  outliers final: 92
  residues processed: 331
  average time/residue: 0.2803
  time to fit residues: 151.7650
Evaluate side-chains
  310 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 106
    poor density    : 204
  time to evaluate  : 1.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  156 MET
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  226 PHE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  168 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  244 THR
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   56 ASP
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain D residue  145 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  284 THR
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  289 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   33 ASN
Chi-restraints excluded: chain F residue   55 ASN
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  111 ASP
Chi-restraints excluded: chain F residue  132 ASN
Chi-restraints excluded: chain F residue  145 VAL
Chi-restraints excluded: chain F residue  166 VAL
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  226 ASP
Chi-restraints excluded: chain F residue  247 ILE
Chi-restraints excluded: chain F residue  250 GLU
Chi-restraints excluded: chain F residue  291 VAL
Chi-restraints excluded: chain G residue   20 ASN
Chi-restraints excluded: chain G residue   48 GLN
Chi-restraints excluded: chain G residue   91 LYS
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  185 LEU
Chi-restraints excluded: chain G residue  191 MET
Chi-restraints excluded: chain G residue  202 SER
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  229 ILE
Chi-restraints excluded: chain G residue  233 ILE
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  268 THR
Chi-restraints excluded: chain G residue  270 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain I residue    6 SER
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   94 VAL
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  147 MET
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   16 ILE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   35 THR
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  132 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  193 LEU
Chi-restraints excluded: chain H residue  226 ASP
Chi-restraints excluded: chain H residue  233 ILE
Chi-restraints excluded: chain H residue  300 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 217 optimal weight:    6.9990
   chunk 196 optimal weight:   30.0000
   chunk 110 optimal weight:    6.9990
   chunk 154 optimal weight:    1.9990
   chunk 139 optimal weight:    0.7980
   chunk 226 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 201 optimal weight:   40.0000
   chunk 17 optimal weight:   10.0000
   chunk 207 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
B  74 GLN
B  78 ASN
** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 ASN
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  72 HIS
F 146 ASN
** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  78 HIS
H  33 ASN
H 146 ASN
H 148 GLN
** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.148182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.108700 restraints weight = 48832.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.108020 restraints weight = 29300.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.108305 restraints weight = 23112.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067  21345  Z= 0.361
  Angle     :  0.756   9.383  29490  Z= 0.402
  Chirality :  0.046   0.243   3438
  Planarity :  0.005   0.054   3410
  Dihedral  : 20.439 177.316   4126
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.49 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 22.73 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -2.22 (0.16), residues: 2379
  helix: -0.88 (0.20), residues: 637
  sheet: -0.86 (0.25), residues: 460
  loop : -2.05 (0.16), residues: 1282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP G 239 
 HIS   0.009   0.002   HIS A 122 
 PHE   0.033   0.003   PHE G 200 
 TYR   0.029   0.002   TYR D  12 
 ARG   0.007   0.001   ARG F 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04391 (  707)
  hydrogen bonds       : angle       5.60970 ( 1930)
  covalent geometry    : bond        0.00789 (21345)
  covalent geometry    : angle       0.75640 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 151
    poor density    : 214
  time to evaluate  : 2.073 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 TYR cc_start: 0.6779 (t80) cc_final: 0.6385 (t80)
REVERT: A   57 GLU cc_start: 0.7255 (mp0) cc_final: 0.6842 (tm-30)
REVERT: A   83 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6311 (tp30)
REVERT: A  106 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5434 (m-80)
REVERT: A  130 TYR cc_start: 0.6954 (t80) cc_final: 0.6745 (t80)
REVERT: A  165 GLN cc_start: 0.8034 (mp10) cc_final: 0.7200 (mp10)
REVERT: B   13 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6939 (t70)
REVERT: B   70 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7649 (mtmt)
REVERT: B  226 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.5926 (m-80)
REVERT: C  168 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7802 (pm20)
REVERT: D   38 MET cc_start: 0.7847 (mmp) cc_final: 0.7589 (mmp)
REVERT: D   56 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6815 (p0)
REVERT: D   88 ASP cc_start: 0.6996 (t70) cc_final: 0.6544 (t0)
REVERT: E   69 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7671 (m110)
REVERT: E   72 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.6975 (t-90)
REVERT: E  133 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8227 (ttm-80)
REVERT: E  273 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7565 (pp)
REVERT: F   55 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7694 (p0)
REVERT: G   48 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7710 (tm-30)
REVERT: G  117 TYR cc_start: 0.8010 (t80) cc_final: 0.7724 (t80)
REVERT: G  185 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8608 (pp)
REVERT: G  270 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8047 (tp)
REVERT: I  118 GLU cc_start: 0.5182 (tp30) cc_final: 0.4696 (tt0)
REVERT: I  121 TYR cc_start: 0.0925 (OUTLIER) cc_final: -0.1128 (t80)
  outliers start: 151
  outliers final: 99
  residues processed: 342
  average time/residue: 0.2831
  time to fit residues: 157.0500
Evaluate side-chains
  307 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 115
    poor density    : 192
  time to evaluate  : 1.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 THR
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   13 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  156 MET
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  226 PHE
Chi-restraints excluded: chain C residue   55 ASN
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  168 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  244 THR
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   56 ASP
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain D residue  145 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  284 THR
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   69 ASN
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   74 LYS
Chi-restraints excluded: chain E residue   82 ASN
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  289 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   33 ASN
Chi-restraints excluded: chain F residue   55 ASN
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  111 ASP
Chi-restraints excluded: chain F residue  132 ASN
Chi-restraints excluded: chain F residue  145 VAL
Chi-restraints excluded: chain F residue  166 VAL
Chi-restraints excluded: chain F residue  172 MET
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  226 ASP
Chi-restraints excluded: chain F residue  247 ILE
Chi-restraints excluded: chain F residue  250 GLU
Chi-restraints excluded: chain F residue  256 VAL
Chi-restraints excluded: chain F residue  294 ASN
Chi-restraints excluded: chain G residue   10 LEU
Chi-restraints excluded: chain G residue   19 THR
Chi-restraints excluded: chain G residue   20 ASN
Chi-restraints excluded: chain G residue   48 GLN
Chi-restraints excluded: chain G residue   91 LYS
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  185 LEU
Chi-restraints excluded: chain G residue  191 MET
Chi-restraints excluded: chain G residue  197 SER
Chi-restraints excluded: chain G residue  202 SER
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  229 ILE
Chi-restraints excluded: chain G residue  233 ILE
Chi-restraints excluded: chain G residue  260 VAL
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  270 LEU
Chi-restraints excluded: chain G residue  273 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain I residue    6 SER
Chi-restraints excluded: chain I residue   34 PHE
Chi-restraints excluded: chain I residue   70 LEU
Chi-restraints excluded: chain I residue   94 VAL
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   16 ILE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   35 THR
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  132 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  145 VAL
Chi-restraints excluded: chain H residue  191 MET
Chi-restraints excluded: chain H residue  219 ASN
Chi-restraints excluded: chain H residue  233 ILE
Chi-restraints excluded: chain H residue  260 VAL
Chi-restraints excluded: chain H residue  300 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 153 optimal weight:    0.6980
   chunk 166 optimal weight:    0.8980
   chunk 214 optimal weight:    0.6980
   chunk 212 optimal weight:   10.0000
   chunk 163 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 221 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  74 GLN
C  72 HIS
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  63 GLN
E  82 ASN
** G 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  78 HIS
H  33 ASN
H 148 GLN
** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.150199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.113913 restraints weight = 46917.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.116284 restraints weight = 28805.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.116296 restraints weight = 23974.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  21345  Z= 0.144
  Angle     :  0.631  10.379  29490  Z= 0.335
  Chirality :  0.043   0.213   3438
  Planarity :  0.004   0.069   3410
  Dihedral  : 20.309 179.569   4125
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  6.94 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 25.32 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -1.99 (0.16), residues: 2379
  helix: -0.62 (0.21), residues: 627
  sheet: -0.58 (0.25), residues: 448
  loop : -2.00 (0.16), residues: 1304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 130 
 HIS   0.007   0.001   HIS A 122 
 PHE   0.023   0.001   PHE F 182 
 TYR   0.014   0.001   TYR A  23 
 ARG   0.005   0.000   ARG G 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03455 (  707)
  hydrogen bonds       : angle       5.26319 ( 1930)
  covalent geometry    : bond        0.00323 (21345)
  covalent geometry    : angle       0.63070 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 108
    poor density    : 246
  time to evaluate  : 2.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8079 (m)
REVERT: A   47 TYR cc_start: 0.6563 (t80) cc_final: 0.6160 (t80)
REVERT: A   83 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6210 (tp30)
REVERT: A  106 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5171 (m-80)
REVERT: A  130 TYR cc_start: 0.6503 (t80) cc_final: 0.5816 (t80)
REVERT: A  165 GLN cc_start: 0.7614 (mp10) cc_final: 0.7122 (mp10)
REVERT: B   13 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6795 (t70)
REVERT: C  168 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7839 (pm20)
REVERT: D   56 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7098 (p0)
REVERT: D   88 ASP cc_start: 0.7002 (t70) cc_final: 0.6634 (t0)
REVERT: E    5 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7597 (tptp)
REVERT: E  133 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8006 (ttt-90)
REVERT: E  273 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7233 (pp)
REVERT: G  185 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8409 (pp)
REVERT: G  270 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7940 (tp)
REVERT: I  118 GLU cc_start: 0.5318 (tp30) cc_final: 0.5045 (tt0)
REVERT: I  121 TYR cc_start: 0.1017 (OUTLIER) cc_final: -0.1083 (t80)
REVERT: H  274 MET cc_start: 0.7935 (ttm) cc_final: 0.7563 (ttm)
  outliers start: 108
  outliers final: 72
  residues processed: 332
  average time/residue: 0.2814
  time to fit residues: 151.5330
Evaluate side-chains
  297 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 213
  time to evaluate  : 2.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   73 TYR
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   13 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue  156 MET
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  168 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  244 THR
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain D residue   56 ASP
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  284 THR
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   82 ASN
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  180 GLU
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  289 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain F residue   33 ASN
Chi-restraints excluded: chain F residue  132 ASN
Chi-restraints excluded: chain F residue  166 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  226 ASP
Chi-restraints excluded: chain F residue  250 GLU
Chi-restraints excluded: chain F residue  256 VAL
Chi-restraints excluded: chain G residue   20 ASN
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  185 LEU
Chi-restraints excluded: chain G residue  191 MET
Chi-restraints excluded: chain G residue  202 SER
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  229 ILE
Chi-restraints excluded: chain G residue  260 VAL
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  270 LEU
Chi-restraints excluded: chain G residue  273 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain I residue    6 SER
Chi-restraints excluded: chain I residue   56 PHE
Chi-restraints excluded: chain I residue   94 VAL
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  132 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  233 ILE
Chi-restraints excluded: chain H residue  260 VAL
Chi-restraints excluded: chain H residue  300 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 227 optimal weight:    0.2980
   chunk 144 optimal weight:    3.9990
   chunk 183 optimal weight:    4.9990
   chunk 169 optimal weight:    4.9990
   chunk 243 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 64 optimal weight:    0.7980
   chunk 187 optimal weight:    9.9990
   chunk 198 optimal weight:    9.9990
   chunk 226 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
B  74 GLN
C  72 HIS
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 ASN
** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I   3 ASN
** I  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  78 HIS
H  33 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.149446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.109984 restraints weight = 47256.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.110784 restraints weight = 28998.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.112021 restraints weight = 18874.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  21345  Z= 0.195
  Angle     :  0.662   9.773  29490  Z= 0.350
  Chirality :  0.043   0.199   3438
  Planarity :  0.004   0.053   3410
  Dihedral  : 20.190 178.417   4118
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.44 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 25.38 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -2.01 (0.16), residues: 2379
  helix: -0.63 (0.20), residues: 634
  sheet: -0.63 (0.25), residues: 454
  loop : -2.01 (0.16), residues: 1291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 239 
 HIS   0.007   0.001   HIS A 122 
 PHE   0.033   0.002   PHE B 226 
 TYR   0.022   0.002   TYR H 117 
 ARG   0.004   0.000   ARG H 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03542 (  707)
  hydrogen bonds       : angle       5.24444 ( 1930)
  covalent geometry    : bond        0.00441 (21345)
  covalent geometry    : angle       0.66150 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 110
    poor density    : 218
  time to evaluate  : 2.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.8317 (tpt170) cc_final: 0.8081 (tpt170)
REVERT: A   47 TYR cc_start: 0.6668 (t80) cc_final: 0.6329 (t80)
REVERT: A   83 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6283 (tp30)
REVERT: A  106 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5413 (m-80)
REVERT: A  165 GLN cc_start: 0.7563 (mp10) cc_final: 0.6948 (mp10)
REVERT: B   13 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6990 (t70)
REVERT: B  158 CYS cc_start: 0.6609 (OUTLIER) cc_final: 0.5808 (m)
REVERT: C  168 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8018 (pm20)
REVERT: D   56 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7030 (p0)
REVERT: D   88 ASP cc_start: 0.7007 (t70) cc_final: 0.6617 (t0)
REVERT: E  133 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8043 (ttt-90)
REVERT: E  143 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.7881 (mm)
REVERT: E  273 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7304 (pp)
REVERT: G  117 TYR cc_start: 0.8312 (t80) cc_final: 0.8046 (t80)
REVERT: G  185 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8481 (pp)
REVERT: G  270 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7997 (tp)
REVERT: I  118 GLU cc_start: 0.5076 (tp30) cc_final: 0.4838 (tt0)
REVERT: I  121 TYR cc_start: 0.0650 (OUTLIER) cc_final: -0.1302 (t80)
REVERT: H  274 MET cc_start: 0.8248 (ttm) cc_final: 0.7896 (ttm)
  outliers start: 110
  outliers final: 79
  residues processed: 310
  average time/residue: 0.2730
  time to fit residues: 138.0439
Evaluate side-chains
  300 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 209
  time to evaluate  : 2.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   13 ASP
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue  156 MET
Chi-restraints excluded: chain B residue  158 CYS
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain C residue   55 ASN
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  168 GLU
Chi-restraints excluded: chain C residue  182 PHE
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  244 THR
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain D residue   56 ASP
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   82 ASN
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain E residue  143 ILE
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  180 GLU
Chi-restraints excluded: chain E residue  227 GLN
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  289 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   33 ASN
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue  132 ASN
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  226 ASP
Chi-restraints excluded: chain F residue  250 GLU
Chi-restraints excluded: chain F residue  256 VAL
Chi-restraints excluded: chain G residue   20 ASN
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  185 LEU
Chi-restraints excluded: chain G residue  191 MET
Chi-restraints excluded: chain G residue  202 SER
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  229 ILE
Chi-restraints excluded: chain G residue  260 VAL
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  270 LEU
Chi-restraints excluded: chain G residue  273 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain I residue    6 SER
Chi-restraints excluded: chain I residue   56 PHE
Chi-restraints excluded: chain I residue   70 LEU
Chi-restraints excluded: chain I residue   94 VAL
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  132 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  233 ILE
Chi-restraints excluded: chain H residue  260 VAL
Chi-restraints excluded: chain H residue  300 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 175 optimal weight:    2.9990
   chunk 121 optimal weight:    0.5980
   chunk 138 optimal weight:    0.7980
   chunk 167 optimal weight:    3.9990
   chunk 8 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 118 optimal weight:    0.7980
   chunk 97 optimal weight:    7.9990
   chunk 214 optimal weight:    4.9990
   chunk 223 optimal weight:    5.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
C  72 HIS
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 ASN
** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  78 HIS
H  33 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.150365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.111288 restraints weight = 47238.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.112555 restraints weight = 28632.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.113296 restraints weight = 19953.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  21345  Z= 0.188
  Angle     :  0.657   9.554  29490  Z= 0.349
  Chirality :  0.044   0.306   3438
  Planarity :  0.004   0.053   3410
  Dihedral  : 20.162 178.537   4118
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.82 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 25.48 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -1.99 (0.16), residues: 2379
  helix: -0.60 (0.21), residues: 633
  sheet: -0.66 (0.25), residues: 457
  loop : -1.98 (0.16), residues: 1289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 239 
 HIS   0.007   0.001   HIS A 122 
 PHE   0.025   0.002   PHE F 182 
 TYR   0.021   0.002   TYR D  12 
 ARG   0.003   0.000   ARG F 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  707)
  hydrogen bonds       : angle       5.21625 ( 1930)
  covalent geometry    : bond        0.00432 (21345)
  covalent geometry    : angle       0.65715 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 218
  time to evaluate  : 2.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.8322 (tpt170) cc_final: 0.8012 (tpt170)
REVERT: A   31 PHE cc_start: 0.7193 (m-80) cc_final: 0.6945 (m-10)
REVERT: A   47 TYR cc_start: 0.6737 (t80) cc_final: 0.6513 (t80)
REVERT: A  106 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.5389 (m-80)
REVERT: A  165 GLN cc_start: 0.7515 (mp10) cc_final: 0.6944 (mp10)
REVERT: B   13 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6980 (t70)
REVERT: C   12 TYR cc_start: 0.7265 (m-10) cc_final: 0.7053 (m-10)
REVERT: C  168 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8176 (pm20)
REVERT: C  172 MET cc_start: 0.6434 (ptp) cc_final: 0.5848 (ptp)
REVERT: D   56 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7143 (p0)
REVERT: D   88 ASP cc_start: 0.6911 (t70) cc_final: 0.6654 (t0)
REVERT: D  204 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7217 (mm-30)
REVERT: E  133 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8033 (ttt-90)
REVERT: E  143 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7879 (mt)
REVERT: E  273 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7282 (pp)
REVERT: F  227 GLN cc_start: 0.8252 (pt0) cc_final: 0.8034 (pt0)
REVERT: G  185 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8484 (pp)
REVERT: G  270 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7977 (tp)
REVERT: I  118 GLU cc_start: 0.5298 (tp30) cc_final: 0.5091 (tt0)
REVERT: I  121 TYR cc_start: 0.0698 (OUTLIER) cc_final: -0.1285 (t80)
REVERT: H  172 MET cc_start: 0.8200 (ppp) cc_final: 0.7940 (ppp)
REVERT: H  274 MET cc_start: 0.8220 (ttm) cc_final: 0.7798 (ttm)
  outliers start: 107
  outliers final: 83
  residues processed: 308
  average time/residue: 0.2839
  time to fit residues: 141.2562
Evaluate side-chains
  299 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 206
  time to evaluate  : 2.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   13 ASP
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue  156 MET
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain C residue   55 ASN
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  168 GLU
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain D residue   56 ASP
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   82 ASN
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain E residue  143 ILE
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  180 GLU
Chi-restraints excluded: chain E residue  227 GLN
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  289 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   33 ASN
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue  132 ASN
Chi-restraints excluded: chain F residue  166 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  226 ASP
Chi-restraints excluded: chain F residue  250 GLU
Chi-restraints excluded: chain F residue  256 VAL
Chi-restraints excluded: chain G residue   20 ASN
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue   91 LYS
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  185 LEU
Chi-restraints excluded: chain G residue  191 MET
Chi-restraints excluded: chain G residue  202 SER
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  229 ILE
Chi-restraints excluded: chain G residue  260 VAL
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  270 LEU
Chi-restraints excluded: chain G residue  273 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain I residue    6 SER
Chi-restraints excluded: chain I residue   34 PHE
Chi-restraints excluded: chain I residue   56 PHE
Chi-restraints excluded: chain I residue   94 VAL
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  132 ASN
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  219 ASN
Chi-restraints excluded: chain H residue  233 ILE
Chi-restraints excluded: chain H residue  260 VAL
Chi-restraints excluded: chain H residue  300 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 180 optimal weight:    0.6980
   chunk 171 optimal weight:    0.0370
   chunk 0 optimal weight:   10.0000
   chunk 181 optimal weight:    1.9990
   chunk 244 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 241 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
C  72 HIS
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 ASN
** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  18 ASN
I  78 HIS
H  17 ASN
H  33 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.151673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.110810 restraints weight = 47395.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.114250 restraints weight = 23307.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.116369 restraints weight = 15199.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  21345  Z= 0.146
  Angle     :  0.651   9.885  29490  Z= 0.343
  Chirality :  0.043   0.199   3438
  Planarity :  0.004   0.093   3410
  Dihedral  : 20.095 179.114   4118
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.19 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 26.10 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -1.83 (0.17), residues: 2379
  helix: -0.52 (0.21), residues: 630
  sheet: -0.32 (0.26), residues: 423
  loop : -1.92 (0.16), residues: 1326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 130 
 HIS   0.006   0.001   HIS C  72 
 PHE   0.036   0.001   PHE G 200 
 TYR   0.018   0.002   TYR E  81 
 ARG   0.010   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03289 (  707)
  hydrogen bonds       : angle       5.10222 ( 1930)
  covalent geometry    : bond        0.00334 (21345)
  covalent geometry    : angle       0.65084 (29490)

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

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

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4758 Ramachandran restraints generated.
    2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 100
    poor density    : 238
  time to evaluate  : 2.126 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.8324 (tpt170) cc_final: 0.8028 (tpt170)
REVERT: A   23 TYR cc_start: 0.8230 (m-80) cc_final: 0.8005 (m-80)
REVERT: A   58 GLU cc_start: 0.7263 (pm20) cc_final: 0.6909 (pm20)
REVERT: A  106 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5238 (m-80)
REVERT: A  165 GLN cc_start: 0.7345 (mp10) cc_final: 0.6809 (mp10)
REVERT: B   13 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6984 (t70)
REVERT: C  168 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7842 (pm20)
REVERT: D  121 TYR cc_start: 0.8513 (t80) cc_final: 0.7926 (t80)
REVERT: D  204 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7157 (mm-30)
REVERT: E    5 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7618 (tptp)
REVERT: E  121 TYR cc_start: 0.8668 (t80) cc_final: 0.8466 (t80)
REVERT: E  133 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7929 (ttt-90)
REVERT: E  143 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7899 (mt)
REVERT: E  235 THR cc_start: 0.8486 (m) cc_final: 0.7776 (p)
REVERT: E  273 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7141 (pp)
REVERT: F  227 GLN cc_start: 0.8155 (pt0) cc_final: 0.7753 (pt0)
REVERT: G  185 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8354 (pp)
REVERT: G  270 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7908 (tp)
REVERT: I  121 TYR cc_start: 0.0385 (OUTLIER) cc_final: -0.1351 (t80)
REVERT: H  117 TYR cc_start: 0.8447 (t80) cc_final: 0.8222 (t80)
REVERT: H  172 MET cc_start: 0.8108 (ppp) cc_final: 0.7904 (ppp)
REVERT: H  274 MET cc_start: 0.8042 (ttm) cc_final: 0.7613 (ttm)
  outliers start: 100
  outliers final: 76
  residues processed: 320
  average time/residue: 0.2954
  time to fit residues: 153.2116
Evaluate side-chains
  309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 223
  time to evaluate  : 2.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  132 TRP
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   13 ASP
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LYS
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain C residue   55 ASN
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  168 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  183 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  255 VAL
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  268 THR
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   82 ASN
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain E residue  143 ILE
Chi-restraints excluded: chain E residue  145 VAL
Chi-restraints excluded: chain E residue  146 ASN
Chi-restraints excluded: chain E residue  155 LEU
Chi-restraints excluded: chain E residue  180 GLU
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  289 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain F residue   33 ASN
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue  132 ASN
Chi-restraints excluded: chain F residue  166 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  226 ASP
Chi-restraints excluded: chain F residue  250 GLU
Chi-restraints excluded: chain F residue  256 VAL
Chi-restraints excluded: chain G residue   20 ASN
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue  102 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  185 LEU
Chi-restraints excluded: chain G residue  206 VAL
Chi-restraints excluded: chain G residue  226 ASP
Chi-restraints excluded: chain G residue  229 ILE
Chi-restraints excluded: chain G residue  260 VAL
Chi-restraints excluded: chain G residue  266 ASN
Chi-restraints excluded: chain G residue  270 LEU
Chi-restraints excluded: chain G residue  273 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain I residue    6 SER
Chi-restraints excluded: chain I residue   18 ASN
Chi-restraints excluded: chain I residue   34 PHE
Chi-restraints excluded: chain I residue   56 PHE
Chi-restraints excluded: chain I residue   94 VAL
Chi-restraints excluded: chain I residue  121 TYR
Chi-restraints excluded: chain I residue  145 PHE
Chi-restraints excluded: chain I residue  148 PHE
Chi-restraints excluded: chain H residue   32 ASP
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  191 MET
Chi-restraints excluded: chain H residue  233 ILE
Chi-restraints excluded: chain H residue  260 VAL
Chi-restraints excluded: chain H residue  300 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 180 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 183 optimal weight:    0.9980
   chunk 160 optimal weight:    0.9990
   chunk 200 optimal weight:   20.0000
   chunk 161 optimal weight:   10.0000
   chunk 202 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 121 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 HIS
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  78 HIS
H  33 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.152203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.116985 restraints weight = 47481.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.118644 restraints weight = 29613.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.119219 restraints weight = 24274.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.135  21345  Z= 0.179
  Angle     :  0.789  59.200  29490  Z= 0.444
  Chirality :  0.055   1.961   3438
  Planarity :  0.005   0.127   3410
  Dihedral  : 20.094 179.115   4118
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  7.10 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 26.31 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.21 %
    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: -1.83 (0.17), residues: 2379
  helix: -0.55 (0.21), residues: 630
  sheet: -0.31 (0.26), residues: 423
  loop : -1.91 (0.16), residues: 1326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 239 
 HIS   0.005   0.001   HIS A 122 
 PHE   0.028   0.001   PHE G 200 
 TYR   0.016   0.002   TYR A  47 
 ARG   0.008   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03290 (  707)
  hydrogen bonds       : angle       5.10492 ( 1930)
  covalent geometry    : bond        0.00396 (21345)
  covalent geometry    : angle       0.78907 (29490)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6683.45 seconds
wall clock time: 118 minutes 17.27 seconds (7097.27 seconds total)