Starting phenix.real_space_refine
on Mon Jul 22 23:21:43 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/07_2024/8tsw_41601_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/07_2024/8tsw_41601.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/07_2024/8tsw_41601.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/07_2024/8tsw_41601.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/07_2024/8tsw_41601_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/07_2024/8tsw_41601_neut.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.889
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      98      5.16       5
     C   13184      2.51       5
     N    3474      2.21       5
     O    3570      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  146": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU   86": "OE1" <-> "OE2"
    Residue "C GLU   73": "OE1" <-> "OE2"
    Residue "C GLU  178": "OE1" <-> "OE2"
    Residue "D GLU   31": "OE1" <-> "OE2"
    Residue "D GLU   73": "OE1" <-> "OE2"
    Residue "E GLU   41": "OE1" <-> "OE2"
    Residue "I GLU   74": "OE1" <-> "OE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 20326
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1687
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 4, 'TRANS': 209}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1687
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 4, 'TRANS': 209}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2033
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 16, 'TRANS': 238}
    Chain: "D"
      Number of atoms: 2033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2033
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 16, 'TRANS': 238}
    Chain: "E"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1624
          Classifications: {'peptide': 198}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 189}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 1672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1672
          Classifications: {'peptide': 204}
          Link IDs: {'PTRANS': 8, 'TRANS': 195}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1713
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 8, 'TRANS': 200}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1434
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 8, 'TRANS': 165}
          Chain breaks: 2
    Chain: "I"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1624
          Classifications: {'peptide': 198}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 189}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 1672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1672
          Classifications: {'peptide': 204}
          Link IDs: {'PTRANS': 8, 'TRANS': 195}
          Chain breaks: 2
    Chain: "K"
      Number of atoms: 1713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1713
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 8, 'TRANS': 200}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1434
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 8, 'TRANS': 165}
          Chain breaks: 2
  Time building chain proxies: 10.40, per 1000 atoms: 0.51
  Number of scatterers: 20326
  At special positions: 0
  Unit cell: (132.84, 132.84, 140.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      98     16.00
     O    3570      8.00
     N    3474      7.00
     C   13184      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 7.05
  Conformation dependent library (CDL) restraints added in 3.2 seconds
  

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4760

  Finding SS restraints...
    Secondary structure from input PDB file:
      105 helices and 14 sheets defined
      63.2% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 52
    Processing helix  chain 'A' and resid 74 through 78
    Processing helix  chain 'A' and resid 83 through 95
    Processing helix  chain 'A' and resid 98 through 114
    Processing helix  chain 'A' and resid 127 through 142
      removed outlier: 3.782A  pdb=" N   PHE A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 173
      removed outlier: 3.531A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 190
    Processing helix  chain 'A' and resid 207 through 219
      removed outlier: 3.902A  pdb=" N   GLY A 211 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 213 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 52
    Processing helix  chain 'B' and resid 74 through 78
    Processing helix  chain 'B' and resid 83 through 95
    Processing helix  chain 'B' and resid 98 through 114
    Processing helix  chain 'B' and resid 127 through 142
      removed outlier: 3.951A  pdb=" N   PHE B 142 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 172
      removed outlier: 3.527A  pdb=" N   ARG B 161 " --> pdb=" O   ASP B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 191
    Processing helix  chain 'B' and resid 207 through 219
      removed outlier: 3.844A  pdb=" N   GLY B 211 " --> pdb=" O   ASP B 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 36
    Processing helix  chain 'C' and resid 41 through 69
      removed outlier: 3.694A  pdb=" N   TRP C  45 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
      Proline residue:  C  50  - end of helix
      removed outlier: 6.233A  pdb=" N   LEU C  63 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   ALA C  64 " --> pdb=" O   LEU C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 97
      Proline residue:  C  84  - end of helix
      removed outlier: 4.275A  pdb=" N   LEU C  95 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   MET C  96 " --> pdb=" O   VAL C  92 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLU C  97 " --> pdb=" O   THR C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 106
      removed outlier: 3.528A  pdb=" N   PHE C 106 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 143
      removed outlier: 3.873A  pdb=" N   THR C 116 " --> pdb=" O   LYS C 112 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL C 117 " --> pdb=" O   PRO C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 176
    Processing helix  chain 'C' and resid 179 through 197
      removed outlier: 3.563A  pdb=" N   ARG C 183 " --> pdb=" O   ILE C 179 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   LEU C 191 " --> pdb=" O   ARG C 187 " (cutoff:3.500A)
      Proline residue:  C 192  - end of helix
      removed outlier: 3.595A  pdb=" N   PHE C 195 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 209
      No H-bonds generated for 'chain 'C' and resid 207 through 209'
    Processing helix  chain 'C' and resid 210 through 215
    Processing helix  chain 'C' and resid 217 through 231
      removed outlier: 3.524A  pdb=" N   HIS C 221 " --> pdb=" O   ASN C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 263
    Processing helix  chain 'D' and resid 17 through 36
    Processing helix  chain 'D' and resid 36 through 41
      removed outlier: 4.309A  pdb=" N   TRP D  40 " --> pdb=" O   LEU D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 69
      removed outlier: 3.712A  pdb=" N   TRP D  45 " --> pdb=" O   LEU D  41 " (cutoff:3.500A)
      Proline residue:  D  50  - end of helix
      removed outlier: 6.206A  pdb=" N   LEU D  63 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   ALA D  64 " --> pdb=" O   LEU D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 97
      Proline residue:  D  84  - end of helix
      removed outlier: 4.272A  pdb=" N   LEU D  95 " --> pdb=" O   LEU D  91 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   MET D  96 " --> pdb=" O   VAL D  92 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLU D  97 " --> pdb=" O   THR D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 106
      removed outlier: 3.554A  pdb=" N   PHE D 106 " --> pdb=" O   ARG D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 143
      removed outlier: 3.895A  pdb=" N   THR D 116 " --> pdb=" O   LYS D 112 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL D 117 " --> pdb=" O   PRO D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 176
    Processing helix  chain 'D' and resid 179 through 197
      removed outlier: 3.573A  pdb=" N   ARG D 183 " --> pdb=" O   ILE D 179 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU D 191 " --> pdb=" O   ARG D 187 " (cutoff:3.500A)
      Proline residue:  D 192  - end of helix
      removed outlier: 3.594A  pdb=" N   PHE D 195 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 209
      No H-bonds generated for 'chain 'D' and resid 207 through 209'
    Processing helix  chain 'D' and resid 210 through 215
    Processing helix  chain 'D' and resid 217 through 231
      removed outlier: 3.508A  pdb=" N   HIS D 221 " --> pdb=" O   ASN D 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 242 through 263
    Processing helix  chain 'E' and resid 10 through 19
    Processing helix  chain 'E' and resid 19 through 33
    Processing helix  chain 'E' and resid 72 through 84
      removed outlier: 3.883A  pdb=" N   HIS E  84 " --> pdb=" O   GLN E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 97
    Processing helix  chain 'E' and resid 97 through 102
    Processing helix  chain 'E' and resid 118 through 129
    Processing helix  chain 'E' and resid 149 through 179
      removed outlier: 4.080A  pdb=" N   MET E 175 " --> pdb=" O   LEU E 171 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA E 176 " --> pdb=" O   SER E 172 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   GLN E 179 " --> pdb=" O   MET E 175 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 340 through 362
      removed outlier: 3.541A  pdb=" N   VAL E 362 " --> pdb=" O   VAL E 358 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 10
      removed outlier: 3.823A  pdb=" N   LEU F   9 " --> pdb=" O   LEU F   5 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   THR F  10 " --> pdb=" O   VAL F   6 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 11 through 19
    Processing helix  chain 'F' and resid 19 through 32
    Processing helix  chain 'F' and resid 73 through 84
      removed outlier: 3.893A  pdb=" N   HIS F  84 " --> pdb=" O   GLN F  80 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 85 through 97
      removed outlier: 3.656A  pdb=" N   LEU F  89 " --> pdb=" O   SER F  85 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 103
      removed outlier: 3.639A  pdb=" N   GLY F 103 " --> pdb=" O   ARG F  99 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 118 through 129
    Processing helix  chain 'F' and resid 149 through 176
      removed outlier: 3.913A  pdb=" N   ALA F 176 " --> pdb=" O   SER F 172 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 340 through 371
      removed outlier: 3.646A  pdb=" N   ASN F 344 " --> pdb=" O   ARG F 340 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   ASP F 371 " --> pdb=" O   ARG F 367 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 19
    Processing helix  chain 'G' and resid 19 through 32
    Processing helix  chain 'G' and resid 72 through 84
      removed outlier: 4.022A  pdb=" N   HIS G  84 " --> pdb=" O   GLN G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 86 through 97
    Processing helix  chain 'G' and resid 97 through 103
    Processing helix  chain 'G' and resid 118 through 129
    Processing helix  chain 'G' and resid 149 through 180
      removed outlier: 3.992A  pdb=" N   GLN G 179 " --> pdb=" O   MET G 175 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   GLY G 180 " --> pdb=" O   ALA G 176 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 340 through 368
    Processing helix  chain 'H' and resid 20 through 33
    Processing helix  chain 'H' and resid 72 through 84
      removed outlier: 4.132A  pdb=" N   HIS H  84 " --> pdb=" O   GLN H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 85 through 97
      removed outlier: 3.826A  pdb=" N   LEU H  89 " --> pdb=" O   SER H  85 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 97 through 103
      removed outlier: 3.560A  pdb=" N   GLY H 103 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 108 through 112
      removed outlier: 3.806A  pdb=" N   ARG H 112 " --> pdb=" O   PRO H 109 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 118 through 129
    Processing helix  chain 'H' and resid 149 through 178
      removed outlier: 3.949A  pdb=" N   MET H 175 " --> pdb=" O   LEU H 171 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 340 through 351
    Processing helix  chain 'I' and resid 10 through 19
    Processing helix  chain 'I' and resid 19 through 32
    Processing helix  chain 'I' and resid 72 through 84
      removed outlier: 3.828A  pdb=" N   HIS I  84 " --> pdb=" O   GLN I  80 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 86 through 97
    Processing helix  chain 'I' and resid 97 through 102
    Processing helix  chain 'I' and resid 118 through 129
    Processing helix  chain 'I' and resid 149 through 178
      removed outlier: 3.500A  pdb=" N   GLN I 154 " --> pdb=" O   PRO I 150 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   MET I 175 " --> pdb=" O   LEU I 171 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 340 through 362
      removed outlier: 3.610A  pdb=" N   VAL I 362 " --> pdb=" O   VAL I 358 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 4 through 10
    Processing helix  chain 'J' and resid 11 through 19
    Processing helix  chain 'J' and resid 19 through 32
    Processing helix  chain 'J' and resid 73 through 84
      removed outlier: 3.849A  pdb=" N   HIS J  84 " --> pdb=" O   GLN J  80 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 85 through 97
      removed outlier: 3.636A  pdb=" N   LEU J  89 " --> pdb=" O   SER J  85 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 97 through 103
      removed outlier: 3.631A  pdb=" N   GLY J 103 " --> pdb=" O   ARG J  99 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 118 through 129
    Processing helix  chain 'J' and resid 149 through 176
      removed outlier: 3.917A  pdb=" N   ALA J 176 " --> pdb=" O   SER J 172 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 340 through 371
      removed outlier: 3.627A  pdb=" N   ASN J 344 " --> pdb=" O   ARG J 340 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASP J 371 " --> pdb=" O   ARG J 367 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 10 through 19
    Processing helix  chain 'K' and resid 19 through 32
    Processing helix  chain 'K' and resid 72 through 84
      removed outlier: 4.045A  pdb=" N   HIS K  84 " --> pdb=" O   GLN K  80 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 86 through 97
    Processing helix  chain 'K' and resid 97 through 103
    Processing helix  chain 'K' and resid 118 through 129
    Processing helix  chain 'K' and resid 149 through 180
    Processing helix  chain 'K' and resid 340 through 368
    Processing helix  chain 'K' and resid 369 through 371
      No H-bonds generated for 'chain 'K' and resid 369 through 371'
    Processing helix  chain 'L' and resid 20 through 31
    Processing helix  chain 'L' and resid 72 through 84
      removed outlier: 4.140A  pdb=" N   HIS L  84 " --> pdb=" O   GLN L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 85 through 97
      removed outlier: 3.810A  pdb=" N   LEU L  89 " --> pdb=" O   SER L  85 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 97 through 103
      removed outlier: 3.550A  pdb=" N   GLY L 103 " --> pdb=" O   ARG L  99 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 118 through 129
    Processing helix  chain 'L' and resid 149 through 178
      removed outlier: 3.780A  pdb=" N   MET L 175 " --> pdb=" O   LEU L 171 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 340 through 351
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 27
      removed outlier: 7.171A  pdb=" N   VAL A  20 " --> pdb=" O   TRP A  10 " (cutoff:3.500A)
      removed outlier: 8.291A  pdb=" N   TRP A  10 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ARG A  22 " --> pdb=" O   THR A   8 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   THR A   8 " --> pdb=" O   ARG A  22 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   LEU A  24 " --> pdb=" O   ASN A   6 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A  26 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LEU A   7 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   GLU A  59 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 38
      removed outlier: 3.656A  pdb=" N   GLY A  35 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL A 195 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 149
      removed outlier: 5.759A  pdb=" N   TYR A 147 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 27
      removed outlier: 6.004A  pdb=" N   LEU B   7 " --> pdb=" O   ASN B  23 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ASN B  25 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ARG B   5 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   ARG B  27 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   GLU B   3 " --> pdb=" O   ARG B  27 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   LEU B   4 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL B  63 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   ASN B   6 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   GLU B  61 " --> pdb=" O   ASN B   6 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 38
      removed outlier: 3.518A  pdb=" N   GLY B  35 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL B 195 " --> pdb=" O   GLY B  35 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 149
      removed outlier: 5.993A  pdb=" N   TYR B 147 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 130 through 135
      removed outlier: 6.416A  pdb=" N   VAL E  43 " --> pdb=" O   VAL E 327 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 130 through 134
      removed outlier: 6.497A  pdb=" N   VAL F  43 " --> pdb=" O   VAL F 327 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 130 through 135
      removed outlier: 7.074A  pdb=" N   THR G  45 " --> pdb=" O   VAL G 326 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   VAL G 326 " --> pdb=" O   THR G  45 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ARG G  47 " --> pdb=" O   LEU G 324 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU G 324 " --> pdb=" O   ARG G  47 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 135
      removed outlier: 7.203A  pdb=" N   THR H  45 " --> pdb=" O   VAL H 326 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   VAL H 326 " --> pdb=" O   THR H  45 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ARG H  47 " --> pdb=" O   LEU H 324 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   LEU H 324 " --> pdb=" O   ARG H  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 130 through 135
      removed outlier: 6.427A  pdb=" N   VAL I  43 " --> pdb=" O   VAL I 327 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 130 through 134
      removed outlier: 6.465A  pdb=" N   VAL J  43 " --> pdb=" O   VAL J 327 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 130 through 135
      removed outlier: 6.712A  pdb=" N   THR K  45 " --> pdb=" O   VAL K 326 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   VAL K 326 " --> pdb=" O   THR K  45 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ARG K  47 " --> pdb=" O   LEU K 324 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   LEU K 324 " --> pdb=" O   ARG K  47 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 130 through 135
      removed outlier: 7.223A  pdb=" N   THR L  45 " --> pdb=" O   VAL L 326 " (cutoff:3.500A)
      removed outlier: 5.263A  pdb=" N   VAL L 326 " --> pdb=" O   THR L  45 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   ARG L  47 " --> pdb=" O   LEU L 324 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   LEU L 324 " --> pdb=" O   ARG L  47 " (cutoff:3.500A)

    1243 hydrogen bonds defined for protein.
    3645 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.58

  Time building geometry restraints manager: 7.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6392
        1.34 -     1.46: 3797
        1.46 -     1.58: 10417
        1.58 -     1.70: 0
        1.70 -     1.82: 164
  Bond restraints: 20770
  Sorted by residual:
  bond pdb=" N   VAL E  28 "
       pdb=" CA  VAL E  28 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.11e+00
  bond pdb=" N   VAL E  25 "
       pdb=" CA  VAL E  25 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.87e+00
  bond pdb=" N   LEU E  24 "
       pdb=" CA  LEU E  24 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.19e-02 7.06e+03 5.72e+00
  bond pdb=" N   THR E  27 "
       pdb=" CA  THR E  27 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.20e-02 6.94e+03 5.26e+00
  bond pdb=" N   MET E  23 "
       pdb=" CA  MET E  23 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.19e-02 7.06e+03 5.21e+00
  ... (remaining 20765 not shown)

  Histogram of bond angle deviations from ideal:
       98.68 -   105.75: 417
      105.75 -   112.83: 11031
      112.83 -   119.90: 7062
      119.90 -   126.97: 9417
      126.97 -   134.05: 243
  Bond angle restraints: 28170
  Sorted by residual:
  angle pdb=" C   ASP L  93 "
        pdb=" N   GLN L  94 "
        pdb=" CA  GLN L  94 "
      ideal   model   delta    sigma   weight residual
     122.38  115.94    6.44 1.81e+00 3.05e-01 1.27e+01
  angle pdb=" C   THR F  10 "
        pdb=" N   ALA F  11 "
        pdb=" CA  ALA F  11 "
      ideal   model   delta    sigma   weight residual
     121.54  128.23   -6.69 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" CB  MET B 184 "
        pdb=" CG  MET B 184 "
        pdb=" SD  MET B 184 "
      ideal   model   delta    sigma   weight residual
     112.70  122.84  -10.14 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" CA  GLN L  94 "
        pdb=" CB  GLN L  94 "
        pdb=" CG  GLN L  94 "
      ideal   model   delta    sigma   weight residual
     114.10  120.71   -6.61 2.00e+00 2.50e-01 1.09e+01
  angle pdb=" C   ARG B  22 "
        pdb=" N   ASN B  23 "
        pdb=" CA  ASN B  23 "
      ideal   model   delta    sigma   weight residual
     122.46  127.09   -4.63 1.41e+00 5.03e-01 1.08e+01
  ... (remaining 28165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 10456
       17.93 -    35.87: 1457
       35.87 -    53.80: 373
       53.80 -    71.73: 82
       71.73 -    89.66: 26
  Dihedral angle restraints: 12394
    sinusoidal: 5044
      harmonic: 7350
  Sorted by residual:
  dihedral pdb=" CA  MET J 134 "
           pdb=" C   MET J 134 "
           pdb=" N   ASP J 135 "
           pdb=" CA  ASP J 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.44   17.56     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CG  ARG G 144 "
           pdb=" CD  ARG G 144 "
           pdb=" NE  ARG G 144 "
           pdb=" CZ  ARG G 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.57  -44.43     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CA  ASN A  23 "
           pdb=" C   ASN A  23 "
           pdb=" N   LEU A  24 "
           pdb=" CA  LEU A  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.10   15.90     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 12391 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 2448
       0.044 -    0.088: 548
       0.088 -    0.132: 196
       0.132 -    0.176: 28
       0.176 -    0.219: 4
  Chirality restraints: 3224
  Sorted by residual:
  chirality pdb=" CB  ILE B 115 "
            pdb=" CA  ILE B 115 "
            pdb=" CG1 ILE B 115 "
            pdb=" CG2 ILE B 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  ILE D 240 "
            pdb=" CA  ILE D 240 "
            pdb=" CG1 ILE D 240 "
            pdb=" CG2 ILE D 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  ASN A   6 "
            pdb=" N   ASN A   6 "
            pdb=" C   ASN A   6 "
            pdb=" CB  ASN A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.29e-01
  ... (remaining 3221 not shown)

  Planarity restraints: 3536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C  74 "   -0.045 5.00e-02 4.00e+02   6.84e-02 7.48e+00
        pdb=" N   PRO C  75 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO C  75 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  75 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F  11 "   -0.010 2.00e-02 2.50e+03   2.00e-02 4.02e+00
        pdb=" C   ALA F  11 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ALA F  11 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS F  12 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR D  74 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO D  75 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO D  75 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D  75 "    0.028 5.00e-02 4.00e+02
  ... (remaining 3533 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1967
        2.75 -     3.29: 19517
        3.29 -     3.82: 34518
        3.82 -     4.36: 37720
        4.36 -     4.90: 67189
  Nonbonded interactions: 160911
  Sorted by model distance:
  nonbonded pdb=" O   MET I  23 "
            pdb=" OG1 THR I  27 "
     model   vdw
     2.210 2.440
  nonbonded pdb=" OG  SER D 101 "
            pdb=" OD1 ASN D 102 "
     model   vdw
     2.224 2.440
  nonbonded pdb=" OG  SER C 101 "
            pdb=" OD1 ASN C 102 "
     model   vdw
     2.226 2.440
  nonbonded pdb=" O   GLN H  90 "
            pdb=" NE2 GLN H  94 "
     model   vdw
     2.255 2.520
  nonbonded pdb=" O   MET H  23 "
            pdb=" OG1 THR H  27 "
     model   vdw
     2.273 2.440
  ... (remaining 160906 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'E' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 
 351))
  selection = (chain 'F' and resid 19 through 351)
  selection = (chain 'G' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 
 351))
  selection = (chain 'H' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 
 351))
  selection = (chain 'I' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 
 351))
  selection = (chain 'J' and resid 19 through 351)
  selection = (chain 'K' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 
 351))
  selection = (chain 'L' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 
 351))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.770
  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:          0.690
  Check model and map are aligned:         0.130
  Set scattering table:                    0.160
  Process input model:                     47.970
  Find NCS groups from input model:        0.980
  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:             0.000
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
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      :  0.003   0.044  20770  Z= 0.180
  Angle     :  0.620  10.140  28170  Z= 0.322
  Chirality :  0.043   0.219   3224
  Planarity :  0.004   0.068   3536
  Dihedral  : 17.905  89.663   7634
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 28.39 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.17), residues: 2448
  helix:  1.60 (0.13), residues: 1456
  sheet:  1.09 (0.34), residues: 280
  loop : -1.85 (0.21), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP I  16 
 HIS   0.013   0.001   HIS C  65 
 PHE   0.027   0.001   PHE C  61 
 TYR   0.028   0.001   TYR J  78 
 ARG   0.017   0.000   ARG H 177 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 413
  time to evaluate  : 2.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.8658 (ttt) cc_final: 0.8336 (mmt)
REVERT: B  184 MET cc_start: 0.8507 (tpp) cc_final: 0.8036 (tpt)
REVERT: E   23 MET cc_start: 0.8819 (mmm) cc_final: 0.8543 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 415
  average time/residue: 0.3052
  time to fit residues: 194.6404
Evaluate side-chains
  409 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 406
  time to evaluate  : 2.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  204 HIS
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain E residue   24 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 206 optimal weight:    7.9990
   chunk 184 optimal weight:    0.0370
   chunk 102 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 191 optimal weight:    8.9990
   chunk 74 optimal weight:    0.8980
   chunk 116 optimal weight:    2.9990
   chunk 142 optimal weight:    3.9990
   chunk 221 optimal weight:    5.9990
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
E 169 ASN
F  15 GLN
G 173 HIS
J  15 GLN
K 173 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.0707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  20770  Z= 0.166
  Angle     :  0.493   6.208  28170  Z= 0.251
  Chirality :  0.039   0.156   3224
  Planarity :  0.004   0.056   3536
  Dihedral  :  3.722  35.706   2800
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 26.72 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.17), residues: 2448
  helix:  2.01 (0.13), residues: 1488
  sheet:  0.87 (0.33), residues: 284
  loop : -1.72 (0.21), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP I  16 
 HIS   0.004   0.000   HIS C  65 
 PHE   0.016   0.001   PHE D  61 
 TYR   0.023   0.001   TYR E  20 
 ARG   0.004   0.000   ARG H 177 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  471 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 408
  time to evaluate  : 2.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7938 (mmt) cc_final: 0.7679 (mmp)
REVERT: A  145 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6870 (p0)
REVERT: A  160 PHE cc_start: 0.6568 (OUTLIER) cc_final: 0.5749 (m-80)
REVERT: A  212 ILE cc_start: 0.7738 (mm) cc_final: 0.7422 (mm)
REVERT: B  145 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7022 (p0)
REVERT: B  184 MET cc_start: 0.8543 (tpp) cc_final: 0.8256 (tpt)
REVERT: C   61 PHE cc_start: 0.8699 (m-80) cc_final: 0.8351 (m-80)
REVERT: C  139 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8553 (mp)
REVERT: F    3 MET cc_start: 0.4138 (pmm) cc_final: 0.3614 (pmm)
REVERT: F   23 MET cc_start: 0.8721 (mmm) cc_final: 0.8369 (mmm)
REVERT: F  352 CYS cc_start: 0.8007 (m) cc_final: 0.7745 (m)
REVERT: F  366 ILE cc_start: 0.9107 (mm) cc_final: 0.8755 (tp)
REVERT: H   94 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7644 (mp10)
  outliers start: 63
  outliers final: 26
  residues processed: 453
  average time/residue: 0.3057
  time to fit residues: 215.2378
Evaluate side-chains
  424 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 393
  time to evaluate  : 2.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  140 MET
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain F residue   49 THR
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   94 GLN
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   10 THR
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain I residue  136 ASP
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue  137 ILE
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain K residue  326 VAL
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 184 optimal weight:    1.9990
   chunk 150 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 221 optimal weight:    5.9990
   chunk 239 optimal weight:    4.9990
   chunk 197 optimal weight:    2.9990
   chunk 220 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 178 optimal weight:    3.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
E 169 ASN
F  15 GLN
G 173 HIS
I 169 ASN
** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
K 173 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  20770  Z= 0.231
  Angle     :  0.524   7.760  28170  Z= 0.265
  Chirality :  0.040   0.178   3224
  Planarity :  0.004   0.054   3536
  Dihedral  :  3.627  16.813   2794
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 26.54 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.17), residues: 2448
  helix:  2.09 (0.13), residues: 1492
  sheet:  0.76 (0.33), residues: 284
  loop : -1.73 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  16 
 HIS   0.005   0.001   HIS C  65 
 PHE   0.015   0.001   PHE D  85 
 TYR   0.022   0.001   TYR E  20 
 ARG   0.006   0.000   ARG A  17 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  491 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 87
    poor density    : 404
  time to evaluate  : 2.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.5949 (OUTLIER) cc_final: 0.5142 (tp)
REVERT: A  123 MET cc_start: 0.8043 (mmt) cc_final: 0.7828 (mmp)
REVERT: A  145 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6871 (p0)
REVERT: A  160 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.5843 (m-80)
REVERT: B  145 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6684 (p0)
REVERT: C   61 PHE cc_start: 0.8660 (m-80) cc_final: 0.8298 (m-80)
REVERT: C  139 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8600 (mp)
REVERT: C  217 ASN cc_start: 0.8753 (t0) cc_final: 0.8542 (t0)
REVERT: E  356 TYR cc_start: 0.7718 (t80) cc_final: 0.7510 (t80)
REVERT: F    3 MET cc_start: 0.4337 (pmm) cc_final: 0.3584 (pmm)
REVERT: F  352 CYS cc_start: 0.8008 (m) cc_final: 0.7769 (m)
REVERT: F  366 ILE cc_start: 0.9115 (mm) cc_final: 0.8762 (tp)
  outliers start: 87
  outliers final: 50
  residues processed: 453
  average time/residue: 0.2950
  time to fit residues: 207.2740
Evaluate side-chains
  453 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 398
  time to evaluate  : 2.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  191 CYS
Chi-restraints excluded: chain B residue  140 MET
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  204 HIS
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  176 THR
Chi-restraints excluded: chain D residue  224 GLU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  331 VAL
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain F residue   49 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue  165 GLU
Chi-restraints excluded: chain F residue  363 VAL
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   48 GLN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  324 LEU
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   10 THR
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain I residue  136 ASP
Chi-restraints excluded: chain I residue  331 VAL
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue  165 GLU
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  363 VAL
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain K residue  326 VAL
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   77 CYS
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  325 VAL
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 219 optimal weight:    3.9990
   chunk 166 optimal weight:    1.9990
   chunk 115 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0980
   chunk 105 optimal weight:    0.7980
   chunk 149 optimal weight:    3.9990
   chunk 222 optimal weight:   10.0000
   chunk 235 optimal weight:    4.9990
   chunk 116 optimal weight:    0.8980
   chunk 211 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
E 169 ASN
F  15 GLN
G 173 HIS
I  15 GLN
J  15 GLN
K 173 HIS
** L  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  20770  Z= 0.163
  Angle     :  0.493   6.101  28170  Z= 0.250
  Chirality :  0.040   0.193   3224
  Planarity :  0.003   0.051   3536
  Dihedral  :  3.536  16.368   2794
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 27.44 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.17), residues: 2448
  helix:  2.16 (0.13), residues: 1488
  sheet:  0.97 (0.34), residues: 270
  loop : -1.71 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP I  16 
 HIS   0.005   0.000   HIS C  65 
 PHE   0.023   0.001   PHE B  21 
 TYR   0.022   0.001   TYR E  20 
 ARG   0.005   0.000   ARG L 177 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  478 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 401
  time to evaluate  : 2.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8431 (mtpp)
REVERT: A  123 MET cc_start: 0.8001 (mmt) cc_final: 0.7786 (mmp)
REVERT: A  145 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6831 (p0)
REVERT: A  160 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.5832 (m-80)
REVERT: B  145 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6829 (p0)
REVERT: B  184 MET cc_start: 0.9037 (tpt) cc_final: 0.8544 (tpt)
REVERT: C   61 PHE cc_start: 0.8652 (m-80) cc_final: 0.8268 (m-80)
REVERT: C  139 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8528 (mp)
REVERT: C  217 ASN cc_start: 0.8751 (t0) cc_final: 0.8444 (t0)
REVERT: D  110 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8014 (mp10)
REVERT: D  139 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8559 (mp)
REVERT: E  356 TYR cc_start: 0.7824 (t80) cc_final: 0.7495 (t80)
REVERT: F    3 MET cc_start: 0.4430 (pmm) cc_final: 0.3666 (pmm)
REVERT: F  366 ILE cc_start: 0.9147 (mm) cc_final: 0.8816 (tp)
REVERT: L   94 GLN cc_start: 0.8073 (mp10) cc_final: 0.7848 (mp10)
  outliers start: 77
  outliers final: 41
  residues processed: 448
  average time/residue: 0.3054
  time to fit residues: 212.0752
Evaluate side-chains
  441 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 394
  time to evaluate  : 2.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  191 CYS
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain C residue   54 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  204 HIS
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   96 MET
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  331 VAL
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain F residue   49 THR
Chi-restraints excluded: chain F residue  165 GLU
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain H residue   40 SER
Chi-restraints excluded: chain H residue   48 GLN
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   10 THR
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain K residue  326 VAL
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain L residue   75 ASP
Chi-restraints excluded: chain L residue   77 CYS
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 196 optimal weight:    0.7980
   chunk 133 optimal weight:    3.9990
   chunk 3 optimal weight:   40.0000
   chunk 175 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 201 optimal weight:    3.9990
   chunk 163 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 120 optimal weight:    0.3980
   chunk 211 optimal weight:    9.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
E 169 ASN
** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
G 173 HIS
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 179 GLN
** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
K 173 HIS
** L  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  20770  Z= 0.255
  Angle     :  0.535   6.849  28170  Z= 0.271
  Chirality :  0.041   0.190   3224
  Planarity :  0.004   0.053   3536
  Dihedral  :  3.656  17.686   2794
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 27.08 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.17), residues: 2448
  helix:  2.15 (0.13), residues: 1492
  sheet:  0.72 (0.33), residues: 292
  loop : -1.76 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP I  16 
 HIS   0.005   0.001   HIS D  65 
 PHE   0.015   0.001   PHE D  85 
 TYR   0.022   0.001   TYR E  20 
 ARG   0.007   0.000   ARG L 177 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  489 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 91
    poor density    : 398
  time to evaluate  : 2.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8581 (mtpp)
REVERT: A  145 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6661 (p0)
REVERT: A  160 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.5903 (m-80)
REVERT: B  140 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8466 (ttt)
REVERT: B  145 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6643 (p0)
REVERT: B  160 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.5741 (m-80)
REVERT: C   61 PHE cc_start: 0.8629 (m-80) cc_final: 0.8257 (m-80)
REVERT: C  139 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: C  217 ASN cc_start: 0.8818 (t0) cc_final: 0.8508 (t0)
REVERT: D  110 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8091 (mp10)
REVERT: E   20 TYR cc_start: 0.8393 (m-80) cc_final: 0.8062 (m-80)
REVERT: E   36 ASP cc_start: 0.8511 (p0) cc_final: 0.8158 (p0)
REVERT: E  356 TYR cc_start: 0.7767 (t80) cc_final: 0.7446 (t80)
REVERT: F    3 MET cc_start: 0.4615 (OUTLIER) cc_final: 0.3657 (pmm)
REVERT: F  366 ILE cc_start: 0.9144 (mm) cc_final: 0.8815 (tp)
REVERT: H   94 GLN cc_start: 0.8063 (mp10) cc_final: 0.7860 (pm20)
REVERT: I   36 ASP cc_start: 0.8580 (p0) cc_final: 0.8296 (p0)
REVERT: K   14 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8733 (mp)
REVERT: L   94 GLN cc_start: 0.8102 (mp10) cc_final: 0.7798 (mp10)
  outliers start: 91
  outliers final: 62
  residues processed: 456
  average time/residue: 0.2951
  time to fit residues: 208.9409
Evaluate side-chains
  462 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 391
  time to evaluate  : 2.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  191 CYS
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  140 MET
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain C residue   54 ILE
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   96 MET
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  331 VAL
Chi-restraints excluded: chain F residue    3 MET
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain F residue   49 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue  165 GLU
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain F residue  363 VAL
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   40 SER
Chi-restraints excluded: chain H residue   48 GLN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  324 LEU
Chi-restraints excluded: chain H residue  325 VAL
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   10 THR
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain I residue  136 ASP
Chi-restraints excluded: chain I residue  331 VAL
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue  165 GLU
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  142 THR
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain K residue  326 VAL
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain L residue   77 CYS
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  324 LEU
Chi-restraints excluded: chain L residue  325 VAL
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 212 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   chunk 138 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 236 optimal weight:    4.9990
   chunk 195 optimal weight:    0.2980
   chunk 109 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
E 169 ASN
F  15 GLN
G 173 HIS
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 179 GLN
** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
K 173 HIS
** L  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  20770  Z= 0.258
  Angle     :  0.535   7.487  28170  Z= 0.272
  Chirality :  0.041   0.191   3224
  Planarity :  0.004   0.053   3536
  Dihedral  :  3.702  17.623   2794
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 26.63 %
    Favored  : 69.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.17), residues: 2448
  helix:  2.12 (0.13), residues: 1492
  sheet:  0.72 (0.33), residues: 292
  loop : -1.78 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP I  16 
 HIS   0.006   0.001   HIS C  65 
 PHE   0.021   0.001   PHE D  61 
 TYR   0.022   0.002   TYR B 146 
 ARG   0.003   0.000   ARG F 340 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  488 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 94
    poor density    : 394
  time to evaluate  : 2.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8400 (mtpp)
REVERT: A  126 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6170 (t80)
REVERT: A  130 MET cc_start: 0.6747 (ptt) cc_final: 0.4916 (ptt)
REVERT: A  145 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6557 (p0)
REVERT: A  160 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5686 (m-80)
REVERT: A  163 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7430 (ptpp)
REVERT: B  145 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.6974 (p0)
REVERT: B  184 MET cc_start: 0.8923 (tpt) cc_final: 0.8549 (tpt)
REVERT: C   61 PHE cc_start: 0.8623 (m-80) cc_final: 0.8253 (m-80)
REVERT: C  139 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8584 (mp)
REVERT: C  217 ASN cc_start: 0.8831 (t0) cc_final: 0.8623 (t0)
REVERT: D   39 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6056 (tpt-90)
REVERT: D  110 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8120 (mp10)
REVERT: D  139 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8509 (mp)
REVERT: E   20 TYR cc_start: 0.8465 (m-80) cc_final: 0.8125 (m-80)
REVERT: E   36 ASP cc_start: 0.8519 (p0) cc_final: 0.8161 (p0)
REVERT: E  356 TYR cc_start: 0.7767 (t80) cc_final: 0.7400 (t80)
REVERT: F    3 MET cc_start: 0.4389 (OUTLIER) cc_final: 0.3410 (pmm)
REVERT: F  366 ILE cc_start: 0.9118 (mm) cc_final: 0.8777 (tp)
REVERT: G   14 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (mp)
REVERT: H   94 GLN cc_start: 0.8036 (mp10) cc_final: 0.7753 (mp10)
REVERT: I   36 ASP cc_start: 0.8586 (p0) cc_final: 0.8282 (p0)
REVERT: L   94 GLN cc_start: 0.8071 (mp10) cc_final: 0.7779 (mp10)
  outliers start: 94
  outliers final: 67
  residues processed: 455
  average time/residue: 0.2853
  time to fit residues: 203.2088
Evaluate side-chains
  468 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 390
  time to evaluate  : 2.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  191 CYS
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain C residue   54 ILE
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain D residue   39 ARG
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue   96 MET
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  176 THR
Chi-restraints excluded: chain D residue  224 GLU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  331 VAL
Chi-restraints excluded: chain F residue    3 MET
Chi-restraints excluded: chain F residue    9 LEU
Chi-restraints excluded: chain F residue   49 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue  137 ILE
Chi-restraints excluded: chain F residue  165 GLU
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain F residue  363 VAL
Chi-restraints excluded: chain G residue   14 LEU
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   40 SER
Chi-restraints excluded: chain H residue   48 GLN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  324 LEU
Chi-restraints excluded: chain H residue  325 VAL
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   10 THR
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain I residue  136 ASP
Chi-restraints excluded: chain I residue  331 VAL
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue  165 GLU
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  363 VAL
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  117 THR
Chi-restraints excluded: chain K residue  142 THR
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  324 LEU
Chi-restraints excluded: chain L residue  325 VAL
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 227 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 134 optimal weight:    5.9990
   chunk 172 optimal weight:   10.0000
   chunk 133 optimal weight:    3.9990
   chunk 198 optimal weight:    5.9990
   chunk 131 optimal weight:    0.0050
   chunk 235 optimal weight:    4.9990
   chunk 147 optimal weight:    5.9990
   chunk 143 optimal weight:    0.8980
   chunk 108 optimal weight:    0.6980
   overall best weight:    1.2996

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

Flipped N/Q/H residues before XYZ refinement:
** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
G 173 HIS
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
K 173 HIS
** L  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  20770  Z= 0.202
  Angle     :  0.518   8.133  28170  Z= 0.262
  Chirality :  0.040   0.208   3224
  Planarity :  0.003   0.052   3536
  Dihedral  :  3.644  16.923   2794
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 27.12 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.17), residues: 2448
  helix:  2.17 (0.13), residues: 1488
  sheet:  0.69 (0.32), residues: 302
  loop : -1.78 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP I  16 
 HIS   0.006   0.001   HIS C  65 
 PHE   0.014   0.001   PHE D  85 
 TYR   0.020   0.001   TYR B 146 
 ARG   0.003   0.000   ARG A  17 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  488 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 86
    poor density    : 402
  time to evaluate  : 2.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7216 (tpt) cc_final: 0.6994 (tpp)
REVERT: A   89 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8408 (mtpp)
REVERT: A  126 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6174 (t80)
REVERT: A  130 MET cc_start: 0.6765 (ptt) cc_final: 0.4908 (ptt)
REVERT: A  145 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6517 (p0)
REVERT: A  160 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.5922 (m-80)
REVERT: B  145 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6687 (p0)
REVERT: B  184 MET cc_start: 0.8922 (tpt) cc_final: 0.8568 (tpt)
REVERT: C   61 PHE cc_start: 0.8662 (m-80) cc_final: 0.8260 (m-80)
REVERT: C  139 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8583 (mp)
REVERT: C  217 ASN cc_start: 0.8824 (t0) cc_final: 0.8603 (t0)
REVERT: D   31 GLU cc_start: 0.8380 (tp30) cc_final: 0.8115 (tp30)
REVERT: D  110 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8193 (mp10)
REVERT: D  139 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8536 (mp)
REVERT: E   20 TYR cc_start: 0.8570 (m-80) cc_final: 0.8140 (m-80)
REVERT: E   36 ASP cc_start: 0.8495 (p0) cc_final: 0.8133 (p0)
REVERT: E  356 TYR cc_start: 0.7791 (t80) cc_final: 0.7369 (t80)
REVERT: F    3 MET cc_start: 0.4339 (OUTLIER) cc_final: 0.3354 (pmm)
REVERT: F  366 ILE cc_start: 0.9154 (mm) cc_final: 0.8823 (tp)
REVERT: G   14 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8787 (mp)
REVERT: H   94 GLN cc_start: 0.8024 (mp10) cc_final: 0.7740 (mp10)
REVERT: I   36 ASP cc_start: 0.8542 (p0) cc_final: 0.8262 (p0)
REVERT: K   14 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8733 (mp)
  outliers start: 86
  outliers final: 61
  residues processed: 453
  average time/residue: 0.2898
  time to fit residues: 204.4697
Evaluate side-chains
  466 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 395
  time to evaluate  : 2.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  191 CYS
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain C residue   54 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue   96 MET
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  224 GLU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  331 VAL
Chi-restraints excluded: chain F residue    3 MET
Chi-restraints excluded: chain F residue  137 ILE
Chi-restraints excluded: chain F residue  165 GLU
Chi-restraints excluded: chain F residue  321 LEU
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain F residue  363 VAL
Chi-restraints excluded: chain G residue   14 LEU
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain G residue  371 ASP
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   40 SER
Chi-restraints excluded: chain H residue   48 GLN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue  324 LEU
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   10 THR
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain I residue  136 ASP
Chi-restraints excluded: chain I residue  331 VAL
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue  165 GLU
Chi-restraints excluded: chain J residue  363 VAL
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  142 THR
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain K residue  326 VAL
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  324 LEU
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 145 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 149 optimal weight:    0.8980
   chunk 160 optimal weight:    6.9990
   chunk 116 optimal weight:    3.9990
   chunk 21 optimal weight:   20.0000
   chunk 184 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
F  15 GLN
G 173 HIS
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  15 GLN
** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
K 173 HIS
** L  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  20770  Z= 0.254
  Angle     :  0.545   7.888  28170  Z= 0.276
  Chirality :  0.041   0.195   3224
  Planarity :  0.004   0.053   3536
  Dihedral  :  3.712  17.703   2794
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 27.03 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.17), residues: 2448
  helix:  2.13 (0.13), residues: 1492
  sheet:  0.54 (0.32), residues: 306
  loop : -1.77 (0.22), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP I  16 
 HIS   0.007   0.001   HIS C  65 
 PHE   0.022   0.001   PHE D  61 
 TYR   0.021   0.001   TYR B 146 
 ARG   0.004   0.000   ARG F 340 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  493 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 92
    poor density    : 401
  time to evaluate  : 2.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7222 (tpt) cc_final: 0.7001 (tpp)
REVERT: A   89 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8357 (mtpp)
REVERT: A  126 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6209 (t80)
REVERT: A  130 MET cc_start: 0.6733 (ptt) cc_final: 0.4878 (ptt)
REVERT: A  145 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6372 (p0)
REVERT: A  160 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.5769 (m-80)
REVERT: B  140 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8397 (ttt)
REVERT: B  145 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6543 (p0)
REVERT: B  184 MET cc_start: 0.8933 (tpt) cc_final: 0.8603 (tpt)
REVERT: C   61 PHE cc_start: 0.8618 (m-80) cc_final: 0.8224 (m-80)
REVERT: C  139 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8584 (mp)
REVERT: C  217 ASN cc_start: 0.8840 (t0) cc_final: 0.8599 (t0)
REVERT: D   39 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6079 (tpt-90)
REVERT: D  110 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8202 (mp10)
REVERT: D  139 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8521 (mp)
REVERT: E   20 TYR cc_start: 0.8604 (m-80) cc_final: 0.8150 (m-80)
REVERT: E   36 ASP cc_start: 0.8514 (p0) cc_final: 0.8145 (p0)
REVERT: E  356 TYR cc_start: 0.7817 (t80) cc_final: 0.7372 (t80)
REVERT: F    3 MET cc_start: 0.4515 (OUTLIER) cc_final: 0.3435 (pmm)
REVERT: F  166 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8304 (ttp80)
REVERT: F  366 ILE cc_start: 0.9168 (mm) cc_final: 0.8834 (tp)
REVERT: G   14 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8766 (mp)
REVERT: H   94 GLN cc_start: 0.8049 (mp10) cc_final: 0.7742 (mp10)
REVERT: I   36 ASP cc_start: 0.8550 (p0) cc_final: 0.8262 (p0)
REVERT: K   14 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8756 (mp)
REVERT: L   94 GLN cc_start: 0.8000 (mp10) cc_final: 0.7759 (mp10)
  outliers start: 92
  outliers final: 70
  residues processed: 460
  average time/residue: 0.2977
  time to fit residues: 212.0856
Evaluate side-chains
  476 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 83
    poor density    : 393
  time to evaluate  : 2.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  140 MET
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  168 PHE
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain C residue   54 ILE
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   69 MET
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain D residue   39 ARG
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue   96 MET
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  176 THR
Chi-restraints excluded: chain D residue  224 GLU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  178 GLU
Chi-restraints excluded: chain E residue  331 VAL
Chi-restraints excluded: chain F residue    3 MET
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue  137 ILE
Chi-restraints excluded: chain F residue  165 GLU
Chi-restraints excluded: chain F residue  166 ARG
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain F residue  363 VAL
Chi-restraints excluded: chain G residue   14 LEU
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain G residue  371 ASP
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   40 SER
Chi-restraints excluded: chain H residue   48 GLN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  324 LEU
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   10 THR
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain I residue  136 ASP
Chi-restraints excluded: chain I residue  331 VAL
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue  165 GLU
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  363 VAL
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  117 THR
Chi-restraints excluded: chain K residue  142 THR
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain K residue  326 VAL
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  324 LEU
Chi-restraints excluded: chain L residue  325 VAL
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 213 optimal weight:    1.9990
   chunk 225 optimal weight:    0.8980
   chunk 205 optimal weight:    3.9990
   chunk 219 optimal weight:    2.9990
   chunk 131 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 172 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   chunk 198 optimal weight:    0.4980
   chunk 207 optimal weight:    3.9990
   chunk 218 optimal weight:    3.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
F  15 GLN
G 173 HIS
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  15 GLN
** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
K 173 HIS
** L  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 169 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  20770  Z= 0.219
  Angle     :  0.534   8.447  28170  Z= 0.270
  Chirality :  0.041   0.208   3224
  Planarity :  0.003   0.052   3536
  Dihedral  :  3.677  17.001   2794
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 26.99 %
    Favored  : 69.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.17), residues: 2448
  helix:  2.15 (0.13), residues: 1488
  sheet:  0.67 (0.32), residues: 302
  loop : -1.77 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP I  16 
 HIS   0.007   0.001   HIS C  65 
 PHE   0.015   0.001   PHE D  85 
 TYR   0.020   0.001   TYR B 146 
 ARG   0.003   0.000   ARG A  17 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  483 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 88
    poor density    : 395
  time to evaluate  : 2.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7206 (tpt) cc_final: 0.6974 (tpp)
REVERT: A   89 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8319 (mtpp)
REVERT: A  126 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.5950 (t80)
REVERT: A  130 MET cc_start: 0.6796 (ptt) cc_final: 0.4989 (ptt)
REVERT: A  145 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6357 (p0)
REVERT: A  160 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5695 (m-80)
REVERT: B  145 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6781 (p0)
REVERT: B  184 MET cc_start: 0.8977 (tpt) cc_final: 0.8657 (tpt)
REVERT: C   61 PHE cc_start: 0.8629 (m-80) cc_final: 0.8251 (m-80)
REVERT: C  139 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8592 (mp)
REVERT: C  217 ASN cc_start: 0.8831 (t0) cc_final: 0.8584 (t0)
REVERT: D   39 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6100 (tpt-90)
REVERT: D  110 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8226 (mp10)
REVERT: D  139 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8526 (mp)
REVERT: E   20 TYR cc_start: 0.8520 (m-80) cc_final: 0.7993 (m-80)
REVERT: E   36 ASP cc_start: 0.8498 (p0) cc_final: 0.8126 (p0)
REVERT: E  356 TYR cc_start: 0.7820 (t80) cc_final: 0.7404 (t80)
REVERT: F    3 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.3356 (pmm)
REVERT: F  166 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8291 (ttp80)
REVERT: F  366 ILE cc_start: 0.9159 (mm) cc_final: 0.8829 (tp)
REVERT: G   14 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8795 (mp)
REVERT: H   94 GLN cc_start: 0.8040 (mp10) cc_final: 0.7721 (mp10)
REVERT: I   36 ASP cc_start: 0.8527 (p0) cc_final: 0.8241 (p0)
REVERT: J  166 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8263 (ttp80)
REVERT: K   14 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8746 (mp)
REVERT: L   94 GLN cc_start: 0.8012 (mp10) cc_final: 0.7748 (mp10)
  outliers start: 88
  outliers final: 64
  residues processed: 453
  average time/residue: 0.2983
  time to fit residues: 208.7661
Evaluate side-chains
  468 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 391
  time to evaluate  : 2.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  168 PHE
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain C residue   54 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain D residue   39 ARG
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue   96 MET
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  176 THR
Chi-restraints excluded: chain D residue  224 GLU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  331 VAL
Chi-restraints excluded: chain F residue    3 MET
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue  137 ILE
Chi-restraints excluded: chain F residue  165 GLU
Chi-restraints excluded: chain F residue  166 ARG
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain F residue  363 VAL
Chi-restraints excluded: chain G residue   14 LEU
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain G residue  371 ASP
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   40 SER
Chi-restraints excluded: chain H residue   48 GLN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  324 LEU
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain I residue  136 ASP
Chi-restraints excluded: chain I residue  331 VAL
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue  165 GLU
Chi-restraints excluded: chain J residue  166 ARG
Chi-restraints excluded: chain J residue  363 VAL
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  117 THR
Chi-restraints excluded: chain K residue  142 THR
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain K residue  326 VAL
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  324 LEU
Chi-restraints excluded: chain L residue  325 VAL
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 143 optimal weight:    2.9990
   chunk 231 optimal weight:    4.9990
   chunk 141 optimal weight:    0.6980
   chunk 109 optimal weight:    3.9990
   chunk 161 optimal weight:    2.9990
   chunk 243 optimal weight:    3.9990
   chunk 223 optimal weight:    0.9980
   chunk 193 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 149 optimal weight:    0.5980
   chunk 118 optimal weight:    1.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
F  15 GLN
G 173 HIS
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
K 173 HIS
** L  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  20770  Z= 0.221
  Angle     :  0.538   8.500  28170  Z= 0.272
  Chirality :  0.041   0.211   3224
  Planarity :  0.003   0.052   3536
  Dihedral  :  3.687  17.159   2794
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 27.08 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.17), residues: 2448
  helix:  2.12 (0.13), residues: 1490
  sheet:  0.65 (0.32), residues: 302
  loop : -1.78 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP I  16 
 HIS   0.013   0.001   HIS D  65 
 PHE   0.022   0.001   PHE D  61 
 TYR   0.020   0.001   TYR B 146 
 ARG   0.002   0.000   ARG A  17 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  484 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 83
    poor density    : 401
  time to evaluate  : 2.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7084 (tpt) cc_final: 0.6839 (tpp)
REVERT: A   89 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8332 (mtpp)
REVERT: A  126 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.5948 (t80)
REVERT: A  130 MET cc_start: 0.6885 (ptt) cc_final: 0.5143 (ptt)
REVERT: A  145 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6373 (p0)
REVERT: A  160 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5627 (m-80)
REVERT: B  145 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6792 (p0)
REVERT: B  160 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5888 (m-80)
REVERT: B  184 MET cc_start: 0.9023 (tpt) cc_final: 0.8738 (tpt)
REVERT: C   61 PHE cc_start: 0.8680 (m-80) cc_final: 0.8263 (m-80)
REVERT: C  139 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8593 (mp)
REVERT: C  217 ASN cc_start: 0.8826 (t0) cc_final: 0.8561 (t0)
REVERT: D   39 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6097 (tpt-90)
REVERT: D  110 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8260 (mp10)
REVERT: D  139 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8553 (mp)
REVERT: E   20 TYR cc_start: 0.8613 (m-80) cc_final: 0.8056 (m-80)
REVERT: E   23 MET cc_start: 0.8772 (mmm) cc_final: 0.8388 (mmm)
REVERT: E   36 ASP cc_start: 0.8496 (p0) cc_final: 0.8127 (p0)
REVERT: E  356 TYR cc_start: 0.7881 (t80) cc_final: 0.7485 (t80)
REVERT: F    3 MET cc_start: 0.4481 (OUTLIER) cc_final: 0.3377 (pmm)
REVERT: F  166 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8292 (ttp80)
REVERT: F  366 ILE cc_start: 0.9155 (mm) cc_final: 0.8827 (tp)
REVERT: G   14 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8795 (mp)
REVERT: H   94 GLN cc_start: 0.8058 (mp10) cc_final: 0.7719 (mp10)
REVERT: H  135 ASP cc_start: 0.7733 (t0) cc_final: 0.7171 (t70)
REVERT: I   36 ASP cc_start: 0.8519 (p0) cc_final: 0.8231 (p0)
REVERT: I  320 LYS cc_start: 0.7615 (tppt) cc_final: 0.7336 (tptp)
REVERT: I  356 TYR cc_start: 0.7602 (t80) cc_final: 0.7227 (t80)
REVERT: J  166 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8262 (ttp80)
REVERT: K   14 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8745 (mp)
REVERT: L   94 GLN cc_start: 0.8073 (mp10) cc_final: 0.7817 (mp10)
  outliers start: 83
  outliers final: 66
  residues processed: 458
  average time/residue: 0.3055
  time to fit residues: 215.6916
Evaluate side-chains
  478 residues out of total 2212 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 80
    poor density    : 398
  time to evaluate  : 2.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  145 ASP
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  168 PHE
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain C residue   54 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  102 ASN
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain D residue   39 ARG
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue   96 MET
Chi-restraints excluded: chain D residue  102 ASN
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  176 THR
Chi-restraints excluded: chain D residue  224 GLU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   10 THR
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue  136 ASP
Chi-restraints excluded: chain E residue  331 VAL
Chi-restraints excluded: chain F residue    3 MET
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue  137 ILE
Chi-restraints excluded: chain F residue  165 GLU
Chi-restraints excluded: chain F residue  166 ARG
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain F residue  363 VAL
Chi-restraints excluded: chain G residue   14 LEU
Chi-restraints excluded: chain G residue  142 THR
Chi-restraints excluded: chain G residue  325 VAL
Chi-restraints excluded: chain G residue  353 CYS
Chi-restraints excluded: chain G residue  371 ASP
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   40 SER
Chi-restraints excluded: chain H residue   48 GLN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  324 LEU
Chi-restraints excluded: chain H residue  326 VAL
Chi-restraints excluded: chain I residue   10 THR
Chi-restraints excluded: chain I residue   49 THR
Chi-restraints excluded: chain I residue   90 GLN
Chi-restraints excluded: chain I residue  136 ASP
Chi-restraints excluded: chain I residue  331 VAL
Chi-restraints excluded: chain J residue   75 ASP
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue  165 GLU
Chi-restraints excluded: chain J residue  166 ARG
Chi-restraints excluded: chain J residue  363 VAL
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain K residue  117 THR
Chi-restraints excluded: chain K residue  142 THR
Chi-restraints excluded: chain K residue  321 LEU
Chi-restraints excluded: chain K residue  326 VAL
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   40 SER
Chi-restraints excluded: chain L residue  110 LEU
Chi-restraints excluded: chain L residue  324 LEU
Chi-restraints excluded: chain L residue  325 VAL
Chi-restraints excluded: chain L residue  326 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 153 optimal weight:    2.9990
   chunk 206 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0970
   chunk 178 optimal weight:    0.9980
   chunk 28 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 193 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 199 optimal weight:    0.7980
   chunk 24 optimal weight:   50.0000
   chunk 35 optimal weight:   20.0000
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
F  15 GLN
G 173 HIS
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 169 ASN
** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
K 173 HIS
** L  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 169 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.142902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.102521 restraints weight = 38912.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.46
r_work: 0.3291 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  20770  Z= 0.213
  Angle     :  0.539   8.493  28170  Z= 0.272
  Chirality :  0.041   0.207   3224
  Planarity :  0.003   0.052   3536
  Dihedral  :  3.678  17.046   2794
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 27.17 %
    Favored  : 69.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.17), residues: 2448
  helix:  2.13 (0.13), residues: 1490
  sheet:  0.69 (0.31), residues: 314
  loop : -1.77 (0.22), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP I  16 
 HIS   0.013   0.001   HIS D  65 
 PHE   0.016   0.001   PHE C  85 
 TYR   0.020   0.001   TYR B 146 
 ARG   0.002   0.000   ARG J 340 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4921.35 seconds
wall clock time: 88 minutes 7.71 seconds (5287.71 seconds total)