Starting phenix.real_space_refine
on Thu Feb 15 06:22:04 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/02_2024/6r6b_4734.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/02_2024/6r6b_4734.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/02_2024/6r6b_4734.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/02_2024/6r6b_4734.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/02_2024/6r6b_4734.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/02_2024/6r6b_4734.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      74      5.16       5
     C    7703      2.51       5
     N    1700      2.21       5
     O    1939      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  117": "NH1" <-> "NH2"
    Residue "C TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE   87": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  140": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  166": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 11416
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1502
          Classifications: {'peptide': 189}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 180}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1347
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 7, 'TRANS': 163}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1340
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 7, 'TRANS': 161}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1332
          Classifications: {'peptide': 168}
          Link IDs: {'PTRANS': 7, 'TRANS': 160}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1348
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 7, 'TRANS': 162}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 1923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1923
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 9, 'TRANS': 235}
    Chain: "I"
      Number of atoms: 656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 656
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 656
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
    Chain: "H"
      Number of atoms: 656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 656
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
    Chain: "J"
      Number of atoms: 656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 656
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
  Time building chain proxies: 6.25, per 1000 atoms: 0.55
  Number of scatterers: 11416
  At special positions: 0
  Unit cell: (92.886, 92.886, 124.944, 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      74     16.00
     O    1939      8.00
     N    1700      7.00
     C    7703      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: 4.47
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2720

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 0 sheets defined
      78.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 21
    Processing helix  chain 'A' and resid 26 through 39
      removed outlier: 3.610A  pdb=" N   PHE A  30 " --> pdb=" O   CYS A  26 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   VAL A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   VAL A  35 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 78
      removed outlier: 3.917A  pdb=" N   GLY A  54 " --> pdb=" O   MET A  50 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A  57 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
      Proline residue:  A  66  - end of helix
      removed outlier: 3.812A  pdb=" N   ALA A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ASN A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 95
      removed outlier: 3.761A  pdb=" N   ILE A  88 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 107
      removed outlier: 3.561A  pdb=" N   HIS A 106 " --> pdb=" O   TYR A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
      removed outlier: 3.598A  pdb=" N   PHE A 115 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 159
    Processing helix  chain 'A' and resid 162 through 174
    Processing helix  chain 'A' and resid 181 through 196
      removed outlier: 4.285A  pdb=" N   ILE A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   VAL A 187 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      Proline residue:  A 188  - end of helix
      removed outlier: 3.909A  pdb=" N   PHE A 194 " --> pdb=" O   LYS A 190 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA A 196 " --> pdb=" O   VAL A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 209
    Processing helix  chain 'B' and resid 11 through 16
      removed outlier: 3.930A  pdb=" N   LEU B  16 " --> pdb=" O   SER B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 25
    Processing helix  chain 'B' and resid 26 through 32
      removed outlier: 3.740A  pdb=" N   PHE B  30 " --> pdb=" O   CYS B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 41
    Processing helix  chain 'B' and resid 51 through 73
      removed outlier: 3.722A  pdb=" N   LEU B  57 " --> pdb=" O   ASN B  53 " (cutoff:3.500A)
      Proline residue:  B  66  - end of helix
      removed outlier: 3.883A  pdb=" N   ALA B  70 " --> pdb=" O   PRO B  66 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLU B  73 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 107
      removed outlier: 4.163A  pdb=" N   LYS B 105 " --> pdb=" O   GLN B 101 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   HIS B 106 " --> pdb=" O   TYR B 102 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 113
      removed outlier: 3.533A  pdb=" N   ARG B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 174
      removed outlier: 3.620A  pdb=" N   LEU B 159 " --> pdb=" O   PHE B 155 " (cutoff:3.500A)
      Proline residue:  B 160  - end of helix
      removed outlier: 3.565A  pdb=" N   VAL B 163 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   VAL B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 196
      removed outlier: 4.497A  pdb=" N   ILE B 185 " --> pdb=" O   SER B 181 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL B 187 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      Proline residue:  B 188  - end of helix
      removed outlier: 3.769A  pdb=" N   PHE B 194 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 209
    Processing helix  chain 'C' and resid 10 through 15
    Processing helix  chain 'C' and resid 16 through 25
    Processing helix  chain 'C' and resid 26 through 41
      removed outlier: 3.747A  pdb=" N   PHE C  30 " --> pdb=" O   CYS C  26 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   VAL C  35 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN C  39 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 69
      Proline residue:  C  66  - end of helix
    Processing helix  chain 'C' and resid 99 through 107
      removed outlier: 3.717A  pdb=" N   LYS C 105 " --> pdb=" O   GLN C 101 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   HIS C 106 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 115
      removed outlier: 3.712A  pdb=" N   ARG C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 175
      Proline residue:  C 160  - end of helix
      removed outlier: 3.638A  pdb=" N   VAL C 163 " --> pdb=" O   LEU C 159 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   VAL C 164 " --> pdb=" O   PRO C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 196
      removed outlier: 3.653A  pdb=" N   VAL C 187 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
      Proline residue:  C 188  - end of helix
      removed outlier: 3.716A  pdb=" N   PHE C 194 " --> pdb=" O   LYS C 190 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA C 196 " --> pdb=" O   VAL C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 209
      removed outlier: 3.530A  pdb=" N   GLU C 209 " --> pdb=" O   LYS C 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 25
      removed outlier: 3.513A  pdb=" N   THR D  25 " --> pdb=" O   VAL D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 32
      removed outlier: 3.642A  pdb=" N   PHE D  30 " --> pdb=" O   CYS D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 41
    Processing helix  chain 'D' and resid 49 through 64
    Processing helix  chain 'D' and resid 64 through 72
      removed outlier: 3.631A  pdb=" N   ALA D  70 " --> pdb=" O   PRO D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 106
      removed outlier: 3.538A  pdb=" N   HIS D 106 " --> pdb=" O   TYR D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 117
      removed outlier: 3.795A  pdb=" N   ARG D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   PHE D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE D 115 " --> pdb=" O   LEU D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 175
      Proline residue:  D 160  - end of helix
      removed outlier: 3.612A  pdb=" N   VAL D 163 " --> pdb=" O   LEU D 159 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL D 164 " --> pdb=" O   PRO D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 181 through 196
      removed outlier: 4.592A  pdb=" N   ILE D 185 " --> pdb=" O   SER D 181 " (cutoff:3.500A)
      Proline residue:  D 188  - end of helix
      removed outlier: 3.973A  pdb=" N   PHE D 194 " --> pdb=" O   LYS D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 200 through 209
    Processing helix  chain 'E' and resid 10 through 16
      removed outlier: 3.522A  pdb=" N   PHE E  14 " --> pdb=" O   THR E  10 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU E  16 " --> pdb=" O   SER E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 25
      removed outlier: 4.509A  pdb=" N   ALA E  23 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 26 through 41
      removed outlier: 3.617A  pdb=" N   PHE E  30 " --> pdb=" O   CYS E  26 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL E  35 " --> pdb=" O   SER E  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 48 through 72
      removed outlier: 4.173A  pdb=" N   LEU E  57 " --> pdb=" O   ASN E  53 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL E  63 " --> pdb=" O   MET E  59 " (cutoff:3.500A)
      Proline residue:  E  66  - end of helix
    Processing helix  chain 'E' and resid 97 through 107
      removed outlier: 3.723A  pdb=" N   HIS E 106 " --> pdb=" O   TYR E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 116
      removed outlier: 3.518A  pdb=" N   ARG E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   PHE E 114 " --> pdb=" O   GLU E 110 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   PHE E 115 " --> pdb=" O   LEU E 111 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN E 116 " --> pdb=" O   ALA E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 138 through 175
      removed outlier: 3.537A  pdb=" N   LEU E 157 " --> pdb=" O   ILE E 153 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU E 159 " --> pdb=" O   PHE E 155 " (cutoff:3.500A)
      Proline residue:  E 160  - end of helix
      removed outlier: 3.500A  pdb=" N   VAL E 164 " --> pdb=" O   PRO E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 196
      Proline residue:  E 188  - end of helix
      removed outlier: 3.995A  pdb=" N   PHE E 194 " --> pdb=" O   LYS E 190 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 209
      removed outlier: 4.141A  pdb=" N   ALA E 206 " --> pdb=" O   ILE E 202 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE E 208 " --> pdb=" O   SER E 204 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLU E 209 " --> pdb=" O   LYS E 205 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 11 through 29
      removed outlier: 3.875A  pdb=" N   ILE F  15 " --> pdb=" O   HIS F  11 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU F  16 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU F  17 " --> pdb=" O   PHE F  13 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLY F  19 " --> pdb=" O   ILE F  15 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL F  20 " --> pdb=" O   LEU F  16 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ARG F  23 " --> pdb=" O   GLY F  19 " (cutoff:3.500A)
      Proline residue:  F  26  - end of helix
    Processing helix  chain 'F' and resid 40 through 56
      removed outlier: 4.445A  pdb=" N   ILE F  45 " --> pdb=" O   PRO F  41 " (cutoff:3.500A)
      Proline residue:  F  46  - end of helix
      removed outlier: 3.750A  pdb=" N   SER F  53 " --> pdb=" O   PHE F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 72 through 90
      removed outlier: 3.954A  pdb=" N   PHE F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LYS F  77 " --> pdb=" O   PHE F  73 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU F  83 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LEU F  84 " --> pdb=" O   ILE F  80 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   CYS F  88 " --> pdb=" O   LEU F  84 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU F  89 " --> pdb=" O   LEU F  85 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 108
      removed outlier: 3.748A  pdb=" N   SER F 101 " --> pdb=" O   HIS F  97 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE F 103 " --> pdb=" O   VAL F  99 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   GLN F 106 " --> pdb=" O   ILE F 102 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 126 through 141
      removed outlier: 3.519A  pdb=" N   ALA F 135 " --> pdb=" O   ASN F 131 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 142 through 158
      removed outlier: 3.531A  pdb=" N   PHE F 146 " --> pdb=" O   GLY F 142 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE F 157 " --> pdb=" O   LEU F 153 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 173 through 206
      removed outlier: 3.631A  pdb=" N   ALA F 182 " --> pdb=" O   LEU F 178 " (cutoff:3.500A)
      Proline residue:  F 188  - end of helix
      removed outlier: 3.711A  pdb=" N   ILE F 191 " --> pdb=" O   SER F 187 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   VAL F 192 " --> pdb=" O   PRO F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 211 through 230
      removed outlier: 3.554A  pdb=" N   ILE F 219 " --> pdb=" O   VAL F 215 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU F 222 " --> pdb=" O   THR F 218 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA F 224 " --> pdb=" O   LYS F 220 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 237 through 249
      removed outlier: 4.365A  pdb=" N   GLN F 241 " --> pdb=" O   PHE F 237 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 35
      removed outlier: 3.793A  pdb=" N   TRP I  21 " --> pdb=" O   ILE I  17 " (cutoff:3.500A)
      Proline residue:  I  22  - end of helix
    Processing helix  chain 'I' and resid 36 through 38
      No H-bonds generated for 'chain 'I' and resid 36 through 38'
    Processing helix  chain 'I' and resid 48 through 62
      removed outlier: 5.383A  pdb=" N   ILE I  54 " --> pdb=" O   GLY I  50 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU I  60 " --> pdb=" O   VAL I  56 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 63 through 84
      removed outlier: 4.268A  pdb=" N   LEU I  71 " --> pdb=" O   TYR I  67 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   CYS I  75 " --> pdb=" O   LEU I  71 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   MET I  79 " --> pdb=" O   CYS I  75 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 20
      removed outlier: 3.636A  pdb=" N   LEU G  16 " --> pdb=" O   LEU G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 20 through 36
    Processing helix  chain 'G' and resid 48 through 62
      removed outlier: 4.512A  pdb=" N   ILE G  54 " --> pdb=" O   GLY G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 65 through 84
      removed outlier: 4.127A  pdb=" N   LEU G  71 " --> pdb=" O   TYR G  67 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLU G  77 " --> pdb=" O   SER G  73 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   MET G  79 " --> pdb=" O   CYS G  75 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 19
    Processing helix  chain 'H' and resid 20 through 35
    Processing helix  chain 'H' and resid 36 through 38
      No H-bonds generated for 'chain 'H' and resid 36 through 38'
    Processing helix  chain 'H' and resid 46 through 62
      removed outlier: 4.548A  pdb=" N   ILE H  54 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   LEU H  60 " --> pdb=" O   VAL H  56 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 82
      removed outlier: 4.094A  pdb=" N   LEU H  71 " --> pdb=" O   TYR H  67 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU H  77 " --> pdb=" O   SER H  73 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   MET H  79 " --> pdb=" O   CYS H  75 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 18
    Processing helix  chain 'J' and resid 19 through 33
      removed outlier: 3.568A  pdb=" N   VAL J  23 " --> pdb=" O   SER J  19 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LEU J  31 " --> pdb=" O   THR J  27 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 46 through 62
      removed outlier: 3.881A  pdb=" N   GLY J  50 " --> pdb=" O   THR J  46 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   LYS J  52 " --> pdb=" O   PRO J  48 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE J  54 " --> pdb=" O   GLY J  50 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   SER J  59 " --> pdb=" O   GLY J  55 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 63 through 66
    Processing helix  chain 'J' and resid 70 through 82

    675 hydrogen bonds defined for protein.
    2019 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.65

  Time building geometry restraints manager: 4.85 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: 3237
        1.34 -     1.46: 2874
        1.46 -     1.58: 5421
        1.58 -     1.70: 1
        1.70 -     1.82: 135
  Bond restraints: 11668
  Sorted by residual:
  bond pdb=" C   LEU A 109 "
       pdb=" N   GLU A 110 "
    ideal  model  delta    sigma   weight residual
    1.334  1.467 -0.133 1.61e-02 3.86e+03 6.86e+01
  bond pdb=" CA  VAL F  67 "
       pdb=" C   VAL F  67 "
    ideal  model  delta    sigma   weight residual
    1.523  1.590 -0.067 1.27e-02 6.20e+03 2.78e+01
  bond pdb=" C   LEU C 159 "
       pdb=" N   PRO C 160 "
    ideal  model  delta    sigma   weight residual
    1.334  1.369 -0.035 8.40e-03 1.42e+04 1.73e+01
  bond pdb=" N   VAL F  67 "
       pdb=" CA  VAL F  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.507 -0.048 1.25e-02 6.40e+03 1.48e+01
  bond pdb=" C   LEU J  47 "
       pdb=" N   PRO J  48 "
    ideal  model  delta    sigma   weight residual
    1.334  1.423 -0.089 2.34e-02 1.83e+03 1.44e+01
  ... (remaining 11663 not shown)

  Histogram of bond angle deviations from ideal:
       93.14 -   105.35: 247
      105.35 -   117.55: 8081
      117.55 -   129.76: 7402
      129.76 -   141.97: 83
      141.97 -   154.18: 1
  Bond angle restraints: 15814
  Sorted by residual:
  angle pdb=" C   VAL F  67 "
        pdb=" N   PHE F  68 "
        pdb=" CA  PHE F  68 "
      ideal   model   delta    sigma   weight residual
     126.86  154.18  -27.32 1.57e+00 4.06e-01 3.03e+02
  angle pdb=" C   SER F  86 "
        pdb=" CA  SER F  86 "
        pdb=" CB  SER F  86 "
      ideal   model   delta    sigma   weight residual
     110.67  127.27  -16.60 1.92e+00 2.71e-01 7.47e+01
  angle pdb=" N   LYS H  83 "
        pdb=" CA  LYS H  83 "
        pdb=" C   LYS H  83 "
      ideal   model   delta    sigma   weight residual
     113.38  103.69    9.69 1.23e+00 6.61e-01 6.21e+01
  angle pdb=" N   SER F  66 "
        pdb=" CA  SER F  66 "
        pdb=" C   SER F  66 "
      ideal   model   delta    sigma   weight residual
     108.76  121.99  -13.23 1.69e+00 3.50e-01 6.12e+01
  angle pdb=" N   ILE C  67 "
        pdb=" CA  ILE C  67 "
        pdb=" C   ILE C  67 "
      ideal   model   delta    sigma   weight residual
     112.96  107.06    5.90 1.00e+00 1.00e+00 3.48e+01
  ... (remaining 15809 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.92: 6090
       13.92 -    27.85: 538
       27.85 -    41.77: 188
       41.77 -    55.70: 36
       55.70 -    69.62: 3
  Dihedral angle restraints: 6855
    sinusoidal: 2640
      harmonic: 4215
  Sorted by residual:
  dihedral pdb=" C   SER F  86 "
           pdb=" N   SER F  86 "
           pdb=" CA  SER F  86 "
           pdb=" CB  SER F  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -146.11   23.51     0      2.50e+00 1.60e-01 8.84e+01
  dihedral pdb=" CA  THR G  38 "
           pdb=" C   THR G  38 "
           pdb=" N   VAL G  39 "
           pdb=" CA  VAL G  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.00  -41.00     0      5.00e+00 4.00e-02 6.72e+01
  dihedral pdb=" CA  GLY I  68 "
           pdb=" C   GLY I  68 "
           pdb=" N   GLU I  69 "
           pdb=" CA  GLU I  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.02  -33.98     0      5.00e+00 4.00e-02 4.62e+01
  ... (remaining 6852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.166: 1890
       0.166 -    0.332: 36
       0.332 -    0.498: 0
       0.498 -    0.664: 0
       0.664 -    0.830: 1
  Chirality restraints: 1927
  Sorted by residual:
  chirality pdb=" CA  SER F  86 "
            pdb=" N   SER F  86 "
            pdb=" C   SER F  86 "
            pdb=" CB  SER F  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.68    0.83 2.00e-01 2.50e+01 1.72e+01
  chirality pdb=" CA  VAL C  46 "
            pdb=" N   VAL C  46 "
            pdb=" C   VAL C  46 "
            pdb=" CB  VAL C  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.14    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CB  ILE G  51 "
            pdb=" CA  ILE G  51 "
            pdb=" CG1 ILE G  51 "
            pdb=" CG2 ILE G  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.10e+00
  ... (remaining 1924 not shown)

  Planarity restraints: 1877
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 109 "   -0.033 2.00e-02 2.50e+03   6.10e-02 3.73e+01
        pdb=" C   LEU A 109 "    0.106 2.00e-02 2.50e+03
        pdb=" O   LEU A 109 "   -0.039 2.00e-02 2.50e+03
        pdb=" N   GLU A 110 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  62 "   -0.028 2.00e-02 2.50e+03   5.93e-02 3.52e+01
        pdb=" C   ASP F  62 "    0.102 2.00e-02 2.50e+03
        pdb=" O   ASP F  62 "   -0.041 2.00e-02 2.50e+03
        pdb=" N   ILE F  63 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  67 "    0.019 2.00e-02 2.50e+03   3.94e-02 1.56e+01
        pdb=" C   VAL F  67 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   VAL F  67 "    0.025 2.00e-02 2.50e+03
        pdb=" N   PHE F  68 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1874 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.40: 30
        2.40 -     3.02: 5866
        3.02 -     3.65: 17695
        3.65 -     4.27: 25556
        4.27 -     4.90: 42126
  Nonbonded interactions: 91273
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 115 "
            pdb=" OG  SER A 137 "
     model   vdw
     1.771 2.440
  nonbonded pdb=" OE1 GLU B 209 "
            pdb=" CE  LYS H  83 "
     model   vdw
     1.812 3.440
  nonbonded pdb=" OE1 GLU B 209 "
            pdb=" CD  LYS H  83 "
     model   vdw
     1.926 3.440
  nonbonded pdb=" OG  SER A 134 "
            pdb=" N   LEU A 135 "
     model   vdw
     2.120 2.520
  nonbonded pdb=" O   GLY A  24 "
            pdb=" OH  TYR A  99 "
     model   vdw
     2.260 2.440
  ... (remaining 91268 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' and (resid 11 through 73 or resid 96 through 116 or resid 133 through \ 
 213))
  selection = (chain 'B' and (resid 11 through 73 or resid 96 through 116 or resid 133 through \ 
 213))
  selection = (chain 'C' and (resid 11 through 116 or resid 133 through 213))
  selection = (chain 'D' and (resid 11 through 116 or resid 133 through 213))
  selection = (chain 'E' and (resid 11 through 116 or resid 133 through 213))
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          5.510
  Check model and map are aligned:         0.150
  Set scattering table:                    0.090
  Process input model:                     31.190
  Find NCS groups from input model:        0.710
  Set up NCS constraints:                  0.060
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
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      :  0.010   0.133  11668  Z= 0.644
  Angle     :  1.362  27.323  15814  Z= 0.693
  Chirality :  0.067   0.830   1927
  Planarity :  0.009   0.071   1877
  Dihedral  : 12.493  69.623   4135
  Min Nonbonded Distance : 1.771

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.56 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  6.54 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.29 %

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: -5.15 (0.17), residues: 1414
  helix: -3.10 (0.11), residues: 1064
  sheet:  None (None), residues: 0
  loop : -3.66 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP D 200 
 HIS   0.007   0.002   HIS B 106 
 PHE   0.037   0.003   PHE F 133 
 TYR   0.024   0.003   TYR D 133 
 ARG   0.010   0.002   ARG B  38 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  556 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 531
  time to evaluate  : 1.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7752 (mtpt)
REVERT: B   29 LYS cc_start: 0.7992 (tptt) cc_final: 0.7520 (tptm)
REVERT: B  172 LEU cc_start: 0.7698 (tt) cc_final: 0.7131 (tt)
REVERT: C  175 LEU cc_start: 0.8309 (tp) cc_final: 0.8045 (tt)
REVERT: C  177 MET cc_start: 0.6125 (ptp) cc_final: 0.5719 (ptm)
REVERT: D  197 LEU cc_start: 0.6869 (tp) cc_final: 0.6582 (tt)
REVERT: I   59 SER cc_start: 0.8387 (p) cc_final: 0.8119 (t)
REVERT: G   46 THR cc_start: 0.7333 (p) cc_final: 0.7042 (p)
REVERT: G   59 SER cc_start: 0.7745 (p) cc_final: 0.7399 (t)
  outliers start: 25
  outliers final: 2
  residues processed: 546
  average time/residue: 0.2337
  time to fit residues: 178.6500
Evaluate side-chains
  304 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 302
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain H residue   21 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.0970
   chunk 106 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 127 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  53 ASN
** B  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 GLN
D 101 GLN
F 106 GLN
F 156 ASN
F 247 HIS
** G  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  45 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11668  Z= 0.234
  Angle     :  0.887  13.119  15814  Z= 0.432
  Chirality :  0.045   0.175   1927
  Planarity :  0.005   0.058   1877
  Dihedral  :  6.291  45.082   1518
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.86 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 18.90 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.20), residues: 1414
  helix: -1.52 (0.14), residues: 1090
  sheet:  None (None), residues: 0
  loop : -3.26 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP J  21 
 HIS   0.011   0.001   HIS F 247 
 PHE   0.023   0.002   PHE F  76 
 TYR   0.025   0.002   TYR C  27 
 ARG   0.008   0.001   ARG B 113 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 364
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  178 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.5862 (ppp)
REVERT: D  179 MET cc_start: 0.7611 (mmm) cc_final: 0.7061 (mpp)
REVERT: E  190 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7528 (mtmm)
REVERT: G   56 VAL cc_start: 0.8125 (m) cc_final: 0.7890 (t)
REVERT: G   59 SER cc_start: 0.7736 (p) cc_final: 0.7498 (t)
REVERT: J    7 MET cc_start: 0.7328 (mmt) cc_final: 0.7097 (mmt)
  outliers start: 76
  outliers final: 27
  residues processed: 420
  average time/residue: 0.2074
  time to fit residues: 126.0089
Evaluate side-chains
  326 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 297
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   49 ASN
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  178 MET
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   55 ILE
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain E residue  170 SER
Chi-restraints excluded: chain E residue  190 LYS
Chi-restraints excluded: chain E residue  202 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain I residue   32 SER
Chi-restraints excluded: chain I residue   40 THR
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain G residue   38 THR
Chi-restraints excluded: chain H residue   46 THR
Chi-restraints excluded: chain J residue   27 THR
Chi-restraints excluded: chain J residue   59 SER
Chi-restraints excluded: chain J residue   75 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0970
   chunk 127 optimal weight:    1.9990
   chunk 137 optimal weight:    7.9990
   chunk 113 optimal weight:    0.7980
   chunk 126 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 101 GLN
** G  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11668  Z= 0.224
  Angle     :  0.845  11.756  15814  Z= 0.407
  Chirality :  0.045   0.179   1927
  Planarity :  0.005   0.056   1877
  Dihedral  :  5.747  44.090   1516
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.00 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 23.31 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.22), residues: 1414
  helix: -0.85 (0.15), residues: 1095
  sheet:  None (None), residues: 0
  loop : -3.02 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 200 
 HIS   0.002   0.001   HIS E 106 
 PHE   0.028   0.001   PHE F  76 
 TYR   0.025   0.002   TYR A 158 
 ARG   0.004   0.001   ARG B  38 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 332
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.6222 (tpp) cc_final: 0.5796 (tpp)
REVERT: C   64 MET cc_start: 0.7426 (mmm) cc_final: 0.7106 (mmt)
REVERT: E  190 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7269 (mtmm)
REVERT: F   35 ASN cc_start: 0.5882 (t0) cc_final: 0.5244 (m-40)
REVERT: G   56 VAL cc_start: 0.8246 (m) cc_final: 0.8038 (t)
REVERT: G   59 SER cc_start: 0.7898 (p) cc_final: 0.7637 (t)
  outliers start: 54
  outliers final: 25
  residues processed: 370
  average time/residue: 0.2008
  time to fit residues: 109.3493
Evaluate side-chains
  315 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 289
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue   97 MET
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  204 SER
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain E residue  190 LYS
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  222 LEU
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain H residue   46 THR
Chi-restraints excluded: chain J residue   12 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 125 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9990
   chunk 127 optimal weight:    4.9990
   chunk 135 optimal weight:   40.0000
   chunk 121 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 112 optimal weight:   20.0000
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A  49 ASN
A  53 ASN
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
F 170 ASN
I   9 ASN
** H  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  45 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  11668  Z= 0.305
  Angle     :  0.832  11.062  15814  Z= 0.409
  Chirality :  0.044   0.199   1927
  Planarity :  0.005   0.062   1877
  Dihedral  :  5.522  44.172   1516
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.43 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 24.33 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -1.58 (0.22), residues: 1414
  helix: -0.45 (0.15), residues: 1108
  sheet:  None (None), residues: 0
  loop : -2.92 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 200 
 HIS   0.003   0.001   HIS E 106 
 PHE   0.024   0.001   PHE F  33 
 TYR   0.023   0.002   TYR D 142 
 ARG   0.005   0.001   ARG D 113 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 307
  time to evaluate  : 1.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 MET cc_start: 0.7466 (mmm) cc_final: 0.7207 (mmt)
REVERT: F   35 ASN cc_start: 0.5943 (t0) cc_final: 0.5076 (m110)
REVERT: G   56 VAL cc_start: 0.8302 (m) cc_final: 0.8100 (t)
  outliers start: 73
  outliers final: 43
  residues processed: 358
  average time/residue: 0.1960
  time to fit residues: 104.6591
Evaluate side-chains
  326 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 283
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue  108 ASP
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  204 SER
Chi-restraints excluded: chain D residue   36 MET
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   45 GLN
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue   97 MET
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  108 ASP
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain E residue  190 LYS
Chi-restraints excluded: chain E residue  202 ILE
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  222 LEU
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain I residue   84 SER
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain G residue   46 THR
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain H residue   46 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   27 THR
Chi-restraints excluded: chain J residue   59 SER
Chi-restraints excluded: chain J residue   75 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 100 optimal weight:    0.2980
   chunk 55 optimal weight:    6.9990
   chunk 115 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9980
   chunk 121 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A  49 ASN
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 GLN
C  39 ASN
C 106 HIS
F 106 GLN
** H  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.5375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11668  Z= 0.218
  Angle     :  0.827  10.420  15814  Z= 0.400
  Chirality :  0.044   0.196   1927
  Planarity :  0.005   0.067   1877
  Dihedral  :  5.435  45.211   1516
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.78 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 27.48 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -1.23 (0.23), residues: 1414
  helix: -0.22 (0.15), residues: 1103
  sheet:  None (None), residues: 0
  loop : -2.66 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J  66 
 HIS   0.003   0.001   HIS F 247 
 PHE   0.030   0.001   PHE F  76 
 TYR   0.032   0.002   TYR A 158 
 ARG   0.003   0.001   ARG F  23 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 317
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLU cc_start: 0.6048 (mm-30) cc_final: 0.5381 (mm-30)
REVERT: C   64 MET cc_start: 0.7452 (mmm) cc_final: 0.7249 (mmt)
REVERT: I   52 LYS cc_start: 0.9112 (pttt) cc_final: 0.8721 (ptpp)
REVERT: G   56 VAL cc_start: 0.8274 (m) cc_final: 0.7968 (t)
REVERT: J    4 ILE cc_start: 0.8375 (mp) cc_final: 0.8120 (pt)
  outliers start: 52
  outliers final: 35
  residues processed: 353
  average time/residue: 0.2009
  time to fit residues: 104.7176
Evaluate side-chains
  330 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 295
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain D residue   36 MET
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   45 GLN
Chi-restraints excluded: chain D residue   97 MET
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain E residue  202 ILE
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain I residue   84 SER
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain H residue   46 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   27 THR
Chi-restraints excluded: chain J residue   59 SER
Chi-restraints excluded: chain J residue   75 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 135 optimal weight:   40.0000
   chunk 112 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 44 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 130 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A  53 ASN
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I   9 ASN
** H  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.5680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11668  Z= 0.219
  Angle     :  0.848  13.830  15814  Z= 0.405
  Chirality :  0.044   0.197   1927
  Planarity :  0.005   0.068   1877
  Dihedral  :  5.315  46.132   1516
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.43 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 28.58 %
    Favored  : 67.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.98 (0.23), residues: 1414
  helix: -0.02 (0.16), residues: 1105
  sheet:  None (None), residues: 0
  loop : -2.67 (0.39), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 200 
 HIS   0.002   0.001   HIS F  70 
 PHE   0.031   0.001   PHE H  49 
 TYR   0.023   0.001   TYR D 142 
 ARG   0.004   0.001   ARG F  44 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 314
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.8108 (tppt) cc_final: 0.7875 (tptp)
REVERT: B   39 ASN cc_start: 0.7536 (m-40) cc_final: 0.7285 (m-40)
REVERT: E  177 MET cc_start: 0.7934 (pmm) cc_final: 0.7707 (pmm)
REVERT: G   56 VAL cc_start: 0.8296 (m) cc_final: 0.7912 (t)
  outliers start: 53
  outliers final: 40
  residues processed: 349
  average time/residue: 0.1964
  time to fit residues: 102.5431
Evaluate side-chains
  331 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 291
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain D residue   36 MET
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   45 GLN
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   97 MET
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain E residue  202 ILE
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain I residue   84 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain H residue   46 THR
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   27 THR
Chi-restraints excluded: chain J residue   59 SER
Chi-restraints excluded: chain J residue   75 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 114 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 134 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A  49 ASN
A  53 ASN
B  45 GLN
** H  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.5938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11668  Z= 0.235
  Angle     :  0.877  14.110  15814  Z= 0.418
  Chirality :  0.044   0.231   1927
  Planarity :  0.005   0.069   1877
  Dihedral  :  5.259  46.187   1516
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.00 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 29.61 %
    Favored  : 65.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.77 (0.23), residues: 1414
  helix:  0.13 (0.16), residues: 1109
  sheet:  None (None), residues: 0
  loop : -2.67 (0.39), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 200 
 HIS   0.003   0.001   HIS F  70 
 PHE   0.027   0.001   PHE F  76 
 TYR   0.030   0.001   TYR A 142 
 ARG   0.003   0.000   ARG F  23 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 311
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5576 (mm-30)
REVERT: H   44 GLU cc_start: 0.5038 (mp0) cc_final: 0.4696 (mp0)
  outliers start: 56
  outliers final: 38
  residues processed: 346
  average time/residue: 0.1965
  time to fit residues: 101.4291
Evaluate side-chains
  323 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 285
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain D residue   36 MET
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   45 GLN
Chi-restraints excluded: chain D residue   97 MET
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  177 MET
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain E residue  202 ILE
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain I residue   84 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain G residue   64 SER
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   59 SER
Chi-restraints excluded: chain J residue   75 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 85 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 66 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 106 optimal weight:   10.0000
   chunk 122 optimal weight:    6.9990
   chunk 129 optimal weight:    0.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A  49 ASN
** D  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 ASN
** H  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.6213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091  11668  Z= 0.250
  Angle     :  0.910  14.239  15814  Z= 0.428
  Chirality :  0.045   0.245   1927
  Planarity :  0.005   0.068   1877
  Dihedral  :  5.208  46.262   1516
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.43 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 31.18 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.64 (0.23), residues: 1414
  helix:  0.22 (0.16), residues: 1109
  sheet:  None (None), residues: 0
  loop : -2.58 (0.40), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 200 
 HIS   0.003   0.001   HIS F  70 
 PHE   0.057   0.001   PHE H  49 
 TYR   0.040   0.001   TYR A 142 
 ARG   0.006   0.001   ARG B  38 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 290
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   52 LYS cc_start: 0.9089 (pttt) cc_final: 0.8889 (ptpp)
REVERT: J    1 MET cc_start: 0.4127 (ptt) cc_final: 0.3918 (ptt)
REVERT: J   52 LYS cc_start: 0.8978 (ptpt) cc_final: 0.8733 (mtmm)
  outliers start: 46
  outliers final: 42
  residues processed: 319
  average time/residue: 0.1883
  time to fit residues: 90.0607
Evaluate side-chains
  318 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 276
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain D residue   36 MET
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   45 GLN
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   97 MET
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  177 MET
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   39 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  222 LEU
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue   84 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain G residue   64 SER
Chi-restraints excluded: chain G residue   82 ILE
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue   71 LEU
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   59 SER
Chi-restraints excluded: chain J residue   75 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 125 optimal weight:    1.9990
   chunk 129 optimal weight:    0.6980
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 113 optimal weight:    0.4980
   chunk 118 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 132 optimal weight:    7.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
** D  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.6333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  11668  Z= 0.242
  Angle     :  0.926  15.571  15814  Z= 0.433
  Chirality :  0.045   0.246   1927
  Planarity :  0.005   0.070   1877
  Dihedral  :  5.204  46.356   1516
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 18.07
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.64 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 31.02 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.54 (0.24), residues: 1414
  helix:  0.31 (0.16), residues: 1108
  sheet:  None (None), residues: 0
  loop : -2.64 (0.40), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  66 
 HIS   0.004   0.001   HIS F 247 
 PHE   0.021   0.001   PHE H  49 
 TYR   0.031   0.001   TYR A 142 
 ARG   0.006   0.001   ARG B  38 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 294
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 48
  outliers final: 43
  residues processed: 324
  average time/residue: 0.1892
  time to fit residues: 91.9536
Evaluate side-chains
  321 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 278
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   49 ASN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain D residue   36 MET
Chi-restraints excluded: chain D residue   45 GLN
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   97 MET
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  177 MET
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain D residue  209 GLU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain E residue  202 ILE
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   39 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  222 LEU
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain I residue   84 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain G residue   54 ILE
Chi-restraints excluded: chain G residue   82 ILE
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue   71 LEU
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   59 SER
Chi-restraints excluded: chain J residue   75 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 139 optimal weight:    0.9980
   chunk 128 optimal weight:    6.9990
   chunk 111 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0770
   chunk 88 optimal weight:    0.8980
   chunk 118 optimal weight:    0.6980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A  53 ASN
** D  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 106 GLN
** H  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.6537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  11668  Z= 0.232
  Angle     :  0.968  16.896  15814  Z= 0.447
  Chirality :  0.046   0.250   1927
  Planarity :  0.005   0.063   1877
  Dihedral  :  5.188  46.708   1516
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.43 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 32.05 %
    Favored  : 64.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.58 (0.23), residues: 1414
  helix:  0.26 (0.16), residues: 1107
  sheet:  None (None), residues: 0
  loop : -2.52 (0.40), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 200 
 HIS   0.003   0.001   HIS F  70 
 PHE   0.039   0.001   PHE H  49 
 TYR   0.044   0.001   TYR A 142 
 ARG   0.005   0.000   ARG B  38 

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 290
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  205 LYS cc_start: 0.7169 (tptp) cc_final: 0.6908 (tppt)
REVERT: J   52 LYS cc_start: 0.8996 (ptpt) cc_final: 0.8760 (mtmm)
  outliers start: 40
  outliers final: 36
  residues processed: 316
  average time/residue: 0.1888
  time to fit residues: 89.5974
Evaluate side-chains
  317 residues out of total 1270 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 281
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   97 MET
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  177 MET
Chi-restraints excluded: chain D residue  193 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  147 ILE
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   39 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  140 TYR
Chi-restraints excluded: chain F residue  222 LEU
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   36 LEU
Chi-restraints excluded: chain G residue   82 ILE
Chi-restraints excluded: chain H residue   59 SER
Chi-restraints excluded: chain H residue   71 LEU
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   59 SER
Chi-restraints excluded: chain J residue   75 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 102 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 111 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 114 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
** D  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.067076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.051164 restraints weight = 48817.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.052761 restraints weight = 27760.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.053868 restraints weight = 18812.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.6648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11668  Z= 0.232
  Angle     :  0.974  15.341  15814  Z= 0.449
  Chirality :  0.046   0.242   1927
  Planarity :  0.005   0.062   1877
  Dihedral  :  5.177  46.775   1516
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.21 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 32.68 %
    Favored  : 64.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.59 (0.23), residues: 1414
  helix:  0.27 (0.16), residues: 1114
  sheet:  None (None), residues: 0
  loop : -2.69 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 200 
 HIS   0.004   0.001   HIS F  70 
 PHE   0.028   0.001   PHE H  49 
 TYR   0.026   0.001   TYR A 142 
 ARG   0.005   0.001   ARG B  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2654.89 seconds
wall clock time: 48 minutes 56.50 seconds (2936.50 seconds total)