Starting phenix.real_space_refine
on Sat Dec  9 08:11:40 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/12_2023/7ka3_22757.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/12_2023/7ka3_22757.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/12_2023/7ka3_22757.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/12_2023/7ka3_22757.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/12_2023/7ka3_22757.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/12_2023/7ka3_22757.pdb"
  }
  resolution = 3.3
  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=   0.003
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      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B ASP   17": "OD1" <-> "OD2"
    Residue "B ASP   33": "OD1" <-> "OD2"
    Residue "B PHE  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  187": "OE1" <-> "OE2"
    Residue "B ASP  195": "OD1" <-> "OD2"
    Residue "B GLU  246": "OE1" <-> "OE2"
    Residue "B GLU  276": "OE1" <-> "OE2"
    Residue "B PHE  299": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  318": "OE1" <-> "OE2"
    Residue "A ASP   17": "OD1" <-> "OD2"
    Residue "A ASP   33": "OD1" <-> "OD2"
    Residue "A PHE  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  187": "OE1" <-> "OE2"
    Residue "A ASP  195": "OD1" <-> "OD2"
    Residue "A GLU  246": "OE1" <-> "OE2"
    Residue "A GLU  276": "OE1" <-> "OE2"
    Residue "A PHE  299": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  318": "OE1" <-> "OE2"
    Residue "C ASP   17": "OD1" <-> "OD2"
    Residue "C ASP   33": "OD1" <-> "OD2"
    Residue "C PHE  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  187": "OE1" <-> "OE2"
    Residue "C ASP  195": "OD1" <-> "OD2"
    Residue "C GLU  246": "OE1" <-> "OE2"
    Residue "C GLU  276": "OE1" <-> "OE2"
    Residue "C PHE  299": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  318": "OE1" <-> "OE2"
    Residue "D ASP   17": "OD1" <-> "OD2"
    Residue "D ASP   33": "OD1" <-> "OD2"
    Residue "D PHE  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  187": "OE1" <-> "OE2"
    Residue "D ASP  195": "OD1" <-> "OD2"
    Residue "D GLU  246": "OE1" <-> "OE2"
    Residue "D GLU  276": "OE1" <-> "OE2"
    Residue "D PHE  299": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  318": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "C"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "D"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
  Time building chain proxies: 5.03, per 1000 atoms: 0.48
  Number of scatterers: 10472
  At special positions: 0
  Unit cell: (97.37, 80.99, 105.56, 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      44     16.00
     O    1980      8.00
     N    1860      7.00
     C    6588      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: 3.83
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      55.2% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 23
      removed outlier: 3.599A  pdb=" N   VAL B  23 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 47
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
      removed outlier: 3.522A  pdb=" N   VAL B  69 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.511A  pdb=" N   GLN B  85 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 100
      removed outlier: 3.993A  pdb=" N   LYS B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 180
      removed outlier: 3.703A  pdb=" N   ASN B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 219
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 275 through 287
      removed outlier: 3.503A  pdb=" N   ALA B 279 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   SER B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 3.946A  pdb=" N   GLN B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLY B 314 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 340
    Processing helix  chain 'A' and resid 8 through 23
      removed outlier: 3.600A  pdb=" N   VAL A  23 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 47
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
      removed outlier: 3.522A  pdb=" N   VAL A  69 " --> pdb=" O   ASP A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 85
      removed outlier: 3.512A  pdb=" N   GLN A  85 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
      removed outlier: 3.993A  pdb=" N   LYS A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 180
      removed outlier: 3.703A  pdb=" N   ASN A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 258
    Processing helix  chain 'A' and resid 275 through 287
      removed outlier: 3.502A  pdb=" N   ALA A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   SER A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 3.946A  pdb=" N   GLN A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 340
    Processing helix  chain 'C' and resid 8 through 23
      removed outlier: 3.601A  pdb=" N   VAL C  23 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 47
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
      removed outlier: 3.521A  pdb=" N   VAL C  69 " --> pdb=" O   ASP C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 3.512A  pdb=" N   GLN C  85 " --> pdb=" O   THR C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 100
      removed outlier: 3.993A  pdb=" N   LYS C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 180
      removed outlier: 3.703A  pdb=" N   ASN C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 219
    Processing helix  chain 'C' and resid 222 through 226
      removed outlier: 3.594A  pdb=" N   THR C 226 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 258
    Processing helix  chain 'C' and resid 275 through 287
      removed outlier: 3.502A  pdb=" N   ALA C 279 " --> pdb=" O   SER C 275 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   SER C 280 " --> pdb=" O   GLU C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 3.947A  pdb=" N   GLN C 306 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLY C 314 " --> pdb=" O   LEU C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 340
    Processing helix  chain 'D' and resid 8 through 23
      removed outlier: 3.600A  pdb=" N   VAL D  23 " --> pdb=" O   ALA D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 47
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
      removed outlier: 3.521A  pdb=" N   VAL D  69 " --> pdb=" O   ASP D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 85
      removed outlier: 3.511A  pdb=" N   GLN D  85 " --> pdb=" O   THR D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 100
      removed outlier: 3.993A  pdb=" N   LYS D 100 " --> pdb=" O   VAL D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
      removed outlier: 3.704A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 219
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 258
    Processing helix  chain 'D' and resid 275 through 287
      removed outlier: 3.503A  pdb=" N   ALA D 279 " --> pdb=" O   SER D 275 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   SER D 280 " --> pdb=" O   GLU D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 3.946A  pdb=" N   GLN D 306 " --> pdb=" O   GLY D 302 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLY D 314 " --> pdb=" O   LEU D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 340
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31
      removed outlier: 6.460A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   ILE B  77 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   LEU B  30 " --> pdb=" O   ILE B  77 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY B  74 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   GLY B 105 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   LEU B  78 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   ILE B 185 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ALA B 145 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   GLU B 187 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   TRP B 147 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   GLU B 189 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   CYS B 149 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU B 191 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA B  31 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31
      removed outlier: 6.460A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   ILE A  77 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU A  30 " --> pdb=" O   ILE A  77 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   GLY A  74 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   GLY A 105 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   LEU A  78 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   ILE A 185 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ALA A 145 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   GLU A 187 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   GLU A 189 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   CYS A 149 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU A 191 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA A  31 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31
      removed outlier: 6.461A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  75 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   ILE C  77 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU C  30 " --> pdb=" O   ILE C  77 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY C  74 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   GLY C 105 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   LEU C  78 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   VAL C 104 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ALA C 145 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 5.596A  pdb=" N   ILE C 106 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   ILE C 185 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ALA C 145 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   GLU C 187 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   TRP C 147 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   GLU C 189 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   CYS C 149 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   LEU C 191 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   LEU C 151 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA C  31 " --> pdb=" O   TYR C 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31
      removed outlier: 6.460A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   ILE D  77 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LEU D  30 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY D  74 " --> pdb=" O   VAL D 103 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   GLY D 105 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D 105 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   LYS D 107 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   LEU D  78 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   VAL D 104 " --> pdb=" O   ASP D 143 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ALA D 145 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 5.596A  pdb=" N   ILE D 106 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   ILE D 185 " --> pdb=" O   ASP D 143 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ALA D 145 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   GLU D 187 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   TRP D 147 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   GLU D 189 " --> pdb=" O   TRP D 147 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   CYS D 149 " --> pdb=" O   GLU D 189 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU D 191 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   LEU D 151 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA D  31 " --> pdb=" O   TYR D 301 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    524 hydrogen bonds defined for protein.
    1536 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: 3.00

  Time building geometry restraints manager: 4.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3479
        1.34 -     1.46: 1920
        1.46 -     1.58: 5217
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" C   ASN A  70 "
       pdb=" N   PRO A  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.398 -0.064 2.34e-02 1.83e+03 7.52e+00
  bond pdb=" C   ASN B  70 "
       pdb=" N   PRO B  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.397 -0.064 2.34e-02 1.83e+03 7.37e+00
  bond pdb=" C   ASN D  70 "
       pdb=" N   PRO D  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.397 -0.063 2.34e-02 1.83e+03 7.28e+00
  bond pdb=" C   ASN C  70 "
       pdb=" N   PRO C  71 "
    ideal  model  delta    sigma   weight residual
    1.334  1.397 -0.063 2.34e-02 1.83e+03 7.28e+00
  bond pdb=" C   PHE C  93 "
       pdb=" N   PRO C  94 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.36e-02 5.41e+03 1.94e+00
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
      100.66 -   107.33: 427
      107.33 -   114.00: 6065
      114.00 -   120.67: 4260
      120.67 -   127.34: 3604
      127.34 -   134.01: 108
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" C   ASN D 319 "
        pdb=" N   LEU D 320 "
        pdb=" CA  LEU D 320 "
      ideal   model   delta    sigma   weight residual
     121.19  127.32   -6.13 1.59e+00 3.96e-01 1.49e+01
  angle pdb=" C   ASN A 319 "
        pdb=" N   LEU A 320 "
        pdb=" CA  LEU A 320 "
      ideal   model   delta    sigma   weight residual
     121.19  127.29   -6.10 1.59e+00 3.96e-01 1.47e+01
  angle pdb=" C   ASN B 319 "
        pdb=" N   LEU B 320 "
        pdb=" CA  LEU B 320 "
      ideal   model   delta    sigma   weight residual
     121.19  127.29   -6.10 1.59e+00 3.96e-01 1.47e+01
  angle pdb=" C   ASN C 319 "
        pdb=" N   LEU C 320 "
        pdb=" CA  LEU C 320 "
      ideal   model   delta    sigma   weight residual
     121.19  127.28   -6.09 1.59e+00 3.96e-01 1.46e+01
  angle pdb=" CA  LEU B  61 "
        pdb=" CB  LEU B  61 "
        pdb=" CG  LEU B  61 "
      ideal   model   delta    sigma   weight residual
     116.30  125.75   -9.45 3.50e+00 8.16e-02 7.30e+00
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 5912
       17.48 -    34.95: 485
       34.95 -    52.43: 83
       52.43 -    69.91: 12
       69.91 -    87.38: 12
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  LEU A 270 "
           pdb=" C   LEU A 270 "
           pdb=" N   SER A 271 "
           pdb=" CA  SER A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.16   17.84     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  LEU D 270 "
           pdb=" C   LEU D 270 "
           pdb=" N   SER D 271 "
           pdb=" CA  SER D 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.20   17.80     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  LEU B 270 "
           pdb=" C   LEU B 270 "
           pdb=" N   SER B 271 "
           pdb=" CA  SER B 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.21   17.79     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 960
       0.029 -    0.059: 395
       0.059 -    0.088: 177
       0.088 -    0.117: 96
       0.117 -    0.146: 16
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CA  VAL D 113 "
            pdb=" N   VAL D 113 "
            pdb=" C   VAL D 113 "
            pdb=" CB  VAL D 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  VAL C 113 "
            pdb=" N   VAL C 113 "
            pdb=" C   VAL C 113 "
            pdb=" CB  VAL C 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CA  VAL B 113 "
            pdb=" N   VAL B 113 "
            pdb=" C   VAL B 113 "
            pdb=" CB  VAL B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 329 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.87e+00
        pdb=" C   LYS C 329 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LYS C 329 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ARG C 330 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 329 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.86e+00
        pdb=" C   LYS B 329 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LYS B 329 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ARG B 330 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 329 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.84e+00
        pdb=" C   LYS A 329 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LYS A 329 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 330 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 3100
        2.82 -     3.34: 9356
        3.34 -     3.86: 18013
        3.86 -     4.38: 20884
        4.38 -     4.90: 36001
  Nonbonded interactions: 87354
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 248 "
            pdb=" OG1 THR B 252 "
     model   vdw
     2.294 2.440
  nonbonded pdb=" O   ILE A 248 "
            pdb=" OG1 THR A 252 "
     model   vdw
     2.294 2.440
  nonbonded pdb=" O   ILE C 248 "
            pdb=" OG1 THR C 252 "
     model   vdw
     2.294 2.440
  nonbonded pdb=" O   ILE D 248 "
            pdb=" OG1 THR D 252 "
     model   vdw
     2.295 2.440
  nonbonded pdb=" OE2 GLU D 277 "
            pdb=" OH  TYR D 342 "
     model   vdw
     2.347 2.440
  ... (remaining 87349 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:          6.200
  Check model and map are aligned:         0.150
  Set scattering table:                    0.100
  Process input model:                     28.470
  Find NCS groups from input model:        0.640
  Set up NCS constraints:                  0.050
  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:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
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      :  0.004   0.064  10672  Z= 0.279
  Angle     :  0.761   9.454  14464  Z= 0.441
  Chirality :  0.043   0.146   1644
  Planarity :  0.008   0.059   1880
  Dihedral  : 13.663  87.383   3984
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  7.82 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -2.21 (0.19), residues: 1364
  helix: -1.29 (0.15), residues: 672
  sheet: -2.19 (0.33), residues: 204
  loop : -1.04 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.003   TRP A 295 
   HIS   0.003   0.001   HIS B 245 
   PHE   0.016   0.002   PHE C 144 
   TYR   0.014   0.002   TYR A 213 
   ARG   0.003   0.000   ARG B  55 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 213
  time to evaluate  : 1.282 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 213
  average time/residue: 0.2676
  time to fit residues: 76.6452
Evaluate side-chains
  150 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 146
  time to evaluate  : 1.238 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0890
  time to fit residues: 2.2444
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    0.5980
   chunk 103 optimal weight:    0.8980
   chunk 57 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 106 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  60 GLN
B 125 GLN
B 324 GLN
A  60 GLN
A 125 GLN
A 324 GLN
C  60 GLN
C 125 GLN
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 324 GLN
D  60 GLN
D 125 GLN
D 324 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  10672  Z= 0.182
  Angle     :  0.507   6.801  14464  Z= 0.261
  Chirality :  0.040   0.121   1644
  Planarity :  0.004   0.040   1880
  Dihedral  :  4.283  15.831   1472
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.61 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.31 (0.22), residues: 1364
  helix:  0.75 (0.18), residues: 696
  sheet: -2.16 (0.32), residues: 224
  loop : -0.42 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP C 147 
   HIS   0.002   0.000   HIS B 156 
   PHE   0.007   0.001   PHE B 144 
   TYR   0.012   0.001   TYR A 213 
   ARG   0.005   0.000   ARG B  56 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 1.183 
Fit side-chains
  outliers start: 16
  outliers final: 8
  residues processed: 183
  average time/residue: 0.2633
  time to fit residues: 65.7667
Evaluate side-chains
  163 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 1.133 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1053
  time to fit residues: 3.0661
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 102 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0060
   chunk 123 optimal weight:    2.9990
   chunk 133 optimal weight:    8.9990
   chunk 110 optimal weight:    0.7980
   chunk 122 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.9400

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

Flipped N/Q/H residues before XYZ refinement:
B  50 ASN
B 274 GLN
B 324 GLN
A 274 GLN
A 324 GLN
C 231 ASN
C 274 GLN
C 324 GLN
D  50 ASN
D 274 GLN
D 324 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10672  Z= 0.184
  Angle     :  0.465   5.740  14464  Z= 0.241
  Chirality :  0.039   0.120   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  4.066  15.237   1472
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 13.13 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.69 (0.23), residues: 1364
  helix:  1.74 (0.19), residues: 696
  sheet: -2.14 (0.31), residues: 224
  loop : -0.02 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP D 147 
   HIS   0.002   0.001   HIS B 220 
   PHE   0.007   0.001   PHE B 144 
   TYR   0.013   0.001   TYR B 213 
   ARG   0.004   0.000   ARG C  56 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 1.273 
Fit side-chains
  outliers start: 10
  outliers final: 9
  residues processed: 170
  average time/residue: 0.2868
  time to fit residues: 66.2656
Evaluate side-chains
  159 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 1.368 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1337
  time to fit residues: 3.7004
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 124 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   chunk 117 optimal weight:    0.0570
   chunk 35 optimal weight:    2.9990
   chunk 109 optimal weight:    6.9990
   overall best weight:    1.8106

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
C  95 GLN
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10672  Z= 0.298
  Angle     :  0.507   6.733  14464  Z= 0.262
  Chirality :  0.041   0.124   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  4.140  16.213   1472
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.67 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.82 (0.23), residues: 1364
  helix:  1.95 (0.19), residues: 688
  sheet: -2.12 (0.33), residues: 204
  loop : -0.18 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP A 147 
   HIS   0.002   0.001   HIS C  20 
   PHE   0.008   0.001   PHE A 144 
   TYR   0.016   0.002   TYR C 213 
   ARG   0.006   0.001   ARG D  56 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 1.189 
Fit side-chains
  outliers start: 15
  outliers final: 5
  residues processed: 177
  average time/residue: 0.2899
  time to fit residues: 68.3860
Evaluate side-chains
  159 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 154
  time to evaluate  : 1.195 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1134
  time to fit residues: 2.6417
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 117 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  50 ASN
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  10672  Z= 0.173
  Angle     :  0.461   6.948  14464  Z= 0.235
  Chirality :  0.039   0.122   1644
  Planarity :  0.003   0.033   1880
  Dihedral  :  3.929  15.355   1472
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 13.85 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.22 (0.24), residues: 1364
  helix:  2.32 (0.19), residues: 688
  sheet: -2.01 (0.33), residues: 204
  loop : -0.04 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP B 147 
   HIS   0.002   0.001   HIS A 156 
   PHE   0.007   0.001   PHE D 144 
   TYR   0.011   0.001   TYR C 213 
   ARG   0.003   0.000   ARG A  42 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 169
  time to evaluate  : 1.089 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 172
  average time/residue: 0.3202
  time to fit residues: 73.3260
Evaluate side-chains
  162 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 1.119 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1157
  time to fit residues: 2.9872
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 131 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0060
   chunk 10 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 126 optimal weight:    7.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10672  Z= 0.163
  Angle     :  0.447   6.799  14464  Z= 0.231
  Chirality :  0.039   0.119   1644
  Planarity :  0.003   0.032   1880
  Dihedral  :  3.843  15.460   1472
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 15.11 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.24), residues: 1364
  helix:  2.53 (0.19), residues: 692
  sheet: -1.94 (0.34), residues: 204
  loop :  0.05 (0.31), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP D 147 
   HIS   0.002   0.001   HIS A 156 
   PHE   0.007   0.001   PHE A 144 
   TYR   0.011   0.001   TYR A 213 
   ARG   0.004   0.000   ARG C  42 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 1.255 
Fit side-chains
  outliers start: 10
  outliers final: 2
  residues processed: 166
  average time/residue: 0.3038
  time to fit residues: 66.6712
Evaluate side-chains
  148 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 1.325 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1471
  time to fit residues: 2.3602
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 96 optimal weight:    0.2980
   chunk 110 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 131 optimal weight:    0.0030
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0980
   chunk 60 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10672  Z= 0.139
  Angle     :  0.444   7.107  14464  Z= 0.228
  Chirality :  0.039   0.116   1644
  Planarity :  0.003   0.032   1880
  Dihedral  :  3.714  14.773   1472
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.74 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.65 (0.24), residues: 1364
  helix:  2.67 (0.19), residues: 692
  sheet: -1.78 (0.33), residues: 200
  loop :  0.09 (0.31), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 295 
   HIS   0.002   0.000   HIS B 219 
   PHE   0.008   0.001   PHE D 144 
   TYR   0.010   0.001   TYR A 173 
   ARG   0.004   0.000   ARG A  42 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 1.127 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 166
  average time/residue: 0.2927
  time to fit residues: 64.1838
Evaluate side-chains
  153 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 1.093 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1095
  time to fit residues: 2.6781
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0670
   chunk 83 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 119 optimal weight:    0.8980
   chunk 125 optimal weight:    0.1980
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10672  Z= 0.147
  Angle     :  0.436   6.500  14464  Z= 0.225
  Chirality :  0.039   0.115   1644
  Planarity :  0.003   0.031   1880
  Dihedral  :  3.656  14.697   1472
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 16.19 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.80 (0.24), residues: 1364
  helix:  2.78 (0.19), residues: 692
  sheet: -1.69 (0.34), residues: 200
  loop :  0.18 (0.31), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP C 147 
   HIS   0.002   0.000   HIS D 219 
   PHE   0.007   0.001   PHE D 144 
   TYR   0.012   0.001   TYR A 213 
   ARG   0.004   0.000   ARG C  42 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 152
  time to evaluate  : 1.246 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 156
  average time/residue: 0.3292
  time to fit residues: 68.0418
Evaluate side-chains
  149 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 1.268 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1148
  time to fit residues: 1.8901
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 125 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 110 optimal weight:    0.9990
   chunk 115 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0870
   chunk 80 optimal weight:    0.7980
   chunk 129 optimal weight:    0.8980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10672  Z= 0.162
  Angle     :  0.465   7.078  14464  Z= 0.241
  Chirality :  0.039   0.118   1644
  Planarity :  0.003   0.031   1880
  Dihedral  :  3.654  14.572   1472
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 16.46 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.87 (0.24), residues: 1364
  helix:  2.83 (0.19), residues: 692
  sheet: -1.46 (0.36), residues: 180
  loop :  0.02 (0.30), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A 295 
   HIS   0.002   0.000   HIS D 219 
   PHE   0.007   0.001   PHE C 144 
   TYR   0.015   0.001   TYR A 213 
   ARG   0.004   0.000   ARG C  42 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 146
  time to evaluate  : 1.184 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 147
  average time/residue: 0.3034
  time to fit residues: 58.9815
Evaluate side-chains
  145 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 140
  time to evaluate  : 1.249 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1241
  time to fit residues: 2.9903
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 135 optimal weight:    0.6980
   chunk 124 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10672  Z= 0.183
  Angle     :  0.471   7.180  14464  Z= 0.244
  Chirality :  0.039   0.120   1644
  Planarity :  0.003   0.031   1880
  Dihedral  :  3.700  14.685   1472
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.09 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.86 (0.24), residues: 1364
  helix:  2.84 (0.19), residues: 692
  sheet: -1.46 (0.36), residues: 180
  loop :  0.01 (0.30), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP C 147 
   HIS   0.002   0.000   HIS B 220 
   PHE   0.007   0.001   PHE C 144 
   TYR   0.019   0.001   TYR D 213 
   ARG   0.004   0.000   ARG A  56 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.091 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.3003
  time to fit residues: 56.5680
Evaluate side-chains
  136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.217 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6510
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 99 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0030
   chunk 29 optimal weight:    2.9990
   chunk 108 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.146617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.118986 restraints weight = 13006.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.05
r_work: 0.3322 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10672  Z= 0.163
  Angle     :  0.471   7.473  14464  Z= 0.244
  Chirality :  0.039   0.118   1644
  Planarity :  0.003   0.032   1880
  Dihedral  :  3.644  14.475   1472
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 17.27 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.91 (0.24), residues: 1364
  helix:  2.88 (0.19), residues: 692
  sheet: -1.44 (0.36), residues: 180
  loop :  0.03 (0.30), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 295 
   HIS   0.002   0.000   HIS B 219 
   PHE   0.007   0.001   PHE D 144 
   TYR   0.017   0.001   TYR D 213 
   ARG   0.003   0.000   ARG A  56 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2427.23 seconds
wall clock time: 45 minutes 15.56 seconds (2715.56 seconds total)