Starting phenix.real_space_refine
on Sat Dec  9 17:18:21 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efl_28085/12_2023/8efl_28085_updated.pdb"
  }
  resolution = 3.2
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      98      5.16       5
     Cl      6      4.86       5
     C    7645      2.51       5
     N    1908      2.21       5
     O    2093      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R ARG   97": "NH1" <-> "NH2"
    Residue "R ARG  213": "NH1" <-> "NH2"
    Residue "R ARG  260": "NH1" <-> "NH2"
    Residue "R ARG  275": "NH1" <-> "NH2"
    Residue "R ARG  282": "NH1" <-> "NH2"
    Residue "R ARG  347": "NH1" <-> "NH2"
    Residue "A TYR  287": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   46": "NH1" <-> "NH2"
    Residue "C ARG   27": "NH1" <-> "NH2"
    Residue "E PHE   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ARG  265": "NH1" <-> "NH2"
    Residue "M ARG  275": "NH1" <-> "NH2"
    Residue "M ARG  347": "NH1" <-> "NH2"
  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: 11750
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "R"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2309
          Classifications: {'peptide': 287}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276}
    Chain: "A"
      Number of atoms: 1816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1816
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2576
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
    Chain: "C"
      Number of atoms: 437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 437
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "E"
      Number of atoms: 1788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1788
          Classifications: {'peptide': 233}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2309
          Classifications: {'peptide': 287}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276}
    Chain: "F"
      Number of atoms: 183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 183
          Classifications: {'peptide': 23}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 22}
    Chain: "R"
      Number of atoms: 166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 166
          Unusual residues: {'CLR': 5, 'WH9': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "M"
      Number of atoms: 166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 166
          Unusual residues: {'CLR': 5, 'WH9': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 6.53, per 1000 atoms: 0.56
  Number of scatterers: 11750
  At special positions: 0
  Unit cell: (106.029, 116.739, 153.153, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      6     17.00
     S      98     16.00
     O    2093      8.00
     N    1908      7.00
     C    7645      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 142 " - pdb=" SG  CYS R 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 160 " - pdb=" SG  CYS E 230 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 142 " - pdb=" SG  CYS M 219 " distance=2.03

  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: 4.34
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2734

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      36 helices and 15 sheets defined
      45.4% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.13
  Creating SS restraints...
    Processing helix  chain 'R' and resid 67 through 97
    Processing helix  chain 'R' and resid 104 through 121
    Processing helix  chain 'R' and resid 123 through 132
    Processing helix  chain 'R' and resid 139 through 172
    Processing helix  chain 'R' and resid 174 through 180
      removed outlier: 3.826A  pdb=" N   ASP R 179 " --> pdb=" O   VAL R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 207
      removed outlier: 4.031A  pdb=" N   ILE R 200 " --> pdb=" O   LEU R 196 " (cutoff:3.500A)
      Proline residue:  R 203  - end of helix
    Processing helix  chain 'R' and resid 227 through 263
      removed outlier: 5.333A  pdb=" N   MET R 245 " --> pdb=" O   PHE R 241 " (cutoff:3.500A)
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 271 through 307
      Proline residue:  R 297  - end of helix
    Processing helix  chain 'R' and resid 314 through 338
      removed outlier: 3.939A  pdb=" N   ASN R 330 " --> pdb=" O   LEU R 326 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   SER R 331 " --> pdb=" O   GLY R 327 " (cutoff:3.500A)
      Proline residue:  R 335  - end of helix
    Processing helix  chain 'R' and resid 343 through 351
    Processing helix  chain 'A' and resid 7 through 32
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 46 through 54
    Processing helix  chain 'A' and resid 208 through 216
      removed outlier: 4.652A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   CYS A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   PHE A 215 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLU A 216 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 229
      No H-bonds generated for 'chain 'A' and resid 227 through 229'
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 280
    Processing helix  chain 'A' and resid 296 through 309
    Processing helix  chain 'A' and resid 328 through 351
      removed outlier: 3.646A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 25
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'C' and resid 11 through 23
    Processing helix  chain 'C' and resid 30 through 43
    Processing helix  chain 'E' and resid 29 through 31
      No H-bonds generated for 'chain 'E' and resid 29 through 31'
    Processing helix  chain 'E' and resid 53 through 55
      No H-bonds generated for 'chain 'E' and resid 53 through 55'
    Processing helix  chain 'E' and resid 62 through 64
      No H-bonds generated for 'chain 'E' and resid 62 through 64'
    Processing helix  chain 'M' and resid 67 through 97
    Processing helix  chain 'M' and resid 104 through 132
      removed outlier: 3.995A  pdb=" N   THR M 122 " --> pdb=" O   LEU M 118 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   LEU M 123 " --> pdb=" O   ALA M 119 " (cutoff:3.500A)
      Proline residue:  M 124  - end of helix
    Processing helix  chain 'M' and resid 139 through 172
      removed outlier: 3.689A  pdb=" N   PHE M 154 " --> pdb=" O   TYR M 150 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 174 through 180
      removed outlier: 3.807A  pdb=" N   ASP M 179 " --> pdb=" O   VAL M 175 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 183 through 207
      removed outlier: 3.745A  pdb=" N   ILE M 200 " --> pdb=" O   LEU M 196 " (cutoff:3.500A)
      Proline residue:  M 203  - end of helix
    Processing helix  chain 'M' and resid 227 through 263
      removed outlier: 5.201A  pdb=" N   MET M 245 " --> pdb=" O   PHE M 241 " (cutoff:3.500A)
      Proline residue:  M 246  - end of helix
    Processing helix  chain 'M' and resid 271 through 307
      Proline residue:  M 297  - end of helix
    Processing helix  chain 'M' and resid 314 through 339
      removed outlier: 3.745A  pdb=" N   SER M 331 " --> pdb=" O   GLY M 327 " (cutoff:3.500A)
      Proline residue:  M 335  - end of helix
    Processing helix  chain 'M' and resid 343 through 351
    Processing helix  chain 'F' and resid 333 through 351
    Processing sheet with id=  A, first strand: chain 'R' and resid 208 through 213
    Processing sheet with id=  B, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.749A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.772A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.734A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.791A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.159A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.809A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.852A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.859A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=  K, first strand: chain 'E' and resid 10 through 13
      removed outlier: 3.672A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 116 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   THR E 118 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   SER E 120 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ALA E  40 " --> pdb=" O   LEU E  45 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LEU E  45 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'E' and resid 147 through 149
      removed outlier: 6.949A  pdb=" N   LYS E 245 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  L
    Processing sheet with id=  M, first strand: chain 'E' and resid 156 through 160
    Processing sheet with id=  N, first strand: chain 'E' and resid 226 through 232
      removed outlier: 5.889A  pdb=" N   LEU E 179 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   LEU E 188 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ARG E 181 " --> pdb=" O   PRO E 186 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'M' and resid 208 through 213

    633 hydrogen bonds defined for protein.
    1851 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: 3.73

  Time building geometry restraints manager: 4.68 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1808
        1.30 -     1.43: 3148
        1.43 -     1.56: 6917
        1.56 -     1.69: 9
        1.69 -     1.82: 151
  Bond restraints: 12033
  Sorted by residual:
  bond pdb=" C03 WH9 R 401 "
       pdb=" N01 WH9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.477  1.316  0.161 2.00e-02 2.50e+03 6.50e+01
  bond pdb=" C03 WH9 M 401 "
       pdb=" N01 WH9 M 401 "
    ideal  model  delta    sigma   weight residual
    1.477  1.316  0.161 2.00e-02 2.50e+03 6.46e+01
  bond pdb=" C05 WH9 R 401 "
       pdb=" N02 WH9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.477  1.348  0.129 2.00e-02 2.50e+03 4.18e+01
  bond pdb=" C05 WH9 M 401 "
       pdb=" N02 WH9 M 401 "
    ideal  model  delta    sigma   weight residual
    1.477  1.348  0.129 2.00e-02 2.50e+03 4.13e+01
  bond pdb=" C07 WH9 M 401 "
       pdb=" N01 WH9 M 401 "
    ideal  model  delta    sigma   weight residual
    1.431  1.322  0.109 2.00e-02 2.50e+03 2.95e+01
  ... (remaining 12028 not shown)

  Histogram of bond angle deviations from ideal:
       98.92 -   105.95: 250
      105.95 -   112.98: 6676
      112.98 -   120.02: 4018
      120.02 -   127.05: 5298
      127.05 -   134.08: 137
  Bond angle restraints: 16379
  Sorted by residual:
  angle pdb=" C   ARG E 192 "
        pdb=" N   MET E 193 "
        pdb=" CA  MET E 193 "
      ideal   model   delta    sigma   weight residual
     121.54  130.25   -8.71 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" C06 WH9 R 401 "
        pdb=" C04 WH9 R 401 "
        pdb="CL2  WH9 R 401 "
      ideal   model   delta    sigma   weight residual
     131.83  120.28   11.55 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C06 WH9 M 401 "
        pdb=" C04 WH9 M 401 "
        pdb="CL2  WH9 M 401 "
      ideal   model   delta    sigma   weight residual
     131.83  120.29   11.54 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C02 WH9 M 401 "
        pdb=" C04 WH9 M 401 "
        pdb="CL2  WH9 M 401 "
      ideal   model   delta    sigma   weight residual
     108.07  119.31  -11.24 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" C02 WH9 R 401 "
        pdb=" C04 WH9 R 401 "
        pdb="CL2  WH9 R 401 "
      ideal   model   delta    sigma   weight residual
     108.07  119.22  -11.15 3.00e+00 1.11e-01 1.38e+01
  ... (remaining 16374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.15: 7219
       14.15 -    28.29: 293
       28.29 -    42.44: 62
       42.44 -    56.58: 15
       56.58 -    70.73: 2
  Dihedral angle restraints: 7591
    sinusoidal: 3363
      harmonic: 4228
  Sorted by residual:
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.57   21.43     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.40   18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  ILE B  81 "
           pdb=" C   ILE B  81 "
           pdb=" N   TRP B  82 "
           pdb=" CA  TRP B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.07  -15.93     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 7588 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1697
       0.088 -    0.176: 170
       0.176 -    0.264: 25
       0.264 -    0.352: 8
       0.352 -    0.440: 11
  Chirality restraints: 1911
  Sorted by residual:
  chirality pdb=" C14 CLR M 405 "
            pdb=" C13 CLR M 405 "
            pdb=" C15 CLR M 405 "
            pdb=" C8  CLR M 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.76    0.44 2.00e-01 2.50e+01 4.83e+00
  chirality pdb=" C14 CLR M 402 "
            pdb=" C13 CLR M 402 "
            pdb=" C15 CLR M 402 "
            pdb=" C8  CLR M 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.46e+00
  chirality pdb=" C14 CLR R 403 "
            pdb=" C13 CLR R 403 "
            pdb=" C15 CLR R 403 "
            pdb=" C8  CLR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.73    0.41 2.00e-01 2.50e+01 4.29e+00
  ... (remaining 1908 not shown)

  Planarity restraints: 1969
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.050 5.00e-02 4.00e+02   7.53e-02 9.07e+00
        pdb=" N   PRO B 236 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 278 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.86e+00
        pdb=" C   ARG R 278 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ARG R 278 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG R 279 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B 194 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1966 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2218
        2.79 -     3.32: 10679
        3.32 -     3.84: 19103
        3.84 -     4.37: 21544
        4.37 -     4.90: 38737
  Nonbonded interactions: 92281
  Sorted by model distance:
  nonbonded pdb=" O   ALA M 325 "
            pdb=" OG1 THR M 329 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" OG  SER E 205 "
            pdb=" OG1 THR E 216 "
     model   vdw
     2.279 2.440
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.304 2.440
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.321 2.440
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.330 2.440
  ... (remaining 92276 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 'M'
  selection = chain 'R'
}

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:             0.420
  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:             0.000
  Extract box with map and model:          2.950
  Check model and map are aligned:         0.170
  Set scattering table:                    0.110
  Process input model:                     33.840
  Find NCS groups from input model:        0.490
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
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      :  0.006   0.161  12033  Z= 0.347
  Angle     :  0.894  11.546  16379  Z= 0.468
  Chirality :  0.066   0.440   1911
  Planarity :  0.006   0.075   1969
  Dihedral  :  8.667  70.730   4848
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  0.35 (0.20), residues: 1428
  helix:  1.12 (0.17), residues: 664
  sheet:  0.57 (0.30), residues: 283
  loop : -1.19 (0.24), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.027   0.002   TRP E 111 
   HIS   0.005   0.001   HIS B  54 
   PHE   0.026   0.002   PHE A 189 
   TYR   0.024   0.002   TYR R 108 
   ARG   0.005   0.000   ARG B 314 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.090 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2475
  time to fit residues: 84.3548
Evaluate side-chains
  156 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.316 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.8503
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 119 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 110 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    0.2980
   chunk 82 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
R 111 ASN
R 173 HIS
R 190 ASN
B  35 ASN
B  62 HIS
B  88 ASN
B  91 HIS
B 155 ASN
B 266 HIS
B 293 ASN
** E  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 180 GLN
M 106 ASN
M 330 ASN
M 334 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12033  Z= 0.159
  Angle     :  0.476   6.672  16379  Z= 0.246
  Chirality :  0.039   0.149   1911
  Planarity :  0.004   0.057   1969
  Dihedral  :  6.335  69.639   2236
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  6.88 %
    Favored  : 91.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  1.61 (0.21), residues: 1428
  helix:  2.59 (0.18), residues: 668
  sheet:  0.50 (0.30), residues: 282
  loop : -0.83 (0.25), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B 169 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.021   0.001   PHE A 189 
   TYR   0.012   0.001   TYR M 168 
   ARG   0.003   0.000   ARG B 129 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 1.183 
Fit side-chains
  outliers start: 26
  outliers final: 15
  residues processed: 184
  average time/residue: 0.2238
  time to fit residues: 60.6480
Evaluate side-chains
  156 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 1.421 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 0
  residues processed: 15
  average time/residue: 0.1039
  time to fit residues: 4.7459
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 106 optimal weight:    0.0010
   chunk 87 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 128 optimal weight:    1.9990
   chunk 138 optimal weight:    0.9990
   chunk 114 optimal weight:    4.9990
   chunk 127 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   overall best weight:    1.3792

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
E 180 GLN
M 190 ASN
M 334 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
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      :  0.004   0.038  12033  Z= 0.233
  Angle     :  0.522   7.414  16379  Z= 0.268
  Chirality :  0.040   0.151   1911
  Planarity :  0.004   0.049   1969
  Dihedral  :  6.723  69.602   2236
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  8.70 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  1.78 (0.21), residues: 1428
  helix:  2.81 (0.19), residues: 662
  sheet:  0.41 (0.29), residues: 289
  loop : -0.71 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.002   TRP B  82 
   HIS   0.005   0.001   HIS B  54 
   PHE   0.021   0.002   PHE R 154 
   TYR   0.014   0.002   TYR R 301 
   ARG   0.004   0.000   ARG B 197 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 1.457 
Fit side-chains
  outliers start: 21
  outliers final: 11
  residues processed: 152
  average time/residue: 0.2392
  time to fit residues: 52.9561
Evaluate side-chains
  139 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 1.247 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1073
  time to fit residues: 3.9739
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 126 optimal weight:    0.9990
   chunk 96 optimal weight:   10.0000
   chunk 66 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0050
   chunk 128 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
M 111 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12033  Z= 0.171
  Angle     :  0.468   6.205  16379  Z= 0.240
  Chirality :  0.038   0.147   1911
  Planarity :  0.003   0.043   1969
  Dihedral  :  6.459  67.256   2236
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.97 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  2.00 (0.22), residues: 1428
  helix:  2.97 (0.19), residues: 662
  sheet:  0.56 (0.29), residues: 285
  loop : -0.58 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.001   TRP B  82 
   HIS   0.002   0.001   HIS A 213 
   PHE   0.018   0.001   PHE R 154 
   TYR   0.012   0.001   TYR B  59 
   ARG   0.004   0.000   ARG B 197 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 1.249 
Fit side-chains
  outliers start: 14
  outliers final: 10
  residues processed: 150
  average time/residue: 0.2250
  time to fit residues: 50.0725
Evaluate side-chains
  144 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 1.329 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1053
  time to fit residues: 3.7643
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 113 optimal weight:    0.7980
   chunk 77 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 101 optimal weight:   20.0000
   chunk 56 optimal weight:    2.9990
   chunk 116 optimal weight:    0.6980
   chunk 94 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 69 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12033  Z= 0.190
  Angle     :  0.473   6.125  16379  Z= 0.244
  Chirality :  0.039   0.141   1911
  Planarity :  0.003   0.041   1969
  Dihedral  :  6.538  64.957   2236
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.68 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  2.01 (0.22), residues: 1428
  helix:  2.97 (0.19), residues: 662
  sheet:  0.40 (0.29), residues: 290
  loop : -0.47 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP B  82 
   HIS   0.002   0.001   HIS B  62 
   PHE   0.017   0.001   PHE R 154 
   TYR   0.013   0.001   TYR E  94 
   ARG   0.003   0.000   ARG B 197 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 1.268 
Fit side-chains
  outliers start: 14
  outliers final: 10
  residues processed: 143
  average time/residue: 0.2284
  time to fit residues: 48.6687
Evaluate side-chains
  143 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 1.228 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1129
  time to fit residues: 3.8079
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 122 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 136 optimal weight:    3.9990
   chunk 113 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 131 optimal weight:    0.4980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12033  Z= 0.225
  Angle     :  0.498   6.794  16379  Z= 0.255
  Chirality :  0.039   0.139   1911
  Planarity :  0.004   0.039   1969
  Dihedral  :  6.732  64.281   2236
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.23 %
    Favored  : 87.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  1.97 (0.22), residues: 1428
  helix:  2.96 (0.19), residues: 657
  sheet:  0.38 (0.30), residues: 287
  loop : -0.46 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  82 
   HIS   0.002   0.001   HIS B  54 
   PHE   0.018   0.001   PHE R 154 
   TYR   0.013   0.001   TYR E  94 
   ARG   0.004   0.000   ARG A 208 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 1.436 
Fit side-chains
  outliers start: 14
  outliers final: 10
  residues processed: 151
  average time/residue: 0.2554
  time to fit residues: 55.7148
Evaluate side-chains
  138 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 1.261 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1206
  time to fit residues: 3.9183
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 99 optimal weight:    2.9990
   chunk 114 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0770
   chunk 135 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0040
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7554

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
E 172 ASN
M 106 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12033  Z= 0.154
  Angle     :  0.462   6.862  16379  Z= 0.237
  Chirality :  0.038   0.139   1911
  Planarity :  0.003   0.039   1969
  Dihedral  :  6.382  61.926   2236
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 12.26 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.22), residues: 1428
  helix:  3.02 (0.19), residues: 663
  sheet:  0.40 (0.30), residues: 284
  loop : -0.40 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.001   TRP B  82 
   HIS   0.002   0.001   HIS A 213 
   PHE   0.014   0.001   PHE A 189 
   TYR   0.012   0.001   TYR M 151 
   ARG   0.004   0.000   ARG B 129 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 1.309 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 139
  average time/residue: 0.2502
  time to fit residues: 49.9525
Evaluate side-chains
  136 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 1.255 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1152
  time to fit residues: 2.8745
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 81 optimal weight:    0.0470
   chunk 40 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 86 optimal weight:   20.0000
   chunk 92 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 106 optimal weight:   10.0000
   chunk 123 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   overall best weight:    0.9282

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12033  Z= 0.170
  Angle     :  0.468   7.242  16379  Z= 0.239
  Chirality :  0.038   0.142   1911
  Planarity :  0.003   0.040   1969
  Dihedral  :  6.218  60.661   2236
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 12.74 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  2.06 (0.22), residues: 1428
  helix:  3.03 (0.19), residues: 665
  sheet:  0.42 (0.30), residues: 279
  loop : -0.48 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.001   TRP B  82 
   HIS   0.002   0.001   HIS A 213 
   PHE   0.014   0.001   PHE A 189 
   TYR   0.013   0.001   TYR R 212 
   ARG   0.004   0.000   ARG B 129 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 1.474 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 144
  average time/residue: 0.2511
  time to fit residues: 52.1707
Evaluate side-chains
  138 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 1.306 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1041
  time to fit residues: 3.2470
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 126 optimal weight:    0.8980
   chunk 130 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 114 optimal weight:    0.0030
   chunk 119 optimal weight:    0.5980
   chunk 83 optimal weight:    3.9990
   chunk 133 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
E 172 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12033  Z= 0.144
  Angle     :  0.453   6.946  16379  Z= 0.232
  Chirality :  0.038   0.149   1911
  Planarity :  0.003   0.040   1969
  Dihedral  :  6.046  57.330   2236
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.21 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  2.12 (0.22), residues: 1428
  helix:  3.11 (0.19), residues: 664
  sheet:  0.47 (0.30), residues: 279
  loop : -0.47 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.001   TRP B  82 
   HIS   0.002   0.000   HIS B 311 
   PHE   0.013   0.001   PHE A 189 
   TYR   0.013   0.001   TYR R 212 
   ARG   0.004   0.000   ARG B 129 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 1.260 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 133
  average time/residue: 0.2724
  time to fit residues: 52.1062
Evaluate side-chains
  134 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 1.374 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1427
  time to fit residues: 2.5017
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 140 optimal weight:    0.9990
   chunk 129 optimal weight:    0.9990
   chunk 111 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 86 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 119 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12033  Z= 0.187
  Angle     :  0.479   6.620  16379  Z= 0.245
  Chirality :  0.039   0.151   1911
  Planarity :  0.003   0.039   1969
  Dihedral  :  6.136  57.546   2236
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 13.21 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.22), residues: 1428
  helix:  3.07 (0.19), residues: 660
  sheet:  0.38 (0.30), residues: 281
  loop : -0.45 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.001   TRP B  82 
   HIS   0.002   0.001   HIS B 311 
   PHE   0.014   0.001   PHE A 189 
   TYR   0.014   0.001   TYR E  94 
   ARG   0.005   0.000   ARG B 129 

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 1.301 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 137
  average time/residue: 0.2771
  time to fit residues: 56.6400
Evaluate side-chains
  136 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 1.276 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1260
  time to fit residues: 2.8951
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 112 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 115 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0270
   chunk 20 optimal weight:    2.9990
   chunk 98 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.204346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.164443 restraints weight = 12100.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.75
r_work: 0.3174 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12033  Z= 0.132
  Angle     :  0.451   7.542  16379  Z= 0.231
  Chirality :  0.038   0.146   1911
  Planarity :  0.003   0.039   1969
  Dihedral  :  5.827  53.162   2236
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 13.13 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    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:  2.16 (0.22), residues: 1428
  helix:  3.14 (0.19), residues: 664
  sheet:  0.49 (0.31), residues: 279
  loop : -0.46 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.001   TRP B  82 
   HIS   0.001   0.000   HIS E  35 
   PHE   0.012   0.001   PHE A 189 
   TYR   0.013   0.001   TYR M 151 
   ARG   0.005   0.000   ARG B 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2586.81 seconds
wall clock time: 48 minutes 5.94 seconds (2885.94 seconds total)