Starting phenix.real_space_refine
on Fri Dec  8 05:37:21 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/12_2023/7cye_30498_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/12_2023/7cye_30498.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/12_2023/7cye_30498.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/12_2023/7cye_30498.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/12_2023/7cye_30498_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/12_2023/7cye_30498_neut.pdb"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      39      5.16       5
     C    4797      2.51       5
     N    1146      2.21       5
     O    1281      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  162": "NH1" <-> "NH2"
    Residue "A ARG  252": "NH1" <-> "NH2"
    Residue "A ARG  274": "NH1" <-> "NH2"
    Residue "A TYR  304": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  333": "NH1" <-> "NH2"
    Residue "A TYR  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  162": "NH1" <-> "NH2"
    Residue "B ARG  252": "NH1" <-> "NH2"
    Residue "B ARG  274": "NH1" <-> "NH2"
    Residue "B ARG  333": "NH1" <-> "NH2"
    Residue "B TYR  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  162": "NH1" <-> "NH2"
    Residue "C ARG  252": "NH1" <-> "NH2"
    Residue "C ARG  274": "NH1" <-> "NH2"
    Residue "C TYR  304": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  333": "NH1" <-> "NH2"
    Residue "C TYR  344": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7263
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2421
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 17, 'TRANS': 308}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2421
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 17, 'TRANS': 308}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2421
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 17, 'TRANS': 308}
          Chain breaks: 1
  Time building chain proxies: 4.28, per 1000 atoms: 0.59
  Number of scatterers: 7263
  At special positions: 0
  Unit cell: (96.235, 100.287, 69.897, 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      39     16.00
     O    1281      8.00
     N    1146      7.00
     C    4797      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: 2.54
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1764

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 0 sheets defined
      62.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 15
      removed outlier: 3.977A  pdb=" N   THR A   9 " --> pdb=" O   SER A   5 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A  10 " --> pdb=" O   ASN A   6 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 31
      removed outlier: 3.844A  pdb=" N   LEU A  23 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL A  28 " --> pdb=" O   ILE A  24 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE A  29 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 3.541A  pdb=" N   THR A  44 " --> pdb=" O   ALA A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.558A  pdb=" N   ILE A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG A  63 " --> pdb=" O   GLY A  59 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 92
      removed outlier: 3.522A  pdb=" N   SER A  77 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU A  80 " --> pdb=" O   PHE A  76 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   VAL A  85 " --> pdb=" O   GLY A  81 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   PHE A  86 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 104
    Processing helix  chain 'A' and resid 120 through 126
      removed outlier: 3.815A  pdb=" N   GLU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 140
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 3.549A  pdb=" N   VAL A 149 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL A 154 " --> pdb=" O   THR A 150 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 220
      removed outlier: 4.174A  pdb=" N   GLU A 217 " --> pdb=" O   PRO A 213 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   SER A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 236
      removed outlier: 3.503A  pdb=" N   LEU A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 265
      removed outlier: 3.752A  pdb=" N   SER A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE A 257 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY A 263 " --> pdb=" O   MET A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 277
      removed outlier: 3.576A  pdb=" N   GLY A 271 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG A 274 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   LYS A 275 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   VAL A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 297
      Proline residue:  A 288  - end of helix
      removed outlier: 4.382A  pdb=" N   GLY A 292 " --> pdb=" O   PRO A 288 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 294 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA A 295 " --> pdb=" O   HIS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
      removed outlier: 3.849A  pdb=" N   ILE A 301 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 302 " --> pdb=" O   GLY A 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 302'
    Processing helix  chain 'A' and resid 309 through 318
      removed outlier: 3.717A  pdb=" N   VAL A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 359
    Processing helix  chain 'A' and resid 360 through 371
      removed outlier: 3.663A  pdb=" N   LEU A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 15
      removed outlier: 3.976A  pdb=" N   THR B   9 " --> pdb=" O   SER B   5 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP B  10 " --> pdb=" O   ASN B   6 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY B  13 " --> pdb=" O   THR B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 31
      removed outlier: 3.844A  pdb=" N   LEU B  23 " --> pdb=" O   THR B  19 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B  28 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE B  29 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 45
      removed outlier: 3.542A  pdb=" N   THR B  44 " --> pdb=" O   ALA B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.558A  pdb=" N   ILE B  62 " --> pdb=" O   GLY B  58 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG B  63 " --> pdb=" O   GLY B  59 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASN B  64 " --> pdb=" O   MET B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 92
      removed outlier: 3.522A  pdb=" N   SER B  77 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU B  80 " --> pdb=" O   PHE B  76 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   VAL B  85 " --> pdb=" O   GLY B  81 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE B  86 " --> pdb=" O   ILE B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 104
    Processing helix  chain 'B' and resid 120 through 126
      removed outlier: 3.815A  pdb=" N   GLU B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 140
    Processing helix  chain 'B' and resid 144 through 161
      removed outlier: 3.549A  pdb=" N   VAL B 149 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR B 150 " --> pdb=" O   PRO B 146 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA B 151 " --> pdb=" O   ALA B 147 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 154 " --> pdb=" O   THR B 150 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 220
      removed outlier: 4.173A  pdb=" N   GLU B 217 " --> pdb=" O   PRO B 213 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   SER B 218 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 236
      removed outlier: 3.503A  pdb=" N   LEU B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLY B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 265
      removed outlier: 3.752A  pdb=" N   SER B 256 " --> pdb=" O   ARG B 252 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE B 257 " --> pdb=" O   GLY B 253 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY B 263 " --> pdb=" O   MET B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 277
      removed outlier: 3.575A  pdb=" N   GLY B 271 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG B 274 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LYS B 275 " --> pdb=" O   GLY B 271 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL B 276 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 297
      Proline residue:  B 288  - end of helix
      removed outlier: 4.382A  pdb=" N   GLY B 292 " --> pdb=" O   PRO B 288 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE B 293 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B 294 " --> pdb=" O   VAL B 290 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 295 " --> pdb=" O   HIS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 302
      removed outlier: 3.846A  pdb=" N   ILE B 301 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 302 " --> pdb=" O   GLY B 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 302'
    Processing helix  chain 'B' and resid 309 through 318
      removed outlier: 3.717A  pdb=" N   VAL B 314 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL B 315 " --> pdb=" O   GLY B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 359
    Processing helix  chain 'B' and resid 360 through 371
      removed outlier: 3.663A  pdb=" N   LEU B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 15
      removed outlier: 3.975A  pdb=" N   THR C   9 " --> pdb=" O   SER C   5 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP C  10 " --> pdb=" O   ASN C   6 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY C  13 " --> pdb=" O   THR C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 31
      removed outlier: 3.844A  pdb=" N   LEU C  23 " --> pdb=" O   THR C  19 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL C  28 " --> pdb=" O   ILE C  24 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE C  29 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 45
      removed outlier: 3.541A  pdb=" N   THR C  44 " --> pdb=" O   ALA C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 64
      removed outlier: 3.558A  pdb=" N   ILE C  62 " --> pdb=" O   GLY C  58 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ARG C  63 " --> pdb=" O   GLY C  59 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN C  64 " --> pdb=" O   MET C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 92
      removed outlier: 3.522A  pdb=" N   SER C  77 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE C  79 " --> pdb=" O   ALA C  75 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU C  80 " --> pdb=" O   PHE C  76 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE C  84 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL C  85 " --> pdb=" O   GLY C  81 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   PHE C  86 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 104
    Processing helix  chain 'C' and resid 120 through 126
      removed outlier: 3.815A  pdb=" N   GLU C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 140
    Processing helix  chain 'C' and resid 144 through 161
      removed outlier: 3.550A  pdb=" N   VAL C 149 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR C 150 " --> pdb=" O   PRO C 146 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA C 151 " --> pdb=" O   ALA C 147 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL C 154 " --> pdb=" O   THR C 150 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU C 159 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 220
      removed outlier: 4.174A  pdb=" N   GLU C 217 " --> pdb=" O   PRO C 213 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   SER C 218 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 236
      removed outlier: 3.503A  pdb=" N   LEU C 228 " --> pdb=" O   LEU C 224 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLY C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 265
      removed outlier: 3.752A  pdb=" N   SER C 256 " --> pdb=" O   ARG C 252 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE C 257 " --> pdb=" O   GLY C 253 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY C 263 " --> pdb=" O   MET C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 277
      removed outlier: 3.576A  pdb=" N   GLY C 271 " --> pdb=" O   TRP C 267 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG C 274 " --> pdb=" O   ILE C 270 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   LYS C 275 " --> pdb=" O   GLY C 271 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   VAL C 276 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA C 277 " --> pdb=" O   LEU C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 297
      Proline residue:  C 288  - end of helix
      removed outlier: 4.382A  pdb=" N   GLY C 292 " --> pdb=" O   PRO C 288 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE C 294 " --> pdb=" O   VAL C 290 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA C 295 " --> pdb=" O   HIS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 301
      removed outlier: 3.831A  pdb=" N   ILE C 301 " --> pdb=" O   LEU C 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 298 through 301'
    Processing helix  chain 'C' and resid 309 through 318
      removed outlier: 3.717A  pdb=" N   VAL C 314 " --> pdb=" O   LEU C 310 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL C 315 " --> pdb=" O   GLY C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 351 through 359
    Processing helix  chain 'C' and resid 360 through 371
      removed outlier: 3.662A  pdb=" N   LEU C 371 " --> pdb=" O   LEU C 367 " (cutoff:3.500A)

    267 hydrogen bonds defined for protein.
    756 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: 1.41

  Time building geometry restraints manager: 2.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2089
        1.34 -     1.45: 1256
        1.45 -     1.57: 3996
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 7416
  Sorted by residual:
  bond pdb=" N   ILE B 301 "
       pdb=" CA  ILE B 301 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.09e-02 8.42e+03 9.31e+00
  bond pdb=" N   ILE A 301 "
       pdb=" CA  ILE A 301 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.033 1.22e-02 6.72e+03 7.53e+00
  bond pdb=" N   TYR B 304 "
       pdb=" CA  TYR B 304 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.16e-02 7.43e+03 6.51e+00
  bond pdb=" N   THR A 306 "
       pdb=" CA  THR A 306 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.19e+00
  bond pdb=" N   TYR A 304 "
       pdb=" CA  TYR A 304 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.19e-02 7.06e+03 5.96e+00
  ... (remaining 7411 not shown)

  Histogram of bond angle deviations from ideal:
       97.81 -   106.49: 277
      106.49 -   115.17: 4443
      115.17 -   123.84: 5128
      123.84 -   132.52: 237
      132.52 -   141.20: 19
  Bond angle restraints: 10104
  Sorted by residual:
  angle pdb=" C   PHE B 308 "
        pdb=" N   SER B 309 "
        pdb=" CA  SER B 309 "
      ideal   model   delta    sigma   weight residual
     121.54  141.20  -19.66 1.91e+00 2.74e-01 1.06e+02
  angle pdb=" N   ILE C 357 "
        pdb=" CA  ILE C 357 "
        pdb=" C   ILE C 357 "
      ideal   model   delta    sigma   weight residual
     113.53  106.04    7.49 9.80e-01 1.04e+00 5.84e+01
  angle pdb=" N   ILE A 357 "
        pdb=" CA  ILE A 357 "
        pdb=" C   ILE A 357 "
      ideal   model   delta    sigma   weight residual
     113.53  106.08    7.45 9.80e-01 1.04e+00 5.79e+01
  angle pdb=" N   ILE B 357 "
        pdb=" CA  ILE B 357 "
        pdb=" C   ILE B 357 "
      ideal   model   delta    sigma   weight residual
     113.53  106.11    7.42 9.80e-01 1.04e+00 5.73e+01
  angle pdb=" C   GLN C  16 "
        pdb=" N   SER C  17 "
        pdb=" CA  SER C  17 "
      ideal   model   delta    sigma   weight residual
     120.68  131.37  -10.69 1.52e+00 4.33e-01 4.94e+01
  ... (remaining 10099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.02: 3704
       11.02 -    22.03: 422
       22.03 -    33.05: 154
       33.05 -    44.06: 65
       44.06 -    55.08: 14
  Dihedral angle restraints: 4359
    sinusoidal: 1596
      harmonic: 2763
  Sorted by residual:
  dihedral pdb=" CA  PRO B  96 "
           pdb=" C   PRO B  96 "
           pdb=" N   ASN B  97 "
           pdb=" CA  ASN B  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.05  -27.95     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  PRO A  96 "
           pdb=" C   PRO A  96 "
           pdb=" N   ASN A  97 "
           pdb=" CA  ASN A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.06  -27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  PRO C  96 "
           pdb=" C   PRO C  96 "
           pdb=" N   ASN C  97 "
           pdb=" CA  ASN C  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.13  -27.87     0      5.00e+00 4.00e-02 3.11e+01
  ... (remaining 4356 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1037
       0.088 -    0.176: 193
       0.176 -    0.264: 12
       0.264 -    0.352: 3
       0.352 -    0.441: 3
  Chirality restraints: 1248
  Sorted by residual:
  chirality pdb=" CB  ILE A 361 "
            pdb=" CA  ILE A 361 "
            pdb=" CG1 ILE A 361 "
            pdb=" CG2 ILE A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.44 2.00e-01 2.50e+01 4.85e+00
  chirality pdb=" CB  ILE C 361 "
            pdb=" CA  ILE C 361 "
            pdb=" CG1 ILE C 361 "
            pdb=" CG2 ILE C 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.44 2.00e-01 2.50e+01 4.84e+00
  chirality pdb=" CB  ILE B 361 "
            pdb=" CA  ILE B 361 "
            pdb=" CG1 ILE B 361 "
            pdb=" CG2 ILE B 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.81e+00
  ... (remaining 1245 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 329 "    0.055 5.00e-02 4.00e+02   8.26e-02 1.09e+01
        pdb=" N   PRO C 330 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO C 330 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C 330 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 329 "   -0.055 5.00e-02 4.00e+02   8.24e-02 1.09e+01
        pdb=" N   PRO B 330 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO B 330 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 330 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 329 "    0.055 5.00e-02 4.00e+02   8.24e-02 1.09e+01
        pdb=" N   PRO A 330 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 330 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 330 "    0.047 5.00e-02 4.00e+02
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1459
        2.77 -     3.30: 6805
        3.30 -     3.83: 11453
        3.83 -     4.37: 13588
        4.37 -     4.90: 23044
  Nonbonded interactions: 56349
  Sorted by model distance:
  nonbonded pdb=" O   SER C 309 "
            pdb=" N   GLY C 312 "
     model   vdw
     2.232 2.520
  nonbonded pdb=" O   SER A  43 "
            pdb=" OG  SER A  43 "
     model   vdw
     2.397 2.440
  nonbonded pdb=" O   SER B  43 "
            pdb=" OG  SER B  43 "
     model   vdw
     2.398 2.440
  nonbonded pdb=" O   SER C  43 "
            pdb=" OG  SER C  43 "
     model   vdw
     2.399 2.440
  nonbonded pdb=" CZ  PHE B 308 "
            pdb=" O   GLY B 312 "
     model   vdw
     2.414 3.340
  ... (remaining 56344 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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  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:          2.120
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     21.770
  Find NCS groups from input model:        0.460
  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:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.078   7416  Z= 0.624
  Angle     :  1.423  19.656  10104  Z= 0.759
  Chirality :  0.071   0.441   1248
  Planarity :  0.010   0.083   1236
  Dihedral  : 12.312  55.076   2595
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 12.42 %
    Favored  : 86.96 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.98 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -7.38 (0.15), residues: 966
  helix: -4.67 (0.08), residues: 663
  sheet:  None (None), residues: 0
  loop : -4.90 (0.27), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.002   TRP C 267 
   HIS   0.003   0.001   HIS B 291 
   PHE   0.045   0.004   PHE B  22 
   TYR   0.016   0.003   TYR B 132 
   ARG   0.006   0.001   ARG C 269 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 258
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 1
  residues processed: 264
  average time/residue: 0.1786
  time to fit residues: 63.1226
Evaluate side-chains
  184 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.772 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0834
  time to fit residues: 1.1846
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0030
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
A 291 HIS
A 340 ASN
B 291 HIS
C 160 ASN
C 220 GLN
C 291 HIS
C 303 HIS
C 340 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7416  Z= 0.245
  Angle     :  0.876  12.816  10104  Z= 0.430
  Chirality :  0.046   0.295   1248
  Planarity :  0.007   0.070   1236
  Dihedral  :  6.544  24.961   1026
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 16.02 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -5.68 (0.20), residues: 966
  helix: -3.40 (0.15), residues: 627
  sheet:  None (None), residues: 0
  loop : -4.22 (0.27), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.001   TRP C 135 
   HIS   0.002   0.000   HIS C 303 
   PHE   0.021   0.001   PHE C 364 
   TYR   0.011   0.001   TYR B 132 
   ARG   0.007   0.001   ARG C  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 191
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 38
  outliers final: 20
  residues processed: 215
  average time/residue: 0.1500
  time to fit residues: 45.6816
Evaluate side-chains
  189 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 0.766 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0676
  time to fit residues: 3.5064
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 59 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 94 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
C 291 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7416  Z= 0.249
  Angle     :  0.831  10.092  10104  Z= 0.401
  Chirality :  0.045   0.187   1248
  Planarity :  0.006   0.068   1236
  Dihedral  :  5.825  22.362   1026
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.27 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.75 (0.22), residues: 966
  helix: -2.44 (0.18), residues: 624
  sheet:  None (None), residues: 0
  loop : -4.38 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.001   TRP C 135 
   HIS   0.003   0.001   HIS C 291 
   PHE   0.017   0.001   PHE A  22 
   TYR   0.011   0.001   TYR B 140 
   ARG   0.003   0.000   ARG B 252 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 186
  time to evaluate  : 0.771 
Fit side-chains
  outliers start: 26
  outliers final: 11
  residues processed: 202
  average time/residue: 0.1678
  time to fit residues: 46.6889
Evaluate side-chains
  180 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 169
  time to evaluate  : 0.748 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0682
  time to fit residues: 2.3340
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
C 291 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.5245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7416  Z= 0.346
  Angle     :  0.898  12.772  10104  Z= 0.428
  Chirality :  0.047   0.173   1248
  Planarity :  0.006   0.067   1236
  Dihedral  :  5.945  22.881   1026
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.70 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.18 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.69 (0.23), residues: 966
  helix: -2.35 (0.18), residues: 666
  sheet:  None (None), residues: 0
  loop : -4.66 (0.26), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.002   TRP C 135 
   HIS   0.002   0.000   HIS B 303 
   PHE   0.023   0.002   PHE C   7 
   TYR   0.014   0.002   TYR C 132 
   ARG   0.004   0.001   ARG A 333 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.794 
Fit side-chains
  outliers start: 29
  outliers final: 13
  residues processed: 204
  average time/residue: 0.1648
  time to fit residues: 46.8928
Evaluate side-chains
  183 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.732 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0716
  time to fit residues: 2.6212
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0980
   chunk 79 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
C 291 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.5645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7416  Z= 0.222
  Angle     :  0.836  12.654  10104  Z= 0.388
  Chirality :  0.045   0.163   1248
  Planarity :  0.006   0.066   1236
  Dihedral  :  5.489  20.751   1026
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.66 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 22.79 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.16 (0.24), residues: 966
  helix: -1.85 (0.19), residues: 675
  sheet:  None (None), residues: 0
  loop : -4.81 (0.25), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP A 135 
   HIS   0.001   0.000   HIS B 291 
   PHE   0.029   0.001   PHE B 308 
   TYR   0.011   0.001   TYR B 280 
   ARG   0.004   0.000   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 184
  time to evaluate  : 0.776 
Fit side-chains
  outliers start: 15
  outliers final: 9
  residues processed: 193
  average time/residue: 0.1605
  time to fit residues: 43.2971
Evaluate side-chains
  177 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 168
  time to evaluate  : 0.775 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0694
  time to fit residues: 2.1829
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 92 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0040
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.5811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7416  Z= 0.179
  Angle     :  0.787  13.326  10104  Z= 0.365
  Chirality :  0.043   0.160   1248
  Planarity :  0.005   0.059   1236
  Dihedral  :  5.204  22.761   1026
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.46 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 24.48 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.78 (0.25), residues: 966
  helix: -1.56 (0.20), residues: 678
  sheet:  None (None), residues: 0
  loop : -4.70 (0.26), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP A 135 
   HIS   0.001   0.000   HIS C 303 
   PHE   0.023   0.001   PHE B 308 
   TYR   0.010   0.001   TYR B 132 
   ARG   0.004   0.000   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 167
  time to evaluate  : 0.757 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 167
  average time/residue: 0.1706
  time to fit residues: 39.3049
Evaluate side-chains
  164 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.778 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0679
  time to fit residues: 1.1987
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 52 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0010
   chunk 78 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0370
   chunk 92 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0060
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.5882

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.6019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7416  Z= 0.180
  Angle     :  0.785  12.879  10104  Z= 0.364
  Chirality :  0.043   0.148   1248
  Planarity :  0.005   0.058   1236
  Dihedral  :  4.964  21.843   1026
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.97 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 23.96 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.44 (0.26), residues: 966
  helix: -1.25 (0.21), residues: 669
  sheet:  None (None), residues: 0
  loop : -4.62 (0.26), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP A 135 
   HIS   0.001   0.000   HIS C 303 
   PHE   0.017   0.001   PHE B 308 
   TYR   0.008   0.001   TYR B 132 
   ARG   0.002   0.000   ARG B  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 0.866 
Fit side-chains
  outliers start: 10
  outliers final: 5
  residues processed: 173
  average time/residue: 0.1693
  time to fit residues: 40.9887
Evaluate side-chains
  165 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 160
  time to evaluate  : 0.726 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1275
  time to fit residues: 1.9242
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    0.4980
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0870
   overall best weight:    0.8760

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.6182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7416  Z= 0.189
  Angle     :  0.780  13.780  10104  Z= 0.358
  Chirality :  0.043   0.143   1248
  Planarity :  0.005   0.058   1236
  Dihedral  :  4.900  21.241   1026
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 24.09 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.19 (0.26), residues: 966
  helix: -1.08 (0.21), residues: 672
  sheet:  None (None), residues: 0
  loop : -4.53 (0.27), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP A 135 
   HIS   0.001   0.000   HIS B 291 
   PHE   0.013   0.001   PHE C  90 
   TYR   0.006   0.001   TYR B 280 
   ARG   0.005   0.000   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 0.785 
Fit side-chains
  outliers start: 11
  outliers final: 8
  residues processed: 172
  average time/residue: 0.1551
  time to fit residues: 37.7160
Evaluate side-chains
  169 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 161
  time to evaluate  : 0.754 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0724
  time to fit residues: 2.0660
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 88 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0870
   chunk 26 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 81 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.9360

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.6316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7416  Z= 0.190
  Angle     :  0.784  13.624  10104  Z= 0.358
  Chirality :  0.043   0.144   1248
  Planarity :  0.005   0.058   1236
  Dihedral  :  4.825  21.064   1026
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 24.48 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.11 (0.26), residues: 966
  helix: -0.99 (0.21), residues: 654
  sheet:  None (None), residues: 0
  loop : -4.38 (0.26), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP A 135 
   HIS   0.001   0.000   HIS B 291 
   PHE   0.010   0.001   PHE C   7 
   TYR   0.007   0.001   TYR C 132 
   ARG   0.007   0.000   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 167
  time to evaluate  : 0.796 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 168
  average time/residue: 0.1687
  time to fit residues: 39.2566
Evaluate side-chains
  167 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 0.767 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0869
  time to fit residues: 1.3434
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    0.3980
   chunk 63 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0170
   chunk 60 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    1.0222

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.6439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7416  Z= 0.196
  Angle     :  0.791  13.804  10104  Z= 0.361
  Chirality :  0.043   0.141   1248
  Planarity :  0.005   0.058   1236
  Dihedral  :  4.835  20.810   1026
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 25.26 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.01 (0.26), residues: 966
  helix: -0.93 (0.21), residues: 657
  sheet:  None (None), residues: 0
  loop : -4.34 (0.26), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP A 135 
   HIS   0.001   0.000   HIS C 303 
   PHE   0.010   0.001   PHE C   7 
   TYR   0.006   0.001   TYR C 132 
   ARG   0.005   0.000   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.777 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 167
  average time/residue: 0.1817
  time to fit residues: 42.3332
Evaluate side-chains
  167 residues out of total 768 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.814 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.3662
  time to fit residues: 1.4982
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 70 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 76 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 GLN ** 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 = 0.3680 r_free = 0.3680 target = 0.148779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.116330 restraints weight = 10570.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.118772 restraints weight = 7232.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.119361 restraints weight = 6302.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.6525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7416  Z= 0.195
  Angle     :  0.790  13.719  10104  Z= 0.360
  Chirality :  0.043   0.142   1248
  Planarity :  0.005   0.058   1236
  Dihedral  :  4.777  20.645   1026
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.78 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.91 (0.26), residues: 966
  helix: -0.84 (0.21), residues: 657
  sheet:  None (None), residues: 0
  loop : -4.34 (0.26), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP A 135 
   HIS   0.001   0.000   HIS C 303 
   PHE   0.010   0.001   PHE C   7 
   TYR   0.009   0.001   TYR C 132 
   ARG   0.006   0.000   ARG A  89 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1675.73 seconds
wall clock time: 31 minutes 8.34 seconds (1868.34 seconds total)