Starting phenix.real_space_refine (version: dev)
on Sat Feb 18 16:35:29 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0745/02_2023/6n4b_0745_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0745/02_2023/6n4b_0745.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0745/02_2023/6n4b_0745.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0745/02_2023/6n4b_0745.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0745/02_2023/6n4b_0745_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4b_0745/02_2023/6n4b_0745_neut_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.004
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
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  208": "NH1" <-> "NH2"
    Residue "B ARG   19": "NH1" <-> "NH2"
    Residue "B ARG   96": "NH1" <-> "NH2"
    Residue "B ARG  137": "NH1" <-> "NH2"
    Residue "B ARG  256": "NH1" <-> "NH2"
    Residue "B ARG  314": "NH1" <-> "NH2"
    Residue "C ARG   13": "NH1" <-> "NH2"
    Residue "R ARG  186": "NH1" <-> "NH2"
    Residue "R ARG  230": "NH1" <-> "NH2"
    Residue "R ARG  311": "NH1" <-> "NH2"
    Residue "R ARG  336": "NH1" <-> "NH2"
    Residue "R ARG  400": "NH1" <-> "NH2"
    Residue "R ARG  405": "NH1" <-> "NH2"
    Residue "S ARG   98": "NH1" <-> "NH2"
    Residue "S ARG  148": "NH1" <-> "NH2"
    Residue "S ARG  206": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 8453
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1646
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 131
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 72
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2553
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 1988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 1988
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 71}
          Link IDs: {'PTRANS': 8, 'TRANS': 267}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 215
          Unresolved non-hydrogen angles: 269
          Unresolved non-hydrogen dihedrals: 167
          Unresolved non-hydrogen chiralities: 29
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 88
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 85
          Unusual residues: {'CLR': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 5.06, per 1000 atoms: 0.60
  Number of scatterers: 8453
  At special positions: 0
  Unit cell: (110.24, 123.76, 110.24, 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)
     S      58     16.00
     F       1      9.00
     O    1514      8.00
     N    1457      7.00
     C    5423      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 257 " - pdb=" SG  CYS R 264 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.55
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      31.9% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 27
      removed outlier: 3.718A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 208 through 215
      removed outlier: 4.798A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   CYS A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   PHE A 215 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 4.244A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ILE A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 296 through 308
      removed outlier: 3.577A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   TYR A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 350
      removed outlier: 3.987A  pdb=" N   VAL A 332 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   VAL A 339 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   THR A 340 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A 344 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LEU A 348 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 17
      removed outlier: 3.550A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    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 12 through 23
      removed outlier: 3.622A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU C  22 " --> pdb=" O   GLN C  18 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ALA C  23 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 33
      No H-bonds generated for 'chain 'C' and resid 30 through 33'
    Processing helix  chain 'C' and resid 35 through 38
      No H-bonds generated for 'chain 'C' and resid 35 through 38'
    Processing helix  chain 'C' and resid 45 through 47
      No H-bonds generated for 'chain 'C' and resid 45 through 47'
    Processing helix  chain 'R' and resid 113 through 142
      removed outlier: 4.519A  pdb=" N   VAL R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU R 122 " --> pdb=" O   ALA R 118 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER R 123 " --> pdb=" O   ILE R 119 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   VAL R 140 " --> pdb=" O   LEU R 136 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE R 141 " --> pdb=" O   VAL R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 149
      No H-bonds generated for 'chain 'R' and resid 146 through 149'
    Processing helix  chain 'R' and resid 151 through 177
      removed outlier: 3.937A  pdb=" N   PHE R 155 " --> pdb=" O   PRO R 151 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE R 156 " --> pdb=" O   SER R 152 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA R 162 " --> pdb=" O   SER R 158 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU R 164 " --> pdb=" O   ALA R 160 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR R 172 " --> pdb=" O   VAL R 168 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 186 through 190
      removed outlier: 4.288A  pdb=" N   LEU R 190 " --> pdb=" O   ARG R 186 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 186 through 190'
    Processing helix  chain 'R' and resid 194 through 219
      removed outlier: 3.622A  pdb=" N   ILE R 212 " --> pdb=" O   PHE R 208 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE R 216 " --> pdb=" O   ILE R 212 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ILE R 218 " --> pdb=" O   ARG R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 221 through 227
      removed outlier: 4.523A  pdb=" N   LYS R 225 " --> pdb=" O   PRO R 221 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   ARG R 226 " --> pdb=" O   LEU R 222 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 230 through 253
      removed outlier: 3.568A  pdb=" N   LEU R 250 " --> pdb=" O   VAL R 246 " (cutoff:3.500A)
      Proline residue:  R 251  - end of helix
    Processing helix  chain 'R' and resid 273 through 276
      No H-bonds generated for 'chain 'R' and resid 273 through 276'
    Processing helix  chain 'R' and resid 279 through 310
      removed outlier: 3.580A  pdb=" N   ILE R 290 " --> pdb=" O   LEU R 286 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   MET R 295 " --> pdb=" O   VAL R 291 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ILE R 297 " --> pdb=" O   ALA R 293 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE R 309 " --> pdb=" O   ALA R 305 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 336 through 357
      removed outlier: 3.842A  pdb=" N   ALA R 342 " --> pdb=" O   ASP R 338 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS R 343 " --> pdb=" O   ILE R 339 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   THR R 344 " --> pdb=" O   ARG R 340 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU R 347 " --> pdb=" O   LYS R 343 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL R 351 " --> pdb=" O   LEU R 347 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE R 353 " --> pdb=" O   LEU R 349 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   TRP R 356 " --> pdb=" O   LEU R 352 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 359 through 362
      No H-bonds generated for 'chain 'R' and resid 359 through 362'
    Processing helix  chain 'R' and resid 375 through 398
      removed outlier: 3.708A  pdb=" N   ALA R 380 " --> pdb=" O   LYS R 376 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE R 381 " --> pdb=" O   THR R 377 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   MET R 384 " --> pdb=" O   ALA R 380 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU R 385 " --> pdb=" O   PHE R 381 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   CYS R 386 " --> pdb=" O   CYS R 382 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU R 387 " --> pdb=" O   SER R 383 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU R 388 " --> pdb=" O   MET R 384 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER R 390 " --> pdb=" O   CYS R 386 " (cutoff:3.500A)
      Proline residue:  R 394  - end of helix
    Processing helix  chain 'R' and resid 402 through 409
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing sheet with id=  A, first strand: chain 'A' and resid 263 through 269
      removed outlier: 3.946A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.918A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.568A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 150
      removed outlier: 7.090A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.765A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 295 through 298
      removed outlier: 3.775A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.601A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.888A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'S' and resid 4 through 7
      removed outlier: 3.660A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'S' and resid 10 through 12
    Processing sheet with id=  K, first strand: chain 'S' and resid 93 through 99
      removed outlier: 3.708A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TRP S  36 " --> pdb=" O   ALA S  49 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'S' and resid 143 through 148
    Processing sheet with id=  M, first strand: chain 'S' and resid 213 through 219
      removed outlier: 3.900A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    819 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.76

  Time building geometry restraints manager: 3.80 seconds

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

  Histogram of bond lengths:
        1.10 -     1.24: 1206
        1.24 -     1.39: 2297
        1.39 -     1.53: 4598
        1.53 -     1.67: 451
        1.67 -     1.81: 84
  Bond restraints: 8636
  Sorted by residual:
  bond pdb=" CAT KCA R 501 "
       pdb=" FAU KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.342  1.101  0.241 2.00e-02 2.50e+03 1.45e+02
  bond pdb=" CAB KCA R 501 "
       pdb=" CAM KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.476  1.351  0.125 2.00e-02 2.50e+03 3.91e+01
  bond pdb=" CA  TRP B 339 "
       pdb=" C   TRP B 339 "
    ideal  model  delta    sigma   weight residual
    1.523  1.457  0.067 1.18e-02 7.18e+03 3.19e+01
  bond pdb=" CAP KCA R 501 "
       pdb=" CAQ KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.507  1.395  0.112 2.00e-02 2.50e+03 3.12e+01
  bond pdb=" CA  LEU B 336 "
       pdb=" C   LEU B 336 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 1.19e-02 7.06e+03 2.07e+01
  ... (remaining 8631 not shown)

  Histogram of bond angle deviations from ideal:
       97.43 -   105.71: 182
      105.71 -   113.99: 4945
      113.99 -   122.27: 5238
      122.27 -   130.55: 1331
      130.55 -   138.82: 52
  Bond angle restraints: 11748
  Sorted by residual:
  angle pdb=" N   PHE R 177 "
        pdb=" CA  PHE R 177 "
        pdb=" C   PHE R 177 "
      ideal   model   delta    sigma   weight residual
     111.14  123.07  -11.93 1.08e+00 8.57e-01 1.22e+02
  angle pdb=" C   TYR S 223 "
        pdb=" N   PRO S 224 "
        pdb=" CD  PRO S 224 "
      ideal   model   delta    sigma   weight residual
     120.60  137.91  -17.31 2.20e+00 2.07e-01 6.19e+01
  angle pdb=" N   TYR R 397 "
        pdb=" CA  TYR R 397 "
        pdb=" C   TYR R 397 "
      ideal   model   delta    sigma   weight residual
     111.36  119.69   -8.33 1.09e+00 8.42e-01 5.84e+01
  angle pdb=" N   LEU R 193 "
        pdb=" CA  LEU R 193 "
        pdb=" C   LEU R 193 "
      ideal   model   delta    sigma   weight residual
     114.39  103.36   11.03 1.45e+00 4.76e-01 5.78e+01
  angle pdb=" N   LEU S 225 "
        pdb=" CA  LEU S 225 "
        pdb=" C   LEU S 225 "
      ideal   model   delta    sigma   weight residual
     111.17  121.84  -10.67 1.41e+00 5.03e-01 5.73e+01
  ... (remaining 11743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 4834
       17.03 -    34.07: 159
       34.07 -    51.10: 33
       51.10 -    68.14: 7
       68.14 -    85.17: 2
  Dihedral angle restraints: 5035
    sinusoidal: 1785
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" N   TYR S 178 "
           pdb=" C   TYR S 178 "
           pdb=" CA  TYR S 178 "
           pdb=" CB  TYR S 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  143.79  -20.99     0      2.50e+00 1.60e-01 7.05e+01
  dihedral pdb=" C   TYR S 178 "
           pdb=" N   TYR S 178 "
           pdb=" CA  TYR S 178 "
           pdb=" CB  TYR S 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -142.31   19.71     0      2.50e+00 1.60e-01 6.21e+01
  dihedral pdb=" C   TRP R 241 "
           pdb=" N   TRP R 241 "
           pdb=" CA  TRP R 241 "
           pdb=" CB  TRP R 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.20   16.60     0      2.50e+00 1.60e-01 4.41e+01
  ... (remaining 5032 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.187: 1319
       0.187 -    0.374: 42
       0.374 -    0.561: 7
       0.561 -    0.749: 1
       0.749 -    0.936: 1
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CA  TYR S 178 "
            pdb=" N   TYR S 178 "
            pdb=" C   TYR S 178 "
            pdb=" CB  TYR S 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.57    0.94 2.00e-01 2.50e+01 2.19e+01
  chirality pdb=" CA  TRP R 241 "
            pdb=" N   TRP R 241 "
            pdb=" C   TRP R 241 "
            pdb=" CB  TRP R 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.83    0.68 2.00e-01 2.50e+01 1.16e+01
  chirality pdb=" CA  LEU S 225 "
            pdb=" N   LEU S 225 "
            pdb=" C   LEU S 225 "
            pdb=" CB  LEU S 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.56e+00
  ... (remaining 1367 not shown)

  Planarity restraints: 1463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP S 111 "   -0.032 2.00e-02 2.50e+03   2.56e-02 1.64e+01
        pdb=" CG  TRP S 111 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 TRP S 111 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP S 111 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP S 111 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP S 111 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP S 111 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP S 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP S 111 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP S 111 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 394 "    0.020 2.00e-02 2.50e+03   4.04e-02 1.63e+01
        pdb=" C   PRO R 394 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PRO R 394 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ILE R 395 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 256 "    0.020 2.00e-02 2.50e+03   3.97e-02 1.57e+01
        pdb=" CG  ASN A 256 "   -0.069 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 256 "    0.026 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 256 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1460 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 52
        2.46 -     3.07: 5970
        3.07 -     3.68: 11478
        3.68 -     4.29: 16720
        4.29 -     4.90: 28836
  Nonbonded interactions: 63056
  Sorted by model distance:
  nonbonded pdb=" CE  MET R 371 "
            pdb=" CB  ILE R 375 "
     model   vdw
     1.855 3.890
  nonbonded pdb=" O   ASP B  66 "
            pdb=" OG  SER B  67 "
     model   vdw
     1.962 2.440
  nonbonded pdb=" O   ASP B  38 "
            pdb=" OD1 ASP B  38 "
     model   vdw
     1.981 3.040
  nonbonded pdb=" O   HIS S 220 "
            pdb=" ND1 HIS S 220 "
     model   vdw
     2.011 2.520
  nonbonded pdb=" CD1 ILE S 126 "
            pdb=" OE2 GLU S 222 "
     model   vdw
     2.077 3.460
  ... (remaining 63051 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5423      2.51       5
     N    1457      2.21       5
     O    1514      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
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:             0.960
  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:          3.590
  Check model and map are aligned:         0.140
  Process input model:                     25.630
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Set scattering table:                    0.090
  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:13.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0113
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      :  0.011   0.241   8636  Z= 0.736
  Angle     :  1.400  17.310  11748  Z= 0.876
  Chirality :  0.091   0.936   1370
  Planarity :  0.008   0.075   1463
  Dihedral  :  9.547  85.169   2932
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer Outliers :  0.84 %
  Cbeta Deviations :  0.38 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -2.27 (0.23), residues: 1101
  helix: -1.09 (0.27), residues: 320
  sheet: -1.55 (0.30), residues: 253
  loop : -1.65 (0.24), residues: 528

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 1
  residues processed: 80
  average time/residue: 1.0019
  time to fit residues: 87.0617
Evaluate side-chains
  55 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.938 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 1
  residues processed: 0
  time to fit residues: 1.3980
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0270
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    0.8840

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B  91 HIS
B 259 GLN
B 266 HIS
** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS
R 219 HIS
S 182 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0362
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8636  Z= 0.184
  Angle     :  0.609   6.368  11748  Z= 0.328
  Chirality :  0.043   0.153   1370
  Planarity :  0.004   0.047   1463
  Dihedral  :  5.993  70.731   1226
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer Outliers :  1.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.24), residues: 1101
  helix: -0.06 (0.28), residues: 332
  sheet: -0.72 (0.31), residues: 261
  loop : -1.51 (0.24), residues: 508

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 3
  residues processed: 68
  average time/residue: 0.9679
  time to fit residues: 72.0054
Evaluate side-chains
  58 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.958 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.6644
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 30 optimal weight:    0.1980
   chunk 82 optimal weight:   20.0000
   chunk 67 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0670
   chunk 107 optimal weight:   30.0000
   chunk 88 optimal weight:    6.9990
   chunk 98 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0471
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8636  Z= 0.138
  Angle     :  0.509   7.958  11748  Z= 0.270
  Chirality :  0.039   0.141   1370
  Planarity :  0.003   0.040   1463
  Dihedral  :  5.546  75.460   1226
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer Outliers :  1.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.91 (0.24), residues: 1101
  helix:  0.38 (0.28), residues: 345
  sheet: -0.28 (0.32), residues: 255
  loop : -1.44 (0.24), residues: 501

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 4
  residues processed: 63
  average time/residue: 0.8521
  time to fit residues: 59.7218
Evaluate side-chains
  57 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.860 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 1.3806
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 99 optimal weight:   50.0000
   chunk 105 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0000
   chunk 28 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.5992

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
S 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0830
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8636  Z= 0.203
  Angle     :  0.594   8.806  11748  Z= 0.313
  Chirality :  0.041   0.157   1370
  Planarity :  0.005   0.058   1463
  Dihedral  :  6.002  85.346   1226
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer Outliers :  1.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.78 (0.24), residues: 1101
  helix:  0.33 (0.28), residues: 349
  sheet:  0.02 (0.32), residues: 259
  loop : -1.41 (0.25), residues: 493

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 4
  residues processed: 62
  average time/residue: 0.9326
  time to fit residues: 63.8761
Evaluate side-chains
  51 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.962 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 1.1823
  time to fit residues: 2.7109
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0170
   chunk 43 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 72 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 94 optimal weight:    0.3980
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0570
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0733
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8636  Z= 0.114
  Angle     :  0.479   6.800  11748  Z= 0.247
  Chirality :  0.038   0.143   1370
  Planarity :  0.003   0.054   1463
  Dihedral  :  5.479  88.894   1226
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer Outliers :  1.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.42 (0.24), residues: 1101
  helix:  0.69 (0.28), residues: 350
  sheet:  0.26 (0.32), residues: 258
  loop : -1.26 (0.25), residues: 493

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 4
  residues processed: 57
  average time/residue: 0.9111
  time to fit residues: 57.4346
Evaluate side-chains
  52 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.846 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 1.2120
  time to fit residues: 2.6825
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    0.3980
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 105 optimal weight:   50.0000
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:   20.0000
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0770
   chunk 101 optimal weight:   20.0000
   overall best weight:    1.0542

-------------------------------------------------------------------------------
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: 0.0897
moved from start:          0.5215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8636  Z= 0.149
  Angle     :  0.525   7.193  11748  Z= 0.272
  Chirality :  0.039   0.144   1370
  Planarity :  0.004   0.040   1463
  Dihedral  :  5.442  81.816   1226
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer Outliers :  1.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.32 (0.24), residues: 1101
  helix:  0.77 (0.28), residues: 352
  sheet:  0.50 (0.33), residues: 250
  loop : -1.31 (0.25), residues: 499

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 7
  residues processed: 64
  average time/residue: 0.9329
  time to fit residues: 65.7817
Evaluate side-chains
  57 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.879 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 5
  residues processed: 2
  average time/residue: 1.1597
  time to fit residues: 3.8764
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 60 optimal weight:   20.0000
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 88 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 105 optimal weight:   40.0000
   chunk 65 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   overall best weight:    4.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 304 GLN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1430
moved from start:          0.7144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.079   8636  Z= 0.408
  Angle     :  0.962  20.548  11748  Z= 0.500
  Chirality :  0.051   0.305   1370
  Planarity :  0.007   0.147   1463
  Dihedral  :  7.335  55.781   1226
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer Outliers :  2.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.04 (0.24), residues: 1101
  helix:  0.11 (0.28), residues: 351
  sheet:  0.40 (0.35), residues: 213
  loop : -1.72 (0.24), residues: 537

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 8
  residues processed: 72
  average time/residue: 1.1067
  time to fit residues: 86.2717
Evaluate side-chains
  61 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.908 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 5
  residues processed: 3
  average time/residue: 0.1867
  time to fit residues: 2.0860
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0010
   chunk 71 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 82 optimal weight:    0.3980
   chunk 95 optimal weight:    6.9990
   chunk 100 optimal weight:    0.0970
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1133
moved from start:          0.6949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8636  Z= 0.140
  Angle     :  0.536   9.015  11748  Z= 0.278
  Chirality :  0.040   0.202   1370
  Planarity :  0.003   0.051   1463
  Dihedral  :  5.420  56.552   1226
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer Outliers :  1.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.24), residues: 1101
  helix:  0.60 (0.28), residues: 342
  sheet:  0.47 (0.33), residues: 236
  loop : -1.49 (0.24), residues: 523

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.957 
Fit side-chains
  outliers start: 11
  outliers final: 10
  residues processed: 59
  average time/residue: 0.9340
  time to fit residues: 60.8930
Evaluate side-chains
  62 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 1.006 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 5
  residues processed: 5
  average time/residue: 0.9831
  time to fit residues: 6.5741
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   chunk 103 optimal weight:   20.0000
   chunk 63 optimal weight:    0.0970
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1252
moved from start:          0.7332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8636  Z= 0.190
  Angle     :  0.613  11.329  11748  Z= 0.316
  Chirality :  0.041   0.217   1370
  Planarity :  0.004   0.050   1463
  Dihedral  :  5.654  57.768   1226
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer Outliers :  0.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.25), residues: 1101
  helix:  0.75 (0.28), residues: 343
  sheet:  0.34 (0.34), residues: 241
  loop : -1.50 (0.25), residues: 517

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.973 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 57
  average time/residue: 0.9392
  time to fit residues: 59.5753
Evaluate side-chains
  57 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.991 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 6
  residues processed: 1
  average time/residue: 1.8106
  time to fit residues: 3.3038
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 108 optimal weight:    6.9990
   chunk 99 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0570
   chunk 8 optimal weight:    0.0970
   chunk 66 optimal weight:    0.0050
   chunk 53 optimal weight:    8.9990
   chunk 68 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.3110

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 220 GLN
R 304 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1108
moved from start:          0.7281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8636  Z= 0.119
  Angle     :  0.500  10.509  11748  Z= 0.257
  Chirality :  0.039   0.141   1370
  Planarity :  0.003   0.056   1463
  Dihedral  :  5.062  58.807   1226
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer Outliers :  0.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.28 (0.25), residues: 1101
  helix:  1.09 (0.29), residues: 346
  sheet:  0.33 (0.34), residues: 250
  loop : -1.38 (0.25), residues: 505

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.871 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 60
  average time/residue: 0.8886
  time to fit residues: 59.2458
Evaluate side-chains
  58 residues out of total 962 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.926 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 6
  residues processed: 0
  time to fit residues: 1.3668
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0020
   chunk 86 optimal weight:   40.0000
   chunk 36 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 10 optimal weight:   30.0000
   chunk 15 optimal weight:   20.0000
   chunk 76 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    2.1594

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
S 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5405 r_free = 0.5405 target = 0.340486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5284 r_free = 0.5284 target = 0.320827 restraints weight = 13199.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.5264 rms_B_bonded: 2.20
r_work: 0.5139 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.5139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1377
moved from start:          0.7924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8636  Z= 0.232
  Angle     :  0.695  16.356  11748  Z= 0.355
  Chirality :  0.043   0.172   1370
  Planarity :  0.004   0.050   1463
  Dihedral  :  5.869  57.415   1226
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer Outliers :  0.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.45 (0.25), residues: 1101
  helix:  1.00 (0.29), residues: 337
  sheet:  0.35 (0.35), residues: 229
  loop : -1.48 (0.25), residues: 535

===============================================================================
Job complete
usr+sys time: 2238.26 seconds
wall clock time: 41 minutes 33.57 seconds (2493.57 seconds total)