Starting phenix.real_space_refine (version: 1.21rc1)
on Tue Jul  4 19:36:18 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/07_2023/6wi9_21683.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/07_2023/6wi9_21683.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/07_2023/6wi9_21683.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/07_2023/6wi9_21683.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/07_2023/6wi9_21683.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/07_2023/6wi9_21683.pdb"
  }
  resolution = 4.3
  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
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5410      2.51       5
     N    1526      2.21       5
     O    1561      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   21": "OE1" <-> "OE2"
    Residue "A ARG  265": "NH1" <-> "NH2"
    Residue "A GLU  327": "OE1" <-> "OE2"
    Residue "B GLU    3": "OE1" <-> "OE2"
    Residue "B ARG  129": "NH1" <-> "NH2"
    Residue "B GLU  226": "OE1" <-> "OE2"
    Residue "G GLU   22": "OE1" <-> "OE2"
    Residue "N GLU   89": "OE1" <-> "OE2"
    Residue "P ARG   21": "NH1" <-> "NH2"
    Residue "R ARG  135": "NH1" <-> "NH2"
    Residue "R GLU  236": "OE1" <-> "OE2"
    Residue "R GLU  328": "OE1" <-> "OE2"
    Residue "R GLU  373": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib"
  Total number of atoms: 8550
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1646
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 6, 'TRANS': 187}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "P"
      Number of atoms: 213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 213
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "R"
      Number of atoms: 2706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2706
          Classifications: {'peptide': 368}
          Incomplete info: {'truncation_to_alanine': 85}
          Link IDs: {'PTRANS': 11, 'TRANS': 356}
          Chain breaks: 1
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 303
          Unresolved non-hydrogen angles: 394
          Unresolved non-hydrogen dihedrals: 253
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 189
  Time building chain proxies: 4.53, per 1000 atoms: 0.53
  Number of scatterers: 8550
  At special positions: 0
  Unit cell: (78.26, 173.72, 97.18, 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      53     16.00
     O    1561      8.00
     N    1526      7.00
     C    5410      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  45 " - pdb=" SG  CYS R  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  89 " - pdb=" SG  CYS R 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 215 " - pdb=" SG  CYS R 285 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.43
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2074

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      40.1% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.503A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASP A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 240
      removed outlier: 3.702A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.720A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.761A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 390
      removed outlier: 3.685A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.962A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 36
      removed outlier: 4.187A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 12
      No H-bonds generated for 'chain 'G' and resid 10 through 12'
    Processing helix  chain 'G' and resid 13 through 18
    Processing helix  chain 'G' and resid 20 through 25
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.796A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.756A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 27
    Processing helix  chain 'R' and resid 31 through 46
      removed outlier: 4.010A  pdb=" N   ASP R  43 " --> pdb=" O   TRP R  39 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   GLN R  44 " --> pdb=" O   GLU R  40 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS R  45 " --> pdb=" O   GLU R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 47 through 50
    Processing helix  chain 'R' and resid 93 through 97
    Processing helix  chain 'R' and resid 131 through 165
      removed outlier: 3.509A  pdb=" N   ARG R 135 " --> pdb=" O   SER R 131 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   HIS R 136 " --> pdb=" O   ASN R 132 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   SER R 137 " --> pdb=" O   GLU R 133 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   VAL R 155 " --> pdb=" O   SER R 151 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU R 158 " --> pdb=" O   LEU R 154 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ILE R 163 " --> pdb=" O   VAL R 159 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LEU R 164 " --> pdb=" O   ALA R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 200
      removed outlier: 3.541A  pdb=" N   TYR R 176 " --> pdb=" O   CYS R 172 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE R 177 " --> pdb=" O   THR R 173 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   HIS R 180 " --> pdb=" O   TYR R 176 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE R 193 " --> pdb=" O   ALA R 189 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE R 194 " --> pdb=" O   LEU R 190 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ASP R 196 " --> pdb=" O   ASN R 192 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   ALA R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 213 through 246
      removed outlier: 3.948A  pdb=" N   VAL R 220 " --> pdb=" O   LYS R 216 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASN R 229 " --> pdb=" O   CYS R 225 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 265
      removed outlier: 3.603A  pdb=" N   GLY R 257 " --> pdb=" O   LYS R 253 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER R 265 " --> pdb=" O   PHE R 261 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 280
      removed outlier: 4.095A  pdb=" N   ALA R 271 " --> pdb=" O   ALA R 267 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS R 278 " --> pdb=" O   ALA R 274 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 325
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 336 through 352
      removed outlier: 4.617A  pdb=" N   ARG R 342 " --> pdb=" O   LYS R 338 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LEU R 346 " --> pdb=" O   ARG R 342 " (cutoff:3.500A)
      Proline residue:  R 349  - end of helix
    Processing helix  chain 'R' and resid 353 through 359
      removed outlier: 3.977A  pdb=" N   PHE R 358 " --> pdb=" O   TYR R 355 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 368
      removed outlier: 5.821A  pdb=" N   GLU R 367 " --> pdb=" O   ASP R 364 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ILE R 368 " --> pdb=" O   ALA R 365 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 369 through 374
      removed outlier: 3.569A  pdb=" N   GLU R 373 " --> pdb=" O   GLN R 369 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 376 through 378
      No H-bonds generated for 'chain 'R' and resid 376 through 378'
    Processing helix  chain 'R' and resid 379 through 390
    Processing helix  chain 'R' and resid 393 through 408
      removed outlier: 3.514A  pdb=" N   GLU R 398 " --> pdb=" O   GLU R 394 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   VAL R 399 " --> pdb=" O   VAL R 395 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS R 401 " --> pdb=" O   LEU R 397 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS R 402 " --> pdb=" O   GLU R 398 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   HIS R 407 " --> pdb=" O   TRP R 403 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 3.590A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   HIS A 220 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 9.337A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.066A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.183A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.991A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.414A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.794A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.666A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.789A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 3.807A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 69 through 70
      removed outlier: 3.677A  pdb=" N   MET R  69 " --> pdb=" O   TRP R  76 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   TRP R  76 " --> pdb=" O   MET R  69 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'R' and resid 85 through 87
      removed outlier: 4.269A  pdb=" N   LEU R 103 " --> pdb=" O   VAL R  87 " (cutoff:3.500A)

    369 hydrogen bonds defined for protein.
    1026 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: 2.30

  Time building geometry restraints manager: 3.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2851
        1.35 -     1.46: 2108
        1.46 -     1.58: 3684
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 8716
  Sorted by residual:
  bond pdb=" CA  THR B 128 "
       pdb=" CB  THR B 128 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.018 1.37e-02 5.33e+03 1.81e+00
  bond pdb=" CA  ILE R 246 "
       pdb=" CB  ILE R 246 "
    ideal  model  delta    sigma   weight residual
    1.533  1.545 -0.012 1.19e-02 7.06e+03 9.69e-01
  bond pdb=" N   GLY B 116 "
       pdb=" CA  GLY B 116 "
    ideal  model  delta    sigma   weight residual
    1.458  1.449  0.009 9.20e-03 1.18e+04 9.13e-01
  bond pdb=" CA  ILE N  51 "
       pdb=" CB  ILE N  51 "
    ideal  model  delta    sigma   weight residual
    1.550  1.541  0.009 1.03e-02 9.43e+03 7.69e-01
  bond pdb=" C   GLU R  67 "
       pdb=" N   GLY R  68 "
    ideal  model  delta    sigma   weight residual
    1.332  1.328  0.004 5.00e-03 4.00e+04 7.03e-01
  ... (remaining 8711 not shown)

  Histogram of bond angle deviations from ideal:
      100.43 -   107.14: 171
      107.14 -   113.85: 4839
      113.85 -   120.55: 3384
      120.55 -   127.26: 3315
      127.26 -   133.97: 88
  Bond angle restraints: 11797
  Sorted by residual:
  angle pdb=" N   GLU A 309 "
        pdb=" CA  GLU A 309 "
        pdb=" C   GLU A 309 "
      ideal   model   delta    sigma   weight residual
     114.56  109.65    4.91 1.27e+00 6.20e-01 1.49e+01
  angle pdb=" N   ILE R  73 "
        pdb=" CA  ILE R  73 "
        pdb=" C   ILE R  73 "
      ideal   model   delta    sigma   weight residual
     111.62  108.73    2.89 7.90e-01 1.60e+00 1.34e+01
  angle pdb=" N   ILE G   9 "
        pdb=" CA  ILE G   9 "
        pdb=" C   ILE G   9 "
      ideal   model   delta    sigma   weight residual
     112.12  109.09    3.03 8.40e-01 1.42e+00 1.30e+01
  angle pdb=" C   GLU R  52 "
        pdb=" N   GLN R  53 "
        pdb=" CA  GLN R  53 "
      ideal   model   delta    sigma   weight residual
     121.54  128.07   -6.53 1.91e+00 2.74e-01 1.17e+01
  angle pdb=" N   VAL N  64 "
        pdb=" CA  VAL N  64 "
        pdb=" C   VAL N  64 "
      ideal   model   delta    sigma   weight residual
     113.20  110.06    3.14 9.60e-01 1.09e+00 1.07e+01
  ... (remaining 11792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4768
       17.83 -    35.67: 347
       35.67 -    53.50: 39
       53.50 -    71.34: 6
       71.34 -    89.17: 15
  Dihedral angle restraints: 5175
    sinusoidal: 1970
      harmonic: 3205
  Sorted by residual:
  dihedral pdb=" CB  CYS R 215 "
           pdb=" SG  CYS R 215 "
           pdb=" SG  CYS R 285 "
           pdb=" CB  CYS R 285 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.54   50.46     1      1.00e+01 1.00e-02 3.49e+01
  dihedral pdb=" CB  CYS R  45 "
           pdb=" SG  CYS R  45 "
           pdb=" SG  CYS R  75 "
           pdb=" CB  CYS R  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.25  -35.25     1      1.00e+01 1.00e-02 1.76e+01
  dihedral pdb=" CB  GLU R 373 "
           pdb=" CG  GLU R 373 "
           pdb=" CD  GLU R 373 "
           pdb=" OE1 GLU R 373 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.17  -89.17     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 5172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 940
       0.035 -    0.071: 282
       0.071 -    0.106: 87
       0.106 -    0.142: 12
       0.142 -    0.177: 2
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" CB  ILE R 246 "
            pdb=" CA  ILE R 246 "
            pdb=" CG1 ILE R 246 "
            pdb=" CG2 ILE R 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.85e-01
  chirality pdb=" CB  THR B 128 "
            pdb=" CA  THR B 128 "
            pdb=" OG1 THR B 128 "
            pdb=" CG2 THR B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.50e-01
  chirality pdb=" CA  ILE R 288 "
            pdb=" N   ILE R 288 "
            pdb=" C   ILE R 288 "
            pdb=" CB  ILE R 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.57e-01
  ... (remaining 1320 not shown)

  Planarity restraints: 1516
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.021 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO B 236 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "    0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO A 321 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 300 "    0.020 5.00e-02 4.00e+02   2.99e-02 1.43e+00
        pdb=" N   PRO R 301 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO R 301 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R 301 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1513 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1049
        2.75 -     3.29: 8547
        3.29 -     3.83: 13270
        3.83 -     4.36: 15713
        4.36 -     4.90: 26736
  Nonbonded interactions: 65315
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B  42 "
            pdb=" O   ILE B  43 "
     model   vdw
     2.214 2.520
  nonbonded pdb=" O   ASP B  76 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.236 2.440
  nonbonded pdb=" O   ARG R 339 "
            pdb=" OG  SER R 343 "
     model   vdw
     2.312 2.440
  nonbonded pdb=" OD1 ASN R 291 "
            pdb=" OG  SER R 293 "
     model   vdw
     2.312 2.440
  nonbonded pdb=" O   GLY B 182 "
            pdb=" NZ  LYS B 209 "
     model   vdw
     2.317 2.520
  ... (remaining 65310 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
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          2.960
  Check model and map are aligned:         0.140
  Set scattering table:                    0.080
  Process input model:                     25.020
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
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      :  0.002   0.020   8716  Z= 0.110
  Angle     :  0.502   6.528  11797  Z= 0.312
  Chirality :  0.038   0.177   1323
  Planarity :  0.002   0.033   1516
  Dihedral  : 12.848  89.170   3086
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer Outliers :  0.00 %
  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: -3.72 (0.21), residues: 1086
  helix: -2.77 (0.18), residues: 377
  sheet: -1.64 (0.32), residues: 208
  loop : -2.50 (0.25), residues: 501

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.2272
  time to fit residues: 96.0518
Evaluate side-chains
  198 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 1.016 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2677
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0270
   chunk 50 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0770
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.0200

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A 218 ASN
B  17 GLN
B  91 HIS
B 220 GLN
N   3 GLN
R 180 HIS
R 223 GLN
R 229 ASN
** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 392 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8716  Z= 0.177
  Angle     :  0.580   7.506  11797  Z= 0.311
  Chirality :  0.042   0.194   1323
  Planarity :  0.004   0.037   1516
  Dihedral  :  3.732  16.184   1203
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer Outliers :  0.00 %
  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: -1.93 (0.24), residues: 1086
  helix: -0.43 (0.26), residues: 375
  sheet: -1.09 (0.34), residues: 201
  loop : -1.99 (0.26), residues: 510

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.2178
  time to fit residues: 79.2519
Evaluate side-chains
  200 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.050 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3914
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 78 optimal weight:   40.0000
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
B  91 HIS
R 229 ASN
** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 392 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8716  Z= 0.183
  Angle     :  0.568  10.918  11797  Z= 0.300
  Chirality :  0.042   0.162   1323
  Planarity :  0.004   0.036   1516
  Dihedral  :  3.908  15.043   1203
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer Outliers :  0.00 %
  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: -1.44 (0.25), residues: 1086
  helix:  0.05 (0.26), residues: 382
  sheet: -0.75 (0.34), residues: 206
  loop : -1.83 (0.27), residues: 498

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2046
  time to fit residues: 68.1197
Evaluate side-chains
  195 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.999 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3576
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 73 optimal weight:   40.0000
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 103 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
B  17 GLN
G  24 ASN
N  53 GLN
R 229 ASN
R 354 HIS
R 392 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8716  Z= 0.246
  Angle     :  0.602   9.236  11797  Z= 0.318
  Chirality :  0.043   0.214   1323
  Planarity :  0.004   0.035   1516
  Dihedral  :  4.214  17.797   1203
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer Outliers :  0.11 %
  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: -1.06 (0.25), residues: 1086
  helix:  0.33 (0.27), residues: 376
  sheet: -0.57 (0.35), residues: 216
  loop : -1.56 (0.28), residues: 494

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 238
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2006
  time to fit residues: 65.8879
Evaluate side-chains
  193 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.010 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3389
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 58 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 77 optimal weight:   20.0000
   chunk 42 optimal weight:    4.9990
   chunk 88 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:   20.0000
   chunk 92 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 229 ASN
** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8716  Z= 0.230
  Angle     :  0.593  10.176  11797  Z= 0.313
  Chirality :  0.042   0.162   1323
  Planarity :  0.004   0.037   1516
  Dihedral  :  4.347  17.003   1203
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer Outliers :  0.00 %
  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: -1.02 (0.26), residues: 1086
  helix:  0.38 (0.26), residues: 376
  sheet: -0.56 (0.35), residues: 214
  loop : -1.54 (0.29), residues: 496

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1942
  time to fit residues: 63.8747
Evaluate side-chains
  195 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.006 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3374
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 229 ASN
** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8716  Z= 0.174
  Angle     :  0.567   9.024  11797  Z= 0.299
  Chirality :  0.041   0.162   1323
  Planarity :  0.003   0.031   1516
  Dihedral  :  4.258  16.410   1203
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer Outliers :  0.00 %
  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: -0.84 (0.26), residues: 1086
  helix:  0.46 (0.27), residues: 384
  sheet: -0.41 (0.35), residues: 213
  loop : -1.42 (0.29), residues: 489

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1998
  time to fit residues: 68.8122
Evaluate side-chains
  193 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.941 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2522
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 75 optimal weight:   30.0000
   chunk 87 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 63 optimal weight:    0.1980
   chunk 41 optimal weight:    8.9990
   overall best weight:    3.3986

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

Flipped N/Q/H residues before XYZ refinement:
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 229 ASN
** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.4246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8716  Z= 0.301
  Angle     :  0.668  10.489  11797  Z= 0.349
  Chirality :  0.044   0.256   1323
  Planarity :  0.004   0.038   1516
  Dihedral  :  4.653  18.288   1203
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer Outliers :  0.11 %
  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: -0.98 (0.26), residues: 1086
  helix:  0.36 (0.26), residues: 383
  sheet: -0.70 (0.34), residues: 227
  loop : -1.41 (0.30), residues: 476

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 230
  average time/residue: 0.1920
  time to fit residues: 61.3623
Evaluate side-chains
  185 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.940 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1081
  time to fit residues: 1.4328
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 31 optimal weight:    0.3980
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 65 optimal weight:    9.9990
   chunk 70 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 93 optimal weight:    0.2980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  53 GLN
N  82 GLN
R 229 ASN
** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8716  Z= 0.160
  Angle     :  0.624   9.448  11797  Z= 0.319
  Chirality :  0.043   0.226   1323
  Planarity :  0.003   0.039   1516
  Dihedral  :  4.504  21.598   1203
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer Outliers :  0.00 %
  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: -0.69 (0.26), residues: 1086
  helix:  0.76 (0.27), residues: 385
  sheet: -0.53 (0.36), residues: 198
  loop : -1.38 (0.29), residues: 503

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2004
  time to fit residues: 67.9950
Evaluate side-chains
  191 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.028 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4008
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 96 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 57 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
N  53 GLN
R 229 ASN
** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8716  Z= 0.169
  Angle     :  0.614   9.252  11797  Z= 0.314
  Chirality :  0.042   0.220   1323
  Planarity :  0.004   0.051   1516
  Dihedral  :  4.374  20.555   1203
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer Outliers :  0.00 %
  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: -0.62 (0.26), residues: 1086
  helix:  0.77 (0.27), residues: 386
  sheet: -0.40 (0.35), residues: 214
  loop : -1.37 (0.30), residues: 486

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1928
  time to fit residues: 64.3783
Evaluate side-chains
  195 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.008 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2924
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 106 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  53 GLN
R 229 ASN
R 392 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8716  Z= 0.184
  Angle     :  0.614   9.653  11797  Z= 0.313
  Chirality :  0.042   0.212   1323
  Planarity :  0.004   0.053   1516
  Dihedral  :  4.367  22.240   1203
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer Outliers :  0.00 %
  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: -0.59 (0.26), residues: 1086
  helix:  0.85 (0.27), residues: 386
  sheet: -0.37 (0.35), residues: 214
  loop : -1.41 (0.29), residues: 486

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1946
  time to fit residues: 63.5920
Evaluate side-chains
  186 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.938 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2878
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 78 optimal weight:   50.0000
   chunk 12 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 74 optimal weight:    0.1980
   chunk 4 optimal weight:    4.9990
   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 218 ASN
B 239 ASN
R 229 ASN
R 392 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.109151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.085738 restraints weight = 23755.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.088349 restraints weight = 14104.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.090168 restraints weight = 9797.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8716  Z= 0.189
  Angle     :  0.615   9.283  11797  Z= 0.313
  Chirality :  0.042   0.204   1323
  Planarity :  0.004   0.047   1516
  Dihedral  :  4.372  19.800   1203
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer Outliers :  0.00 %
  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: -0.60 (0.26), residues: 1086
  helix:  0.88 (0.27), residues: 386
  sheet: -0.41 (0.35), residues: 209
  loop : -1.43 (0.29), residues: 491

===============================================================================
Job complete
usr+sys time: 2039.43 seconds
wall clock time: 37 minutes 36.19 seconds (2256.19 seconds total)