Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 13:26:53 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/04_2023/8avx_15686_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/04_2023/8avx_15686.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/04_2023/8avx_15686.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/04_2023/8avx_15686.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/04_2023/8avx_15686_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avx_15686/04_2023/8avx_15686_updated.pdb"
  }
  resolution = 3.5
  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=   0.014
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      22      5.16       5
     C    4715      2.51       5
     N    1327      2.21       5
     O    1363      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   22": "OE1" <-> "OE2"
    Residue "A GLU   25": "OE1" <-> "OE2"
    Residue "A GLU   50": "OE1" <-> "OE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  127": "OE1" <-> "OE2"
    Residue "A GLU  158": "OE1" <-> "OE2"
    Residue "A GLU  185": "OE1" <-> "OE2"
    Residue "A ARG  192": "NH1" <-> "NH2"
    Residue "A ARG  202": "NH1" <-> "NH2"
    Residue "A ARG  228": "NH1" <-> "NH2"
    Residue "A ARG  254": "NH1" <-> "NH2"
    Residue "A ARG  265": "NH1" <-> "NH2"
    Residue "A ARG  310": "NH1" <-> "NH2"
    Residue "A ARG  337": "NH1" <-> "NH2"
    Residue "A GLU  373": "OE1" <-> "OE2"
    Residue "A ARG  375": "NH1" <-> "NH2"
    Residue "A GLU  381": "OE1" <-> "OE2"
    Residue "A GLU  432": "OE1" <-> "OE2"
    Residue "A ARG  442": "NH1" <-> "NH2"
    Residue "A GLU  474": "OE1" <-> "OE2"
    Residue "A ARG  495": "NH1" <-> "NH2"
    Residue "B GLU   22": "OE1" <-> "OE2"
    Residue "B GLU   25": "OE1" <-> "OE2"
    Residue "B GLU   50": "OE1" <-> "OE2"
    Residue "B GLU  120": "OE1" <-> "OE2"
    Residue "B GLU  127": "OE1" <-> "OE2"
    Residue "B GLU  158": "OE1" <-> "OE2"
    Residue "B GLU  185": "OE1" <-> "OE2"
    Residue "B ARG  192": "NH1" <-> "NH2"
    Residue "B ARG  202": "NH1" <-> "NH2"
    Residue "B ARG  228": "NH1" <-> "NH2"
    Residue "B ARG  254": "NH1" <-> "NH2"
    Residue "B ARG  265": "NH1" <-> "NH2"
    Residue "B ARG  310": "NH1" <-> "NH2"
    Residue "B ARG  337": "NH1" <-> "NH2"
    Residue "B GLU  373": "OE1" <-> "OE2"
    Residue "B ARG  375": "NH1" <-> "NH2"
    Residue "B GLU  381": "OE1" <-> "OE2"
    Residue "B GLU  432": "OE1" <-> "OE2"
    Residue "B ARG  442": "NH1" <-> "NH2"
    Residue "B GLU  474": "OE1" <-> "OE2"
    Residue "B ARG  477": "NH1" <-> "NH2"
    Residue "B ARG  495": "NH1" <-> "NH2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 7427
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3668
          Classifications: {'peptide': 480}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 443}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3673
          Classifications: {'peptide': 481}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 444}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'BLA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'BLA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.40, per 1000 atoms: 0.59
  Number of scatterers: 7427
  At special positions: 0
  Unit cell: (81.8615, 95.6487, 121.5, 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      22     16.00
     O    1363      8.00
     N    1327      7.00
     C    4715      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.06
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1774

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      32 helices and 6 sheets defined
      34.5% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 62
      removed outlier: 3.973A  pdb=" N   ALA A  59 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE A  61 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LEU A  62 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 69
      No H-bonds generated for 'chain 'A' and resid 66 through 69'
    Processing helix  chain 'A' and resid 74 through 77
      No H-bonds generated for 'chain 'A' and resid 74 through 77'
    Processing helix  chain 'A' and resid 82 through 88
      removed outlier: 4.440A  pdb=" N   ALA A  87 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 148
      removed outlier: 3.524A  pdb=" N   PHE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 167
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.578A  pdb=" N   LEU A 215 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 267
      removed outlier: 3.749A  pdb=" N   MET A 267 " --> pdb=" O   TYR A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 330
      removed outlier: 3.916A  pdb=" N   THR A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   THR A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLN A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL A 318 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA A 321 " --> pdb=" O   GLN A 317 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL A 324 " --> pdb=" O   GLU A 320 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA A 325 " --> pdb=" O   ALA A 321 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE A 327 " --> pdb=" O   ASP A 323 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN A 329 " --> pdb=" O   ALA A 325 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 341
      removed outlier: 4.152A  pdb=" N   ARG A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL A 338 " --> pdb=" O   HIS A 334 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 341 " --> pdb=" O   ARG A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 363
      No H-bonds generated for 'chain 'A' and resid 360 through 363'
    Processing helix  chain 'A' and resid 385 through 397
      removed outlier: 3.511A  pdb=" N   ALA A 390 " --> pdb=" O   PRO A 386 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA A 393 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR A 397 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 411
      No H-bonds generated for 'chain 'A' and resid 408 through 411'
    Processing helix  chain 'A' and resid 466 through 473
      removed outlier: 3.901A  pdb=" N   THR A 471 " --> pdb=" O   HIS A 467 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR A 472 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 498
      removed outlier: 3.625A  pdb=" N   GLU A 490 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASP A 493 " --> pdb=" O   GLU A 489 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG A 495 " --> pdb=" O   ALA A 491 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP A 496 " --> pdb=" O   GLN A 492 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR A 497 " --> pdb=" O   ASP A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 520
      removed outlier: 4.050A  pdb=" N   VAL A 508 " --> pdb=" O   GLU A 504 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A 509 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG A 510 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 62
      removed outlier: 3.974A  pdb=" N   ALA B  59 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE B  61 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU B  62 " --> pdb=" O   ALA B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 69
      No H-bonds generated for 'chain 'B' and resid 66 through 69'
    Processing helix  chain 'B' and resid 74 through 77
      No H-bonds generated for 'chain 'B' and resid 74 through 77'
    Processing helix  chain 'B' and resid 82 through 88
      removed outlier: 4.418A  pdb=" N   ALA B  87 " --> pdb=" O   PRO B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 148
      removed outlier: 3.522A  pdb=" N   PHE B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 167
    Processing helix  chain 'B' and resid 210 through 218
      removed outlier: 3.581A  pdb=" N   LEU B 215 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 267
      removed outlier: 3.751A  pdb=" N   MET B 267 " --> pdb=" O   TYR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 330
      removed outlier: 3.933A  pdb=" N   THR B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   THR B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLN B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL B 318 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA B 321 " --> pdb=" O   GLN B 317 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA B 325 " --> pdb=" O   ALA B 321 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE B 327 " --> pdb=" O   ASP B 323 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN B 329 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 341
      removed outlier: 4.150A  pdb=" N   ARG B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL B 338 " --> pdb=" O   HIS B 334 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA B 341 " --> pdb=" O   ARG B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 363
      No H-bonds generated for 'chain 'B' and resid 360 through 363'
    Processing helix  chain 'B' and resid 385 through 397
      removed outlier: 3.512A  pdb=" N   ALA B 390 " --> pdb=" O   PRO B 386 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B 393 " --> pdb=" O   ASP B 389 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR B 397 " --> pdb=" O   ALA B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 411
      No H-bonds generated for 'chain 'B' and resid 408 through 411'
    Processing helix  chain 'B' and resid 466 through 473
      removed outlier: 3.894A  pdb=" N   THR B 471 " --> pdb=" O   HIS B 467 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TYR B 472 " --> pdb=" O   SER B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 498
      removed outlier: 3.624A  pdb=" N   GLU B 490 " --> pdb=" O   GLY B 486 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASP B 493 " --> pdb=" O   GLU B 489 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ARG B 495 " --> pdb=" O   ALA B 491 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP B 496 " --> pdb=" O   GLN B 492 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR B 497 " --> pdb=" O   ASP B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 520
      removed outlier: 4.041A  pdb=" N   VAL B 508 " --> pdb=" O   GLU B 504 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE B 509 " --> pdb=" O   ARG B 505 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG B 510 " --> pdb=" O   LEU B 506 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 99 through 104
      removed outlier: 3.531A  pdb=" N   LEU A 103 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASP A  45 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL A  51 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 183 through 190
      removed outlier: 3.689A  pdb=" N   THR A 183 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   LEU A 175 " --> pdb=" O   ILE A 187 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL A 173 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA A 288 " --> pdb=" O   MET A 174 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   TRP A 284 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 277 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   LEU A 286 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   VAL A 275 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ALA A 288 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU A 273 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   HIS A 290 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   SER A 271 " --> pdb=" O   HIS A 290 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 375 through 380
      removed outlier: 4.585A  pdb=" N   GLU A 436 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 424 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 99 through 105
      removed outlier: 3.521A  pdb=" N   LEU B 103 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASP B  45 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL B  51 " --> pdb=" O   ASP B  45 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 183 through 190
      removed outlier: 3.689A  pdb=" N   THR B 183 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   LEU B 175 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLU B 189 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   VAL B 173 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA B 288 " --> pdb=" O   MET B 174 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   TRP B 284 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL B 277 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL B 275 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   ALA B 288 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LEU B 273 " --> pdb=" O   ALA B 288 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   HIS B 290 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   SER B 271 " --> pdb=" O   HIS B 290 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 375 through 380
      removed outlier: 4.568A  pdb=" N   GLU B 436 " --> pdb=" O   VAL B 430 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY B 424 " --> pdb=" O   ARG B 442 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    717 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: 2.12

  Time building geometry restraints manager: 3.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1481
        1.33 -     1.45: 1744
        1.45 -     1.57: 4349
        1.57 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 7610
  Sorted by residual:
  bond pdb=" C2B BLA B1000 "
       pdb=" C3B BLA B1000 "
    ideal  model  delta    sigma   weight residual
    1.357  1.432 -0.075 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" C2B BLA A1000 "
       pdb=" C3B BLA A1000 "
    ideal  model  delta    sigma   weight residual
    1.357  1.429 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C1D BLA A1000 "
       pdb=" CHD BLA A1000 "
    ideal  model  delta    sigma   weight residual
    1.440  1.373  0.067 2.00e-02 2.50e+03 1.12e+01
  bond pdb=" C2C BLA A1000 "
       pdb=" C3C BLA A1000 "
    ideal  model  delta    sigma   weight residual
    1.351  1.415 -0.064 2.00e-02 2.50e+03 1.03e+01
  bond pdb=" C1D BLA B1000 "
       pdb=" CHD BLA B1000 "
    ideal  model  delta    sigma   weight residual
    1.440  1.377  0.063 2.00e-02 2.50e+03 1.00e+01
  ... (remaining 7605 not shown)

  Histogram of bond angle deviations from ideal:
      100.08 -   107.43: 419
      107.43 -   114.78: 4270
      114.78 -   122.13: 3391
      122.13 -   129.48: 2249
      129.48 -   136.83: 81
  Bond angle restraints: 10410
  Sorted by residual:
  angle pdb=" C   PHE B 203 "
        pdb=" CA  PHE B 203 "
        pdb=" CB  PHE B 203 "
      ideal   model   delta    sigma   weight residual
     108.87  115.23   -6.36 1.55e+00 4.16e-01 1.68e+01
  angle pdb=" C   PHE A 203 "
        pdb=" CA  PHE A 203 "
        pdb=" CB  PHE A 203 "
      ideal   model   delta    sigma   weight residual
     108.87  115.05   -6.18 1.55e+00 4.16e-01 1.59e+01
  angle pdb=" CB  ARG A 375 "
        pdb=" CG  ARG A 375 "
        pdb=" CD  ARG A 375 "
      ideal   model   delta    sigma   weight residual
     111.30  120.43   -9.13 2.30e+00 1.89e-01 1.58e+01
  angle pdb=" C   PRO B 384 "
        pdb=" N   ALA B 385 "
        pdb=" CA  ALA B 385 "
      ideal   model   delta    sigma   weight residual
     120.09  124.82   -4.73 1.25e+00 6.40e-01 1.43e+01
  angle pdb=" C   PRO A 384 "
        pdb=" N   ALA A 385 "
        pdb=" CA  ALA A 385 "
      ideal   model   delta    sigma   weight residual
     120.09  124.79   -4.70 1.25e+00 6.40e-01 1.41e+01
  ... (remaining 10405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 3883
       17.27 -    34.54: 440
       34.54 -    51.80: 120
       51.80 -    69.07: 71
       69.07 -    86.34: 6
  Dihedral angle restraints: 4520
    sinusoidal: 1776
      harmonic: 2744
  Sorted by residual:
  dihedral pdb=" CA  HIS B 219 "
           pdb=" C   HIS B 219 "
           pdb=" N   LEU B 220 "
           pdb=" CA  LEU B 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.72  -19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  HIS A 219 "
           pdb=" C   HIS A 219 "
           pdb=" N   LEU A 220 "
           pdb=" CA  LEU A 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.76  -19.24     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CG  ARG B 514 "
           pdb=" CD  ARG B 514 "
           pdb=" NE  ARG B 514 "
           pdb=" CZ  ARG B 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.38   44.62     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 4517 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 627
       0.050 -    0.100: 285
       0.100 -    0.151: 190
       0.151 -    0.201: 54
       0.201 -    0.251: 17
  Chirality restraints: 1173
  Sorted by residual:
  chirality pdb=" CB  VAL A 237 "
            pdb=" CA  VAL A 237 "
            pdb=" CG1 VAL A 237 "
            pdb=" CG2 VAL A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL A 449 "
            pdb=" CA  VAL A 449 "
            pdb=" CG1 VAL A 449 "
            pdb=" CG2 VAL A 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ASN B 243 "
            pdb=" N   ASN B 243 "
            pdb=" C   ASN B 243 "
            pdb=" CB  ASN B 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1170 not shown)

  Planarity restraints: 1364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C BLA B1000 "   -0.001 2.00e-02 2.50e+03   2.84e-01 2.01e+03
        pdb=" C1D BLA B1000 "    0.520 2.00e-02 2.50e+03
        pdb=" C2C BLA B1000 "   -0.007 2.00e-02 2.50e+03
        pdb=" C3C BLA B1000 "   -0.040 2.00e-02 2.50e+03
        pdb=" C4C BLA B1000 "   -0.264 2.00e-02 2.50e+03
        pdb=" CAC BLA B1000 "    0.147 2.00e-02 2.50e+03
        pdb=" CHD BLA B1000 "   -0.254 2.00e-02 2.50e+03
        pdb=" CMC BLA B1000 "    0.055 2.00e-02 2.50e+03
        pdb=" NC  BLA B1000 "   -0.503 2.00e-02 2.50e+03
        pdb=" OC  BLA B1000 "    0.347 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  BLA B1000 "   -0.384 2.00e-02 2.50e+03   2.82e-01 1.98e+03
        pdb=" OB  BLA B1000 "    0.184 2.00e-02 2.50e+03
        pdb=" C1B BLA B1000 "   -0.180 2.00e-02 2.50e+03
        pdb=" C2B BLA B1000 "   -0.174 2.00e-02 2.50e+03
        pdb=" C3B BLA B1000 "    0.071 2.00e-02 2.50e+03
        pdb=" C4A BLA B1000 "    0.543 2.00e-02 2.50e+03
        pdb=" C4B BLA B1000 "   -0.019 2.00e-02 2.50e+03
        pdb=" CAB BLA B1000 "    0.348 2.00e-02 2.50e+03
        pdb=" CHB BLA B1000 "   -0.032 2.00e-02 2.50e+03
        pdb=" CMB BLA B1000 "   -0.357 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C BLA A1000 "   -0.034 2.00e-02 2.50e+03   2.78e-01 1.93e+03
        pdb=" C1D BLA A1000 "    0.551 2.00e-02 2.50e+03
        pdb=" C2C BLA A1000 "    0.033 2.00e-02 2.50e+03
        pdb=" C3C BLA A1000 "   -0.075 2.00e-02 2.50e+03
        pdb=" C4C BLA A1000 "   -0.247 2.00e-02 2.50e+03
        pdb=" CAC BLA A1000 "    0.008 2.00e-02 2.50e+03
        pdb=" CHD BLA A1000 "   -0.175 2.00e-02 2.50e+03
        pdb=" CMC BLA A1000 "    0.210 2.00e-02 2.50e+03
        pdb=" NC  BLA A1000 "   -0.515 2.00e-02 2.50e+03
        pdb=" OC  BLA A1000 "    0.243 2.00e-02 2.50e+03
  ... (remaining 1361 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1581
        2.83 -     3.35: 6142
        3.35 -     3.87: 12015
        3.87 -     4.38: 13388
        4.38 -     4.90: 23364
  Nonbonded interactions: 56490
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 107 "
            pdb=" N   GLY A 109 "
     model   vdw
     2.316 2.520
  nonbonded pdb=" O   LEU B 516 "
            pdb=" OG  SER B 519 "
     model   vdw
     2.584 2.440
  nonbonded pdb=" O   LEU A 516 "
            pdb=" OG  SER A 519 "
     model   vdw
     2.585 2.440
  nonbonded pdb=" O   GLY A  39 "
            pdb=" ND2 ASN A  57 "
     model   vdw
     2.600 2.520
  nonbonded pdb=" O   GLY B  39 "
            pdb=" ND2 ASN B  57 "
     model   vdw
     2.601 2.520
  ... (remaining 56485 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 22 through 107 or resid 109 through 521 or resid 1000))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.050
  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:          19.160
  Check model and map are aligned:         0.090
  Set scattering table:                    0.050
  Process input model:                     23.320
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.030
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
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      :  0.008   0.075   7610  Z= 0.528
  Angle     :  1.384   9.131  10410  Z= 0.921
  Chirality :  0.079   0.251   1173
  Planarity :  0.015   0.284   1364
  Dihedral  : 17.787  86.341   2746
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.54 %
    Favored  : 95.25 %
  Rotamer Outliers :  4.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.22), residues: 947
  helix: -3.67 (0.16), residues: 369
  sheet: -1.34 (0.36), residues: 180
  loop : -2.13 (0.26), residues: 398

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 4
  residues processed: 174
  average time/residue: 0.2407
  time to fit residues: 53.7629
Evaluate side-chains
  90 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.803 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0693
  time to fit residues: 1.7200
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0050
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A 110 HIS
A 239 ASN
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 HIS
B 334 HIS
B 335 HIS
B 410 GLN
** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7610  Z= 0.201
  Angle     :  0.644   8.993  10410  Z= 0.299
  Chirality :  0.041   0.137   1173
  Planarity :  0.004   0.030   1364
  Dihedral  :  6.542  75.889   1058
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer Outliers :  3.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -2.51 (0.25), residues: 947
  helix: -2.27 (0.23), residues: 361
  sheet: -0.79 (0.37), residues: 188
  loop : -1.29 (0.29), residues: 398

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
  outliers start: 30
  outliers final: 8
  residues processed: 122
  average time/residue: 0.2146
  time to fit residues: 35.0132
Evaluate side-chains
  84 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.920 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0657
  time to fit residues: 2.1695
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
A 262 GLN
A 266 ASN
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 ASN
B 110 HIS
B 241 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.4536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7610  Z= 0.383
  Angle     :  0.798  11.465  10410  Z= 0.378
  Chirality :  0.047   0.169   1173
  Planarity :  0.006   0.039   1364
  Dihedral  :  7.110  59.763   1058
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer Outliers :  3.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -2.45 (0.25), residues: 947
  helix: -2.03 (0.24), residues: 368
  sheet: -0.80 (0.36), residues: 188
  loop : -1.43 (0.29), residues: 391

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
  outliers start: 26
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1971
  time to fit residues: 29.7999
Evaluate side-chains
  88 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.887 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0714
  time to fit residues: 2.6018
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.0970
   chunk 65 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0980
   chunk 9 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 58 optimal weight:    0.1980
   chunk 87 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0010
   chunk 25 optimal weight:    0.0770
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.0942

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

Flipped N/Q/H residues before XYZ refinement:
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6678
moved from start:          0.4664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7610  Z= 0.137
  Angle     :  0.612   9.851  10410  Z= 0.275
  Chirality :  0.040   0.143   1173
  Planarity :  0.004   0.037   1364
  Dihedral  :  6.264  74.783   1058
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer Outliers :  1.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -1.39 (0.26), residues: 947
  helix: -1.02 (0.27), residues: 358
  sheet: -0.48 (0.36), residues: 185
  loop : -0.85 (0.30), residues: 404

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 3
  residues processed: 94
  average time/residue: 0.1911
  time to fit residues: 25.1841
Evaluate side-chains
  69 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.786 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0737
  time to fit residues: 1.4709
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0270
   chunk 69 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0770
   chunk 64 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.4974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7610  Z= 0.164
  Angle     :  0.610   9.233  10410  Z= 0.275
  Chirality :  0.041   0.241   1173
  Planarity :  0.004   0.037   1364
  Dihedral  :  5.885  62.388   1058
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer Outliers :  1.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -1.13 (0.27), residues: 947
  helix: -0.74 (0.27), residues: 367
  sheet: -0.55 (0.36), residues: 194
  loop : -0.63 (0.32), residues: 386

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.859 
Fit side-chains
  outliers start: 15
  outliers final: 6
  residues processed: 86
  average time/residue: 0.1970
  time to fit residues: 23.5785
Evaluate side-chains
  75 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.854 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0767
  time to fit residues: 2.0448
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 54 optimal weight:    0.1980
   chunk 22 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0040
   chunk 43 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
A 484 HIS
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7610  Z= 0.140
  Angle     :  0.574   8.786  10410  Z= 0.258
  Chirality :  0.040   0.152   1173
  Planarity :  0.004   0.038   1364
  Dihedral  :  5.434  48.966   1058
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer Outliers :  1.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.85 (0.27), residues: 947
  helix: -0.45 (0.28), residues: 364
  sheet: -0.45 (0.36), residues: 194
  loop : -0.51 (0.32), residues: 389

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.917 
Fit side-chains
  outliers start: 8
  outliers final: 4
  residues processed: 76
  average time/residue: 0.1829
  time to fit residues: 20.0530
Evaluate side-chains
  70 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.873 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0899
  time to fit residues: 1.7887
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0980
   chunk 42 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 344 HIS
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 ASN
B 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7610  Z= 0.255
  Angle     :  0.678  10.597  10410  Z= 0.312
  Chirality :  0.043   0.157   1173
  Planarity :  0.005   0.037   1364
  Dihedral  :  5.999  52.064   1058
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer Outliers :  2.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -1.08 (0.27), residues: 947
  helix: -0.66 (0.27), residues: 353
  sheet: -0.50 (0.36), residues: 196
  loop : -0.68 (0.31), residues: 398

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.911 
Fit side-chains
  outliers start: 17
  outliers final: 8
  residues processed: 83
  average time/residue: 0.2069
  time to fit residues: 23.9530
Evaluate side-chains
  77 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.840 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0833
  time to fit residues: 2.3172
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 63 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0870
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.5691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7610  Z= 0.163
  Angle     :  0.610  10.572  10410  Z= 0.278
  Chirality :  0.040   0.150   1173
  Planarity :  0.004   0.037   1364
  Dihedral  :  5.541  51.045   1058
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer Outliers :  0.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.73 (0.27), residues: 947
  helix: -0.27 (0.28), residues: 352
  sheet: -0.36 (0.37), residues: 195
  loop : -0.56 (0.31), residues: 400

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.862 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 72
  average time/residue: 0.2051
  time to fit residues: 20.6826
Evaluate side-chains
  66 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.879 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0810
  time to fit residues: 1.7215
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 88 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6820
moved from start:          0.5930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7610  Z= 0.226
  Angle     :  0.658   9.833  10410  Z= 0.307
  Chirality :  0.042   0.172   1173
  Planarity :  0.005   0.040   1364
  Dihedral  :  5.776  50.676   1058
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer Outliers :  0.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.85 (0.27), residues: 947
  helix: -0.32 (0.28), residues: 351
  sheet: -0.44 (0.37), residues: 195
  loop : -0.66 (0.31), residues: 401

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.911 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 68
  average time/residue: 0.2432
  time to fit residues: 22.3482
Evaluate side-chains
  66 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.926 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0819
  time to fit residues: 1.7136
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 95 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.2980
   chunk 60 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.6090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7610  Z= 0.195
  Angle     :  0.622  10.246  10410  Z= 0.289
  Chirality :  0.041   0.165   1173
  Planarity :  0.005   0.046   1364
  Dihedral  :  5.662  51.874   1058
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer Outliers :  0.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.72 (0.27), residues: 947
  helix: -0.24 (0.28), residues: 346
  sheet: -0.39 (0.37), residues: 195
  loop : -0.55 (0.31), residues: 406

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.883 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 69
  average time/residue: 0.2202
  time to fit residues: 20.7936
Evaluate side-chains
  62 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.883 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0664
  time to fit residues: 1.2233
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0470
   chunk 78 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7482

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

Flipped N/Q/H residues before XYZ refinement:
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.180496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.158162 restraints weight = 13359.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.160814 restraints weight = 8556.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.161921 restraints weight = 5819.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.6194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7610  Z= 0.192
  Angle     :  0.625   9.813  10410  Z= 0.288
  Chirality :  0.041   0.159   1173
  Planarity :  0.005   0.045   1364
  Dihedral  :  5.568  52.146   1058
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer Outliers :  0.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.65 (0.27), residues: 947
  helix: -0.20 (0.28), residues: 346
  sheet: -0.37 (0.37), residues: 195
  loop : -0.48 (0.31), residues: 406

===============================================================================
Job complete
usr+sys time: 1746.35 seconds
wall clock time: 32 minutes 12.30 seconds (1932.30 seconds total)