Starting phenix.real_space_refine
on Wed Mar  4 10:28:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vwi_21417/03_2026/6vwi_21417_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vwi_21417/03_2026/6vwi_21417.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vwi_21417/03_2026/6vwi_21417_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vwi_21417/03_2026/6vwi_21417_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vwi_21417/03_2026/6vwi_21417.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vwi_21417/03_2026/6vwi_21417.map"
  }
  resolution = 3.7
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4078      2.51       5
     N    1115      2.21       5
     O    1224      1.98       5
     H    6283      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12752
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 6916
          Classifications: {'peptide': 439}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 422}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 4981
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 11, 'TRANS': 295}
          Chain breaks: 2
    Chain: "I"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 799
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 1, 'TRANS': 52}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.19, per 1000 atoms: 0.17
  Number of scatterers: 12752
  At special positions: 0
  Unit cell: (78.44, 110.24, 107.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     O    1224      8.00
     N    1115      7.00
     C    4078      6.00
     H    6283      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   3 " - pdb=" SG  CYS A  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 120 " - pdb=" SG  CYS A 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 152 " - pdb=" SG  CYS A 175 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 185 " - pdb=" SG  CYS A 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 201 " - pdb=" SG  CYS A 209 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 205 " - pdb=" SG  CYS A 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 221 " - pdb=" SG  CYS A 230 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 252 " - pdb=" SG  CYS A 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 277 " - pdb=" SG  CYS A 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 302 " - pdb=" SG  CYS A 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 302 " - pdb=" SG  CYS B 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 425 " - pdb=" SG  CYS B 458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I   9 " - pdb=" SG  CYS I  47 " distance=2.02
    Simple disulfide: pdb=" SG  CYS I  21 " - pdb=" SG  CYS I  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  46 " - pdb=" SG  CYS I  51 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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
  Links applied
    NAG-ASN
      " NAG A1001 " - " ASN A  21 "
      " NAG A1002 " - " ASN A 387 "
      " NAG A1003 " - " ASN A 105 "
      " NAG B1001 " - " ASN B 504 "
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 348.9 milliseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 18 sheets defined
      21.2% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 22
      removed outlier: 3.791A  pdb=" N   LYS A  17 " --> pdb=" O   GLN A  14 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ASN A  21 " --> pdb=" O   ARG A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 43
      removed outlier: 3.681A  pdb=" N   TYR A  43 " --> pdb=" O   TYR A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 126 through 131
    Processing helix  chain 'A' and resid 133 through 137
    Processing helix  chain 'A' and resid 144 through 148
      removed outlier: 3.798A  pdb=" N   CYS A 148 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 190
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 248 through 253
    Processing helix  chain 'A' and resid 313 through 319
      removed outlier: 3.661A  pdb=" N   MET A 319 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 349
      removed outlier: 4.004A  pdb=" N   ASN A 346 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 436
    Processing helix  chain 'B' and resid 313 through 318
    Processing helix  chain 'B' and resid 319 through 321
      No H-bonds generated for 'chain 'B' and resid 319 through 321'
    Processing helix  chain 'B' and resid 339 through 349
      removed outlier: 3.908A  pdb=" N   GLU B 343 " --> pdb=" O   ASN B 339 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASN B 346 " --> pdb=" O   SER B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 436
      removed outlier: 3.747A  pdb=" N   ILE B 429 " --> pdb=" O   CYS B 425 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR B 430 " --> pdb=" O   VAL B 426 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ARG B 431 " --> pdb=" O   SER B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 447
    Processing helix  chain 'B' and resid 486 through 488
      No H-bonds generated for 'chain 'B' and resid 486 through 488'
    Processing helix  chain 'B' and resid 560 through 564
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 683 through 701
      removed outlier: 5.028A  pdb=" N   ARG B 689 " --> pdb=" O   GLU B 685 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   VAL B 691 " --> pdb=" O   GLU B 687 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   PHE B 692 " --> pdb=" O   TYR B 688 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE B 701 " --> pdb=" O   HIS B 697 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 10 through 22
    Processing helix  chain 'I' and resid 41 through 47
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 3.520A  pdb=" N   ILE A  76 " --> pdb=" O   ASN A 105 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9
      removed outlier: 6.819A  pdb=" N   ILE A   7 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   LEU A  32 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ILE A   9 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LEU A  29 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   PHE A  58 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ILE A  31 " --> pdb=" O   PHE A  58 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   LEU A  55 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   PHE A  90 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   LEU A  57 " --> pdb=" O   PHE A  90 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   ARG A 112 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   VAL A  88 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   GLU A 114 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE A  90 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ILE A 111 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   VAL A 140 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ILE A 113 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165
    Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177
      removed outlier: 3.561A  pdb=" N   THR A 177 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 195
    Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 209
      removed outlier: 3.548A  pdb=" N   ALA A 220 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   SER A 208 " --> pdb=" O   CYS A 218 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   CYS A 218 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 226
    Processing sheet with id=AA8, first strand: chain 'A' and resid 239 through 241
    Processing sheet with id=AA9, first strand: chain 'A' and resid 267 through 269
    Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 283
    Processing sheet with id=AB2, first strand: chain 'A' and resid 301 through 302
    Processing sheet with id=AB3, first strand: chain 'A' and resid 308 through 311
      removed outlier: 3.650A  pdb=" N   LEU A 331 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 358 through 361
      removed outlier: 6.659A  pdb=" N   VAL A 358 " --> pdb=" O   TYR A 391 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   LEU A 393 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE A 360 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 301 through 311
      removed outlier: 5.991A  pdb=" N   ILE B 325 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   GLU B 303 " --> pdb=" O   ILE B 325 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   LYS B 327 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLU B 305 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
      removed outlier: 8.913A  pdb=" N   ASN B 329 " --> pdb=" O   GLU B 305 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LYS B 307 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   LEU B 331 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LYS B 309 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 301 through 311
      removed outlier: 5.991A  pdb=" N   ILE B 325 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   GLU B 303 " --> pdb=" O   ILE B 325 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   LYS B 327 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLU B 305 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
      removed outlier: 8.913A  pdb=" N   ASN B 329 " --> pdb=" O   GLU B 305 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LYS B 307 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   LEU B 331 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LYS B 309 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
      removed outlier: 8.691A  pdb=" N   LYS B 359 " --> pdb=" O   GLY B 328 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LEU B 330 " --> pdb=" O   LYS B 359 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ARG B 361 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE B 332 " --> pdb=" O   ARG B 361 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   TYR B 417 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   TYR B 391 " --> pdb=" O   TYR B 417 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   ALA B 419 " --> pdb=" O   TYR B 391 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   LEU B 393 " --> pdb=" O   ALA B 419 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 461 through 463
      removed outlier: 5.894A  pdb=" N   ASP B 461 " --> pdb=" O   LYS B 568 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 465 through 470
      removed outlier: 3.694A  pdb=" N   SER B 467 " --> pdb=" O   THR B 478 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 520 through 524
      removed outlier: 3.845A  pdb=" N   SER B 492 " --> pdb=" O   VAL B 554 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    315 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: 2.69

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6282
        1.03 -     1.23: 150
        1.23 -     1.43: 2645
        1.43 -     1.63: 3734
        1.63 -     1.83: 67
  Bond restraints: 12878
  Sorted by residual:
  bond pdb=" C1  NAG A1002 "
       pdb=" O5  NAG A1002 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 7.14e+00
  bond pdb=" C1  NAG A1003 "
       pdb=" C2  NAG A1003 "
    ideal  model  delta    sigma   weight residual
    1.532  1.486  0.046 2.00e-02 2.50e+03 5.28e+00
  bond pdb=" C1  NAG B1001 "
       pdb=" O5  NAG B1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.85e+00
  bond pdb=" N   SER I   5 "
       pdb=" CA  SER I   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.68e+00
  bond pdb=" C1  NAG A1001 "
       pdb=" O5  NAG A1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.35e+00
  ... (remaining 12873 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 20886
        1.21 -     2.42: 2053
        2.42 -     3.64: 207
        3.64 -     4.85: 33
        4.85 -     6.06: 9
  Bond angle restraints: 23188
  Sorted by residual:
  angle pdb=" N   LYS A 373 "
        pdb=" CA  LYS A 373 "
        pdb=" C   LYS A 373 "
      ideal   model   delta    sigma   weight residual
     111.11  115.51   -4.40 1.20e+00 6.94e-01 1.35e+01
  angle pdb=" N   ARG B 407 "
        pdb=" CA  ARG B 407 "
        pdb=" C   ARG B 407 "
      ideal   model   delta    sigma   weight residual
     108.69  114.45   -5.76 1.77e+00 3.19e-01 1.06e+01
  angle pdb=" CA  TRP B 544 "
        pdb=" CB  TRP B 544 "
        pdb=" CG  TRP B 544 "
      ideal   model   delta    sigma   weight residual
     113.60  119.04   -5.44 1.90e+00 2.77e-01 8.19e+00
  angle pdb=" N   ASN A  11 "
        pdb=" CA  ASN A  11 "
        pdb=" C   ASN A  11 "
      ideal   model   delta    sigma   weight residual
     110.80  116.86   -6.06 2.13e+00 2.20e-01 8.09e+00
  angle pdb=" N   LEU B 366 "
        pdb=" CA  LEU B 366 "
        pdb=" C   LEU B 366 "
      ideal   model   delta    sigma   weight residual
     107.99  112.67   -4.68 1.77e+00 3.19e-01 6.99e+00
  ... (remaining 23183 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 5496
       17.65 -    35.30: 436
       35.30 -    52.95: 124
       52.95 -    70.60: 82
       70.60 -    88.25: 12
  Dihedral angle restraints: 6150
    sinusoidal: 3404
      harmonic: 2746
  Sorted by residual:
  dihedral pdb=" CB  CYS A 162 "
           pdb=" SG  CYS A 162 "
           pdb=" SG  CYS A 181 "
           pdb=" CB  CYS A 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -164.87   78.87     1      1.00e+01 1.00e-02 7.75e+01
  dihedral pdb=" CA  ASN B 374 "
           pdb=" C   ASN B 374 "
           pdb=" N   LEU B 375 "
           pdb=" CA  LEU B 375 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.07  -28.93     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CB  CYS A 252 "
           pdb=" SG  CYS A 252 "
           pdb=" SG  CYS A 273 "
           pdb=" CB  CYS A 273 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.20   49.20     1      1.00e+01 1.00e-02 3.33e+01
  ... (remaining 6147 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 525
       0.035 -    0.069: 293
       0.069 -    0.104: 126
       0.104 -    0.138: 42
       0.138 -    0.173: 5
  Chirality restraints: 991
  Sorted by residual:
  chirality pdb=" CA  CYS I  46 "
            pdb=" N   CYS I  46 "
            pdb=" C   CYS I  46 "
            pdb=" CB  CYS I  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.47e-01
  chirality pdb=" C2  NAG A1002 "
            pdb=" C1  NAG A1002 "
            pdb=" C3  NAG A1002 "
            pdb=" N2  NAG A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.34   -0.16 2.00e-01 2.50e+01 6.16e-01
  chirality pdb=" C1  NAG A1003 "
            pdb=" ND2 ASN A 105 "
            pdb=" C2  NAG A1003 "
            pdb=" O5  NAG A1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-01 2.50e+01 5.37e-01
  ... (remaining 988 not shown)

  Planarity restraints: 1909
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 395 "    0.055 2.00e-02 2.50e+03   6.42e-02 6.19e+01
        pdb=" CG  ASN A 395 "   -0.061 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 395 "    0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 395 "   -0.094 2.00e-02 2.50e+03
        pdb="HD21 ASN A 395 "   -0.003 2.00e-02 2.50e+03
        pdb="HD22 ASN A 395 "    0.095 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 336 "   -0.150 9.50e-02 1.11e+02   6.80e-02 5.02e+01
        pdb=" NE  ARG A 336 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 336 "    0.063 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 336 "   -0.067 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 336 "    0.025 2.00e-02 2.50e+03
        pdb="HH11 ARG A 336 "   -0.027 2.00e-02 2.50e+03
        pdb="HH12 ARG A 336 "    0.075 2.00e-02 2.50e+03
        pdb="HH21 ARG A 336 "   -0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A 336 "   -0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 395 "   -0.041 2.00e-02 2.50e+03   5.08e-02 3.86e+01
        pdb=" CG  ASN B 395 "    0.038 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 395 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 395 "    0.080 2.00e-02 2.50e+03
        pdb="HD21 ASN B 395 "    0.001 2.00e-02 2.50e+03
        pdb="HD22 ASN B 395 "   -0.077 2.00e-02 2.50e+03
  ... (remaining 1906 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 494
        2.13 -     2.75: 23964
        2.75 -     3.37: 34936
        3.37 -     3.98: 44530
        3.98 -     4.60: 70137
  Nonbonded interactions: 174061
  Sorted by model distance:
  nonbonded pdb=" HG1 THR A 195 "
            pdb=" O   CYS A 209 "
     model   vdw
     1.513 2.450
  nonbonded pdb="HH11 ARG A 174 "
            pdb=" OE1 GLN A 182 "
     model   vdw
     1.546 2.450
  nonbonded pdb=" H   CYS I   9 "
            pdb=" OE2 GLU I  12 "
     model   vdw
     1.548 2.450
  nonbonded pdb=" O   ALA A  61 "
            pdb="HD21 ASN A  94 "
     model   vdw
     1.572 2.450
  nonbonded pdb=" HZ2 LYS A 164 "
            pdb=" OH  TYR A 171 "
     model   vdw
     1.597 2.450
  ... (remaining 174056 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=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:             4.430
  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:             0.070
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.660
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
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      :  0.007   0.053   6617  Z= 0.281
  Angle     :  0.883   6.059   8956  Z= 0.499
  Chirality :  0.051   0.173    991
  Planarity :  0.008   0.108   1140
  Dihedral  : 14.894  88.250   2524
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.89 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  6.60 %
    Favored  : 91.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.28), residues: 782
  helix: -3.51 (0.33), residues: 101
  sheet: -0.76 (0.46), residues: 118
  loop : -1.53 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.080   0.013   ARG A 104 
 TYR   0.040   0.007   TYR A 138 
 PHE   0.022   0.004   PHE A  45 
 TRP   0.038   0.007   TRP A 176 
 HIS   0.009   0.003   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00679 ( 6595)
  covalent geometry    : angle       0.87789 ( 8908)
  SS BOND              : bond        0.00421 (   18)
  SS BOND              : angle       1.26709 (   36)
  hydrogen bonds       : bond        0.22043 (  136)
  hydrogen bonds       : angle       9.91789 (  315)
  link_NAG-ASN         : bond        0.00370 (    4)
  link_NAG-ASN         : angle       2.23797 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.383 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.8325 (t80) cc_final: 0.8116 (t80)
REVERT: A  256 LEU cc_start: 0.8342 (tp) cc_final: 0.7774 (pt)
REVERT: A  266 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.4320 (t80)
REVERT: A  333 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7498 (t0)
REVERT: B  396 GLN cc_start: 0.7956 (mt0) cc_final: 0.7687 (mt0)
REVERT: B  572 LEU cc_start: 0.8623 (tp) cc_final: 0.8322 (tp)
REVERT: I   44 GLU cc_start: 0.7835 (tt0) cc_final: 0.7279 (tt0)
  outliers start: 14
  outliers final: 3
  residues processed: 148
  average time/residue: 0.2128
  time to fit residues: 40.0132
Evaluate side-chains
  80 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  333 ASN
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain B residue  333 ASN
Chi-restraints excluded: chain I residue    8 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
A 197 ASN
B 339 ASN
B 387 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.106688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.090038 restraints weight = 47606.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.094050 restraints weight = 21746.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.096792 restraints weight = 12768.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.098628 restraints weight = 8610.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.099929 restraints weight = 6349.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6617  Z= 0.157
  Angle     :  0.724  13.417   8956  Z= 0.391
  Chirality :  0.047   0.159    991
  Planarity :  0.005   0.083   1140
  Dihedral  :  8.879  56.643    970
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.66 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.29), residues: 782
  helix: -2.08 (0.46), residues: 108
  sheet: -1.16 (0.46), residues: 110
  loop : -1.20 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 455 
 TYR   0.010   0.001   TYR B 391 
 PHE   0.017   0.002   PHE A 326 
 TRP   0.010   0.001   TRP A 402 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6595)
  covalent geometry    : angle       0.69176 ( 8908)
  SS BOND              : bond        0.00483 (   18)
  SS BOND              : angle       3.35062 (   36)
  hydrogen bonds       : bond        0.04692 (  136)
  hydrogen bonds       : angle       7.35253 (  315)
  link_NAG-ASN         : bond        0.00270 (    4)
  link_NAG-ASN         : angle       1.57438 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.339 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ASP cc_start: 0.8191 (t0) cc_final: 0.7959 (t0)
REVERT: A  118 ASP cc_start: 0.7518 (t0) cc_final: 0.7202 (t70)
REVERT: A  312 ASP cc_start: 0.6620 (t0) cc_final: 0.5958 (t0)
REVERT: A  333 ASN cc_start: 0.7482 (t0) cc_final: 0.7223 (t0)
REVERT: A  398 LEU cc_start: 0.8406 (tp) cc_final: 0.8189 (tt)
REVERT: A  439 LYS cc_start: 0.7754 (mttt) cc_final: 0.6712 (tptt)
REVERT: B  406 HIS cc_start: 0.6634 (OUTLIER) cc_final: 0.6378 (m-70)
REVERT: I   44 GLU cc_start: 0.7925 (tt0) cc_final: 0.7407 (tt0)
  outliers start: 14
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1631
  time to fit residues: 22.2126
Evaluate side-chains
  84 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 GLU
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  406 HIS
Chi-restraints excluded: chain B residue  458 CYS
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  539 HIS
Chi-restraints excluded: chain B residue  674 LYS
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN
** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.116098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.099784 restraints weight = 46012.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.103890 restraints weight = 21121.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.106548 restraints weight = 12519.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.108309 restraints weight = 8551.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.109528 restraints weight = 6413.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6617  Z= 0.140
  Angle     :  0.623   7.134   8956  Z= 0.334
  Chirality :  0.046   0.153    991
  Planarity :  0.003   0.031   1140
  Dihedral  :  7.741  54.842    963
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.20 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.29), residues: 782
  helix: -1.55 (0.49), residues: 108
  sheet: -1.45 (0.43), residues: 110
  loop : -1.14 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  41 
 TYR   0.011   0.001   TYR B 391 
 PHE   0.012   0.002   PHE A  45 
 TRP   0.007   0.001   TRP B 402 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6595)
  covalent geometry    : angle       0.61143 ( 8908)
  SS BOND              : bond        0.00527 (   18)
  SS BOND              : angle       1.84584 (   36)
  hydrogen bonds       : bond        0.03965 (  136)
  hydrogen bonds       : angle       6.48569 (  315)
  link_NAG-ASN         : bond        0.00246 (    4)
  link_NAG-ASN         : angle       1.26000 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.269 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  300 LYS cc_start: 0.7662 (ptmt) cc_final: 0.7456 (ptmt)
  outliers start: 14
  outliers final: 9
  residues processed: 91
  average time/residue: 0.1656
  time to fit residues: 19.8647
Evaluate side-chains
  77 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  425 CYS
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  525 ASP
Chi-restraints excluded: chain B residue  539 HIS
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   60 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 76 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.113499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.097268 restraints weight = 45808.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.101283 restraints weight = 21325.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.103880 restraints weight = 12682.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.105635 restraints weight = 8730.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.106885 restraints weight = 6558.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6617  Z= 0.197
  Angle     :  0.639   5.721   8956  Z= 0.347
  Chirality :  0.047   0.160    991
  Planarity :  0.004   0.039   1140
  Dihedral  :  7.709  57.775    963
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.34 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.30), residues: 782
  helix: -1.56 (0.47), residues: 102
  sheet: -1.69 (0.43), residues: 110
  loop : -1.19 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 565 
 TYR   0.014   0.001   TYR B 391 
 PHE   0.015   0.002   PHE A  45 
 TRP   0.008   0.001   TRP B 402 
 HIS   0.005   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 6595)
  covalent geometry    : angle       0.62981 ( 8908)
  SS BOND              : bond        0.00430 (   18)
  SS BOND              : angle       1.69903 (   36)
  hydrogen bonds       : bond        0.03830 (  136)
  hydrogen bonds       : angle       6.62503 (  315)
  link_NAG-ASN         : bond        0.00276 (    4)
  link_NAG-ASN         : angle       1.41562 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.253 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ASP cc_start: 0.8344 (t0) cc_final: 0.8111 (p0)
REVERT: B  402 TRP cc_start: 0.6590 (OUTLIER) cc_final: 0.5944 (p-90)
REVERT: B  420 PHE cc_start: 0.7857 (m-80) cc_final: 0.7612 (m-80)
REVERT: I   44 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7971 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 86
  average time/residue: 0.1689
  time to fit residues: 19.5365
Evaluate side-chains
  78 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue  333 ASN
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  521 MET
Chi-restraints excluded: chain B residue  539 HIS
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   60 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 321 GLN
B 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.113773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.097374 restraints weight = 45639.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.101403 restraints weight = 21421.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.104062 restraints weight = 12852.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.105833 restraints weight = 8818.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.107049 restraints weight = 6627.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.4583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6617  Z= 0.150
  Angle     :  0.579   5.274   8956  Z= 0.311
  Chirality :  0.045   0.154    991
  Planarity :  0.003   0.041   1140
  Dihedral  :  7.289  55.028    963
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.31 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.04 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.29), residues: 782
  helix: -1.40 (0.48), residues: 102
  sheet: -1.77 (0.43), residues: 110
  loop : -1.24 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.011   0.001   TYR B 391 
 PHE   0.011   0.001   PHE A  45 
 TRP   0.006   0.001   TRP B 402 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6595)
  covalent geometry    : angle       0.57346 ( 8908)
  SS BOND              : bond        0.00313 (   18)
  SS BOND              : angle       1.19832 (   36)
  hydrogen bonds       : bond        0.03528 (  136)
  hydrogen bonds       : angle       6.35085 (  315)
  link_NAG-ASN         : bond        0.00227 (    4)
  link_NAG-ASN         : angle       1.24211 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.387 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  396 GLN cc_start: 0.7755 (mt0) cc_final: 0.7495 (mt0)
REVERT: B  402 TRP cc_start: 0.6617 (OUTLIER) cc_final: 0.5998 (p-90)
REVERT: B  420 PHE cc_start: 0.7900 (m-80) cc_final: 0.7657 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 87
  average time/residue: 0.1821
  time to fit residues: 21.1635
Evaluate side-chains
  82 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue  333 ASN
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  525 ASP
Chi-restraints excluded: chain B residue  539 HIS
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   60 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 339 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.113799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.097610 restraints weight = 45558.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.101609 restraints weight = 21239.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.104258 restraints weight = 12638.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.105992 restraints weight = 8633.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.107195 restraints weight = 6469.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.4885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6617  Z= 0.150
  Angle     :  0.568   5.170   8956  Z= 0.305
  Chirality :  0.045   0.153    991
  Planarity :  0.003   0.044   1140
  Dihedral  :  7.115  53.741    963
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.82 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.03 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.29), residues: 782
  helix: -1.33 (0.48), residues: 101
  sheet: -1.87 (0.43), residues: 110
  loop : -1.34 (0.27), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.012   0.001   TYR B 391 
 PHE   0.012   0.001   PHE A  45 
 TRP   0.006   0.001   TRP B 402 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6595)
  covalent geometry    : angle       0.56404 ( 8908)
  SS BOND              : bond        0.00287 (   18)
  SS BOND              : angle       1.04544 (   36)
  hydrogen bonds       : bond        0.03366 (  136)
  hydrogen bonds       : angle       6.18842 (  315)
  link_NAG-ASN         : bond        0.00208 (    4)
  link_NAG-ASN         : angle       1.22009 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.338 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.7044 (tmm) cc_final: 0.6815 (tmm)
REVERT: B  311 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8048 (mp)
REVERT: B  402 TRP cc_start: 0.6728 (OUTLIER) cc_final: 0.5939 (p-90)
  outliers start: 20
  outliers final: 14
  residues processed: 86
  average time/residue: 0.1540
  time to fit residues: 18.5854
Evaluate side-chains
  82 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  333 ASN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  525 ASP
Chi-restraints excluded: chain B residue  539 HIS
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   60 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.113916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.097484 restraints weight = 45744.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.101566 restraints weight = 20927.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.104289 restraints weight = 12373.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.106088 restraints weight = 8394.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.107297 restraints weight = 6233.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6617  Z= 0.135
  Angle     :  0.557   5.059   8956  Z= 0.299
  Chirality :  0.045   0.152    991
  Planarity :  0.003   0.044   1140
  Dihedral  :  6.908  53.721    963
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.57 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.47 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.29), residues: 782
  helix: -1.24 (0.49), residues: 101
  sheet: -1.90 (0.45), residues: 105
  loop : -1.36 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 455 
 TYR   0.010   0.001   TYR B 391 
 PHE   0.017   0.001   PHE B 420 
 TRP   0.006   0.001   TRP B 402 
 HIS   0.002   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6595)
  covalent geometry    : angle       0.55324 ( 8908)
  SS BOND              : bond        0.00266 (   18)
  SS BOND              : angle       1.06731 (   36)
  hydrogen bonds       : bond        0.03264 (  136)
  hydrogen bonds       : angle       6.08154 (  315)
  link_NAG-ASN         : bond        0.00193 (    4)
  link_NAG-ASN         : angle       1.12744 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.338 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.7047 (tmm) cc_final: 0.6824 (tmm)
REVERT: A  394 ASP cc_start: 0.7281 (t0) cc_final: 0.6907 (t0)
REVERT: B  402 TRP cc_start: 0.6776 (OUTLIER) cc_final: 0.6044 (p-90)
REVERT: B  406 HIS cc_start: 0.6613 (OUTLIER) cc_final: 0.6251 (m-70)
  outliers start: 21
  outliers final: 15
  residues processed: 82
  average time/residue: 0.1433
  time to fit residues: 16.4346
Evaluate side-chains
  81 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue  333 ASN
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  406 HIS
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  525 ASP
Chi-restraints excluded: chain B residue  539 HIS
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   60 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 12 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0170
   chunk 51 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.112787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.096972 restraints weight = 45124.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.100941 restraints weight = 21033.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.103501 restraints weight = 12560.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.105247 restraints weight = 8619.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.106469 restraints weight = 6451.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.5280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6617  Z= 0.114
  Angle     :  0.538   4.838   8956  Z= 0.287
  Chirality :  0.044   0.150    991
  Planarity :  0.003   0.041   1140
  Dihedral  :  6.653  53.714    963
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.18 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 14.04 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.30), residues: 782
  helix: -1.10 (0.49), residues: 101
  sheet: -1.86 (0.45), residues: 105
  loop : -1.31 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 450 
 TYR   0.009   0.001   TYR B 391 
 PHE   0.009   0.001   PHE I  19 
 TRP   0.005   0.001   TRP B 402 
 HIS   0.003   0.000   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6595)
  covalent geometry    : angle       0.53430 ( 8908)
  SS BOND              : bond        0.00221 (   18)
  SS BOND              : angle       0.98635 (   36)
  hydrogen bonds       : bond        0.03069 (  136)
  hydrogen bonds       : angle       5.86999 (  315)
  link_NAG-ASN         : bond        0.00175 (    4)
  link_NAG-ASN         : angle       1.10557 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.365 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  387 ASN cc_start: 0.4728 (OUTLIER) cc_final: 0.3681 (t0)
REVERT: B  402 TRP cc_start: 0.6673 (OUTLIER) cc_final: 0.5972 (p-90)
REVERT: B  406 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.6159 (m-70)
  outliers start: 22
  outliers final: 17
  residues processed: 86
  average time/residue: 0.1717
  time to fit residues: 19.9585
Evaluate side-chains
  84 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain B residue  333 ASN
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  387 ASN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  406 HIS
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  525 ASP
Chi-restraints excluded: chain B residue  539 HIS
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   60 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 12 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 50 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.104021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.087563 restraints weight = 48095.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.091384 restraints weight = 22299.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.093969 restraints weight = 13216.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.095688 restraints weight = 9018.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.096911 restraints weight = 6767.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.5423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6617  Z= 0.126
  Angle     :  0.549   6.214   8956  Z= 0.291
  Chirality :  0.044   0.148    991
  Planarity :  0.003   0.043   1140
  Dihedral  :  6.670  53.556    963
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.08 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.33 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.30), residues: 782
  helix: -1.13 (0.50), residues: 101
  sheet: -1.77 (0.46), residues: 105
  loop : -1.33 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 431 
 TYR   0.010   0.001   TYR B 391 
 PHE   0.016   0.001   PHE B 420 
 TRP   0.005   0.001   TRP B 402 
 HIS   0.002   0.000   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6595)
  covalent geometry    : angle       0.54532 ( 8908)
  SS BOND              : bond        0.00224 (   18)
  SS BOND              : angle       0.94380 (   36)
  hydrogen bonds       : bond        0.03063 (  136)
  hydrogen bonds       : angle       5.77649 (  315)
  link_NAG-ASN         : bond        0.00183 (    4)
  link_NAG-ASN         : angle       1.10266 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.365 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  387 ASN cc_start: 0.4589 (OUTLIER) cc_final: 0.3533 (t0)
REVERT: B  402 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.5996 (p-90)
REVERT: B  406 HIS cc_start: 0.6745 (OUTLIER) cc_final: 0.6332 (m-70)
REVERT: B  432 MET cc_start: 0.7695 (tmm) cc_final: 0.7403 (tmm)
  outliers start: 21
  outliers final: 14
  residues processed: 81
  average time/residue: 0.1865
  time to fit residues: 19.9615
Evaluate side-chains
  81 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  387 ASN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  406 HIS
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  525 ASP
Chi-restraints excluded: chain B residue  539 HIS
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   60 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.103189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.086843 restraints weight = 48194.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.090638 restraints weight = 22346.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.093152 restraints weight = 13228.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.094878 restraints weight = 9089.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.096032 restraints weight = 6818.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.5519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6617  Z= 0.149
  Angle     :  0.568   5.864   8956  Z= 0.302
  Chirality :  0.045   0.150    991
  Planarity :  0.003   0.043   1140
  Dihedral  :  6.790  53.594    963
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.34 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.17 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.30), residues: 782
  helix: -1.19 (0.50), residues: 101
  sheet: -1.75 (0.48), residues: 100
  loop : -1.38 (0.27), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.012   0.001   TYR B 391 
 PHE   0.012   0.001   PHE A  45 
 TRP   0.007   0.001   TRP B 402 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6595)
  covalent geometry    : angle       0.56450 ( 8908)
  SS BOND              : bond        0.00282 (   18)
  SS BOND              : angle       1.02976 (   36)
  hydrogen bonds       : bond        0.03211 (  136)
  hydrogen bonds       : angle       5.82429 (  315)
  link_NAG-ASN         : bond        0.00186 (    4)
  link_NAG-ASN         : angle       1.12178 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.343 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  387 ASN cc_start: 0.4607 (OUTLIER) cc_final: 0.3582 (t0)
REVERT: B  402 TRP cc_start: 0.6843 (OUTLIER) cc_final: 0.6110 (p-90)
REVERT: B  406 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.6386 (m-70)
REVERT: B  432 MET cc_start: 0.7829 (tmm) cc_final: 0.7573 (tmm)
REVERT: I   45 GLU cc_start: 0.8519 (tp30) cc_final: 0.8229 (mm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 81
  average time/residue: 0.1938
  time to fit residues: 20.3851
Evaluate side-chains
  81 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  239 TYR
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  387 ASN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  406 HIS
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  486 ASP
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   60 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.103840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.087657 restraints weight = 48083.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.091415 restraints weight = 22084.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.093927 restraints weight = 13018.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.095641 restraints weight = 8848.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.096840 restraints weight = 6602.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.5599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6617  Z= 0.136
  Angle     :  0.561   6.146   8956  Z= 0.297
  Chirality :  0.045   0.149    991
  Planarity :  0.003   0.044   1140
  Dihedral  :  6.682  53.686    963
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.82 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.59 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.30), residues: 782
  helix: -1.14 (0.50), residues: 101
  sheet: -1.68 (0.49), residues: 100
  loop : -1.36 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.011   0.001   TYR B 391 
 PHE   0.012   0.001   PHE B 420 
 TRP   0.006   0.001   TRP B 402 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6595)
  covalent geometry    : angle       0.55667 ( 8908)
  SS BOND              : bond        0.00240 (   18)
  SS BOND              : angle       1.04692 (   36)
  hydrogen bonds       : bond        0.03120 (  136)
  hydrogen bonds       : angle       5.77410 (  315)
  link_NAG-ASN         : bond        0.00185 (    4)
  link_NAG-ASN         : angle       1.11225 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2417.46 seconds
wall clock time: 41 minutes 44.98 seconds (2504.98 seconds total)