Starting phenix.real_space_refine
on Sat May 17 02:16:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gs3_34219/05_2025/8gs3_34219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gs3_34219/05_2025/8gs3_34219.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gs3_34219/05_2025/8gs3_34219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gs3_34219/05_2025/8gs3_34219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gs3_34219/05_2025/8gs3_34219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gs3_34219/05_2025/8gs3_34219.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8368 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    5389      2.51       5
     N    1395      2.21       5
     O    1554      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8376
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 534, 4191
          Classifications: {'peptide': 534}
          Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 491}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4185
          Classifications: {'peptide': 533}
          Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 490}
          Chain breaks: 2
  Time building chain proxies: 5.64, per 1000 atoms: 0.67
  Number of scatterers: 8376
  At special positions: 0
  Unit cell: (113.67, 108.618, 83.358, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1554      8.00
     N    1395      7.00
     C    5389      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 340 " - pdb=" SG  CYS A 351 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 510 " - pdb=" SG  CYS A 544 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 106 " - pdb=" SG  CYS B 141 " distance=2.64
    Simple disulfide: pdb=" SG  CYS B 340 " - pdb=" SG  CYS B 351 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 510 " - pdb=" SG  CYS B 544 " distance=2.04

  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
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1962

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 4 sheets defined
      46.5% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 3.549A  pdb=" N   LYS A  82 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 126
      removed outlier: 3.570A  pdb=" N   ASN A 126 " --> pdb=" O   TRP A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 135
      removed outlier: 3.640A  pdb=" N   THR A 132 " --> pdb=" O   ASP A 128 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 133 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 229
    Processing helix  chain 'A' and resid 239 through 245
    Processing helix  chain 'A' and resid 255 through 272
    Processing helix  chain 'A' and resid 273 through 275
      No H-bonds generated for 'chain 'A' and resid 273 through 275'
    Processing helix  chain 'A' and resid 288 through 299
    Processing helix  chain 'A' and resid 300 through 304
      removed outlier: 3.510A  pdb=" N   GLU A 304 " --> pdb=" O   HIS A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 339
      removed outlier: 3.873A  pdb=" N   TYR A 330 " --> pdb=" O   GLN A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 355
    Processing helix  chain 'A' and resid 356 through 363
      removed outlier: 3.825A  pdb=" N   LEU A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 394
    Processing helix  chain 'A' and resid 395 through 399
      removed outlier: 4.193A  pdb=" N   ASN A 398 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 4.655A  pdb=" N   GLY A 416 " --> pdb=" O   LYS A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 442
    Processing helix  chain 'A' and resid 446 through 458
    Processing helix  chain 'A' and resid 466 through 483
      removed outlier: 3.589A  pdb=" N   ARG A 470 " --> pdb=" O   ASN A 466 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE A 478 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 495
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 526 through 531
    Processing helix  chain 'A' and resid 532 through 537
      removed outlier: 4.160A  pdb=" N   VAL A 536 " --> pdb=" O   GLY A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 568
    Processing helix  chain 'A' and resid 617 through 626
    Processing helix  chain 'A' and resid 626 through 632
      removed outlier: 3.707A  pdb=" N   HIS A 630 " --> pdb=" O   HIS A 626 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TYR A 632 " --> pdb=" O   VAL A 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 120 through 126
      removed outlier: 3.563A  pdb=" N   ASN B 126 " --> pdb=" O   TRP B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 135
      removed outlier: 3.769A  pdb=" N   THR B 132 " --> pdb=" O   ASP B 128 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR B 133 " --> pdb=" O   ILE B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 219
      removed outlier: 3.728A  pdb=" N   MET B 218 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 229
    Processing helix  chain 'B' and resid 240 through 245
    Processing helix  chain 'B' and resid 255 through 272
    Processing helix  chain 'B' and resid 273 through 275
      No H-bonds generated for 'chain 'B' and resid 273 through 275'
    Processing helix  chain 'B' and resid 288 through 299
      removed outlier: 3.501A  pdb=" N   LEU B 299 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 304
    Processing helix  chain 'B' and resid 326 through 339
      removed outlier: 3.903A  pdb=" N   TYR B 330 " --> pdb=" O   GLN B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 355
      removed outlier: 3.876A  pdb=" N   GLN B 354 " --> pdb=" O   ASP B 350 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B 355 " --> pdb=" O   CYS B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 363
      removed outlier: 3.543A  pdb=" N   GLN B 363 " --> pdb=" O   GLU B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 394
    Processing helix  chain 'B' and resid 395 through 399
      removed outlier: 4.051A  pdb=" N   ASN B 398 " --> pdb=" O   GLU B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 416
      removed outlier: 4.488A  pdb=" N   GLY B 416 " --> pdb=" O   LYS B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 442
    Processing helix  chain 'B' and resid 446 through 458
    Processing helix  chain 'B' and resid 466 through 483
      removed outlier: 3.910A  pdb=" N   PHE B 478 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 495
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'B' and resid 526 through 531
    Processing helix  chain 'B' and resid 532 through 537
      removed outlier: 3.932A  pdb=" N   VAL B 536 " --> pdb=" O   GLY B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 568
    Processing helix  chain 'B' and resid 617 through 626
    Processing helix  chain 'B' and resid 626 through 632
      removed outlier: 4.226A  pdb=" N   HIS B 630 " --> pdb=" O   HIS B 626 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU B 631 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   TYR B 632 " --> pdb=" O   VAL B 628 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 626 through 632'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46
      removed outlier: 6.991A  pdb=" N   LYS A  50 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 56
      removed outlier: 5.497A  pdb=" N   GLN A  68 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   VAL A 148 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   LEU A  70 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   VAL A 146 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU A 235 " --> pdb=" O   TYR A 205 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LYS A 200 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ARG A 280 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   VAL A 202 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ILE A 282 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   VAL A 204 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   VAL A 284 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ILE A 206 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   GLY A 286 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ARG A 309 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE A 282 " --> pdb=" O   ARG A 309 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   ILE A 311 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL A 284 " --> pdb=" O   ILE A 311 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   GLN A 313 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   GLY A 286 " --> pdb=" O   GLN A 313 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ILE A 401 " --> pdb=" O   TYR A 502 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   TYR A 504 " --> pdb=" O   ILE A 401 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   LEU A 403 " --> pdb=" O   TYR A 504 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   PHE A 506 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   VAL A 405 " --> pdb=" O   PHE A 506 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   LEU A 602 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   PHE A 503 " --> pdb=" O   LEU A 602 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A 611 " --> pdb=" O   HIS A 605 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 46
    Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 56
      removed outlier: 5.448A  pdb=" N   GLN B  68 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   VAL B 148 " --> pdb=" O   GLN B  68 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   LEU B  70 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL B 146 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   TYR B 143 " --> pdb=" O   ASN B 236 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU B 235 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   LYS B 200 " --> pdb=" O   ASP B 278 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ARG B 280 " --> pdb=" O   LYS B 200 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   VAL B 202 " --> pdb=" O   ARG B 280 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ILE B 282 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   VAL B 204 " --> pdb=" O   ILE B 282 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL B 284 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   ILE B 206 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   GLY B 286 " --> pdb=" O   ILE B 206 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ARG B 309 " --> pdb=" O   ARG B 280 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE B 282 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   ILE B 311 " --> pdb=" O   ILE B 282 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL B 284 " --> pdb=" O   ILE B 311 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   GLN B 313 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   GLY B 286 " --> pdb=" O   GLN B 313 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ILE B 401 " --> pdb=" O   TYR B 502 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   TYR B 504 " --> pdb=" O   ILE B 401 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   LEU B 403 " --> pdb=" O   TYR B 504 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   PHE B 506 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL B 405 " --> pdb=" O   PHE B 506 " (cutoff:3.500A)
      removed outlier: 8.653A  pdb=" N   THR B 501 " --> pdb=" O   LEU B 602 " (cutoff:3.500A)
      removed outlier: 8.983A  pdb=" N   LEU B 604 " --> pdb=" O   THR B 501 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   PHE B 503 " --> pdb=" O   LEU B 604 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   ILE B 606 " --> pdb=" O   PHE B 503 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ALA B 505 " --> pdb=" O   ILE B 606 " (cutoff:3.500A)

    330 hydrogen bonds defined for protein.
    936 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: 2.65

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        0.84 -     1.12: 1
        1.12 -     1.41: 3654
        1.41 -     1.69: 4911
        1.69 -     1.98: 60
        1.98 -     2.26: 2
  Bond restraints: 8628
  Sorted by residual:
  bond pdb=" CG  PRO B 201 "
       pdb=" CD  PRO B 201 "
    ideal  model  delta    sigma   weight residual
    1.503  0.839  0.664 3.40e-02 8.65e+02 3.81e+02
  bond pdb=" CB  PRO B 201 "
       pdb=" CG  PRO B 201 "
    ideal  model  delta    sigma   weight residual
    1.492  2.264 -0.772 5.00e-02 4.00e+02 2.38e+02
  bond pdb=" N   PRO B 201 "
       pdb=" CD  PRO B 201 "
    ideal  model  delta    sigma   weight residual
    1.473  1.636 -0.163 1.40e-02 5.10e+03 1.36e+02
  bond pdb=" CA  PRO B 201 "
       pdb=" CB  PRO B 201 "
    ideal  model  delta    sigma   weight residual
    1.533  1.420  0.114 1.42e-02 4.96e+03 6.39e+01
  bond pdb=" CB  CYS B 141 "
       pdb=" SG  CYS B 141 "
    ideal  model  delta    sigma   weight residual
    1.808  2.054 -0.246 3.30e-02 9.18e+02 5.54e+01
  ... (remaining 8623 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    21.21: 11789
       21.21 -    42.42: 2
       42.42 -    63.64: 0
       63.64 -    84.85: 0
       84.85 -   106.06: 1
  Bond angle restraints: 11792
  Sorted by residual:
  angle pdb=" CB  PRO B 201 "
        pdb=" CG  PRO B 201 "
        pdb=" CD  PRO B 201 "
      ideal   model   delta    sigma   weight residual
     106.10    0.04  106.06 3.20e+00 9.77e-02 1.10e+03
  angle pdb=" CA  PRO B 201 "
        pdb=" N   PRO B 201 "
        pdb=" CD  PRO B 201 "
      ideal   model   delta    sigma   weight residual
     112.00   77.60   34.40 1.40e+00 5.10e-01 6.04e+02
  angle pdb=" CA  PRO B 201 "
        pdb=" CB  PRO B 201 "
        pdb=" CG  PRO B 201 "
      ideal   model   delta    sigma   weight residual
     104.50   84.71   19.79 1.90e+00 2.77e-01 1.08e+02
  angle pdb=" CA  LYS B 200 "
        pdb=" C   LYS B 200 "
        pdb=" O   LYS B 200 "
      ideal   model   delta    sigma   weight residual
     120.60  111.42    9.18 9.00e-01 1.23e+00 1.04e+02
  angle pdb=" C   LYS B 200 "
        pdb=" N   PRO B 201 "
        pdb=" CD  PRO B 201 "
      ideal   model   delta    sigma   weight residual
     125.00  160.46  -35.46 4.10e+00 5.95e-02 7.48e+01
  ... (remaining 11787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.65: 4553
       19.65 -    39.31: 401
       39.31 -    58.96: 98
       58.96 -    78.62: 12
       78.62 -    98.27: 8
  Dihedral angle restraints: 5072
    sinusoidal: 1993
      harmonic: 3079
  Sorted by residual:
  dihedral pdb=" CB  CYS B 106 "
           pdb=" SG  CYS B 106 "
           pdb=" SG  CYS B 141 "
           pdb=" CB  CYS B 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -28.48  -57.52     1      1.00e+01 1.00e-02 4.44e+01
  dihedral pdb=" CB  CYS B 510 "
           pdb=" SG  CYS B 510 "
           pdb=" SG  CYS B 544 "
           pdb=" CB  CYS B 544 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -37.20  -48.80     1      1.00e+01 1.00e-02 3.28e+01
  dihedral pdb=" CA  PRO B 201 "
           pdb=" CB  PRO B 201 "
           pdb=" CG  PRO B 201 "
           pdb=" CD  PRO B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -38.00 -136.27   98.27     1      2.00e+01 2.50e-03 2.75e+01
  ... (remaining 5069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1114
       0.071 -    0.141: 158
       0.141 -    0.211: 3
       0.211 -    0.282: 1
       0.282 -    0.352: 1
  Chirality restraints: 1277
  Sorted by residual:
  chirality pdb=" CA  LYS B 200 "
            pdb=" N   LYS B 200 "
            pdb=" C   LYS B 200 "
            pdb=" CB  LYS B 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.10e+00
  chirality pdb=" CA  PRO B 201 "
            pdb=" N   PRO B 201 "
            pdb=" C   PRO B 201 "
            pdb=" CB  PRO B 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CB  VAL A 230 "
            pdb=" CA  VAL A 230 "
            pdb=" CG1 VAL A 230 "
            pdb=" CG2 VAL A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.77e-01
  ... (remaining 1274 not shown)

  Planarity restraints: 1539
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 102 "   -0.059 5.00e-02 4.00e+02   8.86e-02 1.26e+01
        pdb=" N   PRO B 103 "    0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO B 103 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 103 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 102 "    0.057 5.00e-02 4.00e+02   8.56e-02 1.17e+01
        pdb=" N   PRO A 103 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 103 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 103 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 383 "    0.053 5.00e-02 4.00e+02   7.95e-02 1.01e+01
        pdb=" N   PRO A 384 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 384 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 384 "    0.044 5.00e-02 4.00e+02
  ... (remaining 1536 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 33
        2.43 -     3.05: 5540
        3.05 -     3.66: 13549
        3.66 -     4.28: 19743
        4.28 -     4.90: 32430
  Nonbonded interactions: 71295
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 250 "
            pdb=" OE1 GLN A 250 "
     model   vdw
     1.810 3.040
  nonbonded pdb=" CD1 LEU B  58 "
            pdb=" CD1 LEU B  63 "
     model   vdw
     1.918 3.880
  nonbonded pdb=" OD1 ASP B 492 "
            pdb=" OH  TYR B 596 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" O   HIS A 207 "
            pdb=" OH  TYR A 237 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" O   ILE B 389 "
            pdb=" OE2 GLU B 392 "
     model   vdw
     2.198 3.040
  ... (remaining 71290 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 41 through 150 or resid 198 through 633))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.250
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
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      :  0.014   0.772   8634  Z= 0.524
  Angle     :  1.358 106.059  11804  Z= 0.594
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  : 15.895  98.273   3092
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 20.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.50 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17362 (  330)
  hydrogen bonds       : angle       6.70764 (  936)
  SS BOND              : bond        0.25012 (    6)
  SS BOND              : angle      10.23309 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31853 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9006 (t) cc_final: 0.8781 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1810
  time to fit residues: 21.3135
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 80 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.053846 restraints weight = 38854.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.055466 restraints weight = 24765.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056602 restraints weight = 18267.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22314 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9109 (t) cc_final: 0.8887 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1675
  time to fit residues: 19.7875
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 94 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 88 optimal weight:    0.0270
   chunk 83 optimal weight:    0.9990
   chunk 69 optimal weight:    8.9990
   overall best weight:    1.7844

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.053807 restraints weight = 39447.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.055428 restraints weight = 24990.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056586 restraints weight = 18344.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22314 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9108 (t) cc_final: 0.8887 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1603
  time to fit residues: 18.9326
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0770
   chunk 67 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    3.2146

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053820 restraints weight = 39116.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.055453 restraints weight = 24889.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056588 restraints weight = 18350.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22314 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9108 (t) cc_final: 0.8886 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1586
  time to fit residues: 18.7768
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.053838 restraints weight = 38929.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.055458 restraints weight = 24796.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.056614 restraints weight = 18271.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22314 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9109 (t) cc_final: 0.8887 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1571
  time to fit residues: 18.6162
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 59 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053811 restraints weight = 39226.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.055450 restraints weight = 24940.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056583 restraints weight = 18375.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22312 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9108 (t) cc_final: 0.8887 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1693
  time to fit residues: 19.9033
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 103 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 50 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0170
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053805 restraints weight = 39306.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.055439 restraints weight = 24982.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056582 restraints weight = 18407.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22312 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9109 (t) cc_final: 0.8887 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1747
  time to fit residues: 20.4291
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 76 optimal weight:    0.0770
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.1342

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053797 restraints weight = 39385.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.055422 restraints weight = 25018.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056583 restraints weight = 18387.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22312 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9110 (t) cc_final: 0.8888 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1727
  time to fit residues: 20.2754
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053764 restraints weight = 39788.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.055390 restraints weight = 25185.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.056542 restraints weight = 18531.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22312 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9108 (t) cc_final: 0.8886 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1638
  time to fit residues: 19.4297
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 52 optimal weight:    0.3980
   chunk 68 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0870
   chunk 64 optimal weight:   50.0000
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.0964

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053812 restraints weight = 39210.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.055432 restraints weight = 24929.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056587 restraints weight = 18360.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22312 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  556 VAL cc_start: 0.9109 (t) cc_final: 0.8887 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1640
  time to fit residues: 19.1836
Evaluate side-chains
  77 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 91 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 64 optimal weight:   50.0000
   chunk 13 optimal weight:    2.9990
   chunk 101 optimal weight:    0.3980
   chunk 92 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.053764 restraints weight = 39757.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.055405 restraints weight = 25179.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.056538 restraints weight = 18463.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.0014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.772   8634  Z= 0.521
  Angle     :  1.357 106.100  11804  Z= 0.592
  Chirality :  0.047   0.352   1277
  Planarity :  0.007   0.089   1539
  Dihedral  :  4.783  26.199   1157
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.16 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1055
  helix:  0.93 (0.27), residues: 378
  sheet:  0.05 (0.41), residues: 140
  loop : -0.25 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 518 
 HIS   0.008   0.001   HIS B 207 
 PHE   0.014   0.002   PHE B 546 
 TYR   0.039   0.002   TYR B  69 
 ARG   0.008   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17345 (  330)
  hydrogen bonds       : angle       6.70665 (  936)
  SS BOND              : bond        0.24859 (    6)
  SS BOND              : angle      10.22312 (   12)
  covalent geometry    : bond        0.01268 ( 8628)
  covalent geometry    : angle       1.31802 (11792)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2227.86 seconds
wall clock time: 40 minutes 25.47 seconds (2425.47 seconds total)