Starting phenix.real_space_refine
on Wed Mar  4 09:32:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wjo_32547/03_2026/7wjo_32547.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wjo_32547/03_2026/7wjo_32547.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wjo_32547/03_2026/7wjo_32547.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wjo_32547/03_2026/7wjo_32547.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wjo_32547/03_2026/7wjo_32547.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wjo_32547/03_2026/7wjo_32547.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    8394      2.51       5
     N    2156      2.21       5
     O    2310      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 12932
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 801, 6431
          Classifications: {'peptide': 801}
          Link IDs: {'PTRANS': 30, 'TRANS': 770}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'BGI': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.03, per 1000 atoms: 0.47
  Number of scatterers: 12932
  At special positions: 0
  Unit cell: (116.63, 114.49, 129.47, 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      72     16.00
     O    2310      8.00
     N    2156      7.00
     C    8394      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 1.13
  Conformation dependent library (CDL) restraints added in 600.1 milliseconds
  

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3012

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      65.8% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 74
    Processing helix  chain 'A' and resid 76 through 90
      removed outlier: 3.612A  pdb=" N   SER A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 110
    Processing helix  chain 'A' and resid 112 through 134
      removed outlier: 3.676A  pdb=" N   ALA A 116 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ARG A 133 " --> pdb=" O   ASN A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 163
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 221 through 227
    Processing helix  chain 'A' and resid 242 through 262
      removed outlier: 3.801A  pdb=" N   LEU A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 282
      removed outlier: 3.505A  pdb=" N   GLN A 282 " --> pdb=" O   ASP A 279 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 279 through 282'
    Processing helix  chain 'A' and resid 297 through 307
    Processing helix  chain 'A' and resid 311 through 319
    Processing helix  chain 'A' and resid 357 through 374
    Processing helix  chain 'A' and resid 390 through 403
    Processing helix  chain 'A' and resid 423 through 447
      removed outlier: 3.670A  pdb=" N   SER A 427 " --> pdb=" O   ASN A 423 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   PHE A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 474
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 3.626A  pdb=" N   LEU A 484 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 490
    Processing helix  chain 'A' and resid 494 through 505
      removed outlier: 3.545A  pdb=" N   VAL A 504 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 554
      removed outlier: 3.782A  pdb=" N   LYS A 537 " --> pdb=" O   ILE A 533 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   ARG A 538 " --> pdb=" O   SER A 534 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   TRP A 539 " --> pdb=" O   GLN A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 564 through 587
      removed outlier: 3.682A  pdb=" N   PHE A 587 " --> pdb=" O   ALA A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 606
    Processing helix  chain 'A' and resid 619 through 647
      removed outlier: 3.882A  pdb=" N   ASP A 623 " --> pdb=" O   GLN A 619 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   VAL A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 681
    Processing helix  chain 'A' and resid 684 through 705
      removed outlier: 5.333A  pdb=" N   VAL A 697 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   TYR A 698 " --> pdb=" O   THR A 694 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 720
      removed outlier: 5.265A  pdb=" N   THR A 716 " --> pdb=" O   PHE A 712 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   HIS A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 736
    Processing helix  chain 'A' and resid 764 through 819
    Processing helix  chain 'A' and resid 824 through 857
      removed outlier: 5.049A  pdb=" N   GLY A 854 " --> pdb=" O   ILE A 850 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   LEU A 855 " --> pdb=" O   HIS A 851 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 74
    Processing helix  chain 'B' and resid 76 through 90
      removed outlier: 3.612A  pdb=" N   SER B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 110
    Processing helix  chain 'B' and resid 112 through 134
      removed outlier: 3.676A  pdb=" N   ALA B 116 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLU B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ARG B 133 " --> pdb=" O   ASN B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 163
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 210 through 214
    Processing helix  chain 'B' and resid 221 through 227
    Processing helix  chain 'B' and resid 242 through 262
      removed outlier: 3.800A  pdb=" N   LEU B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 282
      removed outlier: 3.505A  pdb=" N   GLN B 282 " --> pdb=" O   ASP B 279 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 279 through 282'
    Processing helix  chain 'B' and resid 297 through 307
    Processing helix  chain 'B' and resid 311 through 319
    Processing helix  chain 'B' and resid 357 through 374
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 423 through 447
      removed outlier: 3.670A  pdb=" N   SER B 427 " --> pdb=" O   ASN B 423 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   PHE B 447 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 474
    Processing helix  chain 'B' and resid 474 through 479
    Processing helix  chain 'B' and resid 480 through 485
      removed outlier: 3.626A  pdb=" N   LEU B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 490
    Processing helix  chain 'B' and resid 494 through 505
      removed outlier: 3.545A  pdb=" N   VAL B 504 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 554
      removed outlier: 3.781A  pdb=" N   LYS B 537 " --> pdb=" O   ILE B 533 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ARG B 538 " --> pdb=" O   SER B 534 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   TRP B 539 " --> pdb=" O   GLN B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 560
    Processing helix  chain 'B' and resid 564 through 587
      removed outlier: 3.682A  pdb=" N   PHE B 587 " --> pdb=" O   ALA B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 606
    Processing helix  chain 'B' and resid 619 through 647
      removed outlier: 3.882A  pdb=" N   ASP B 623 " --> pdb=" O   GLN B 619 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   VAL B 626 " --> pdb=" O   LEU B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 652 through 681
    Processing helix  chain 'B' and resid 684 through 705
      removed outlier: 5.333A  pdb=" N   VAL B 697 " --> pdb=" O   LEU B 693 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   TYR B 698 " --> pdb=" O   THR B 694 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   PHE B 699 " --> pdb=" O   VAL B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 720
      removed outlier: 5.265A  pdb=" N   THR B 716 " --> pdb=" O   PHE B 712 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   HIS B 717 " --> pdb=" O   MET B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 736
    Processing helix  chain 'B' and resid 764 through 819
    Processing helix  chain 'B' and resid 824 through 857
      removed outlier: 5.049A  pdb=" N   GLY B 854 " --> pdb=" O   ILE B 850 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   LEU B 855 " --> pdb=" O   HIS B 851 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
      removed outlier: 6.174A  pdb=" N   HIS B 175 " --> pdb=" O   PRO B 205 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ARG B 200 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   THR B 332 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLN B 346 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LYS B 352 " --> pdb=" O   ALA B 290 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU B 232 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   CYS B 287 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE B 234 " --> pdb=" O   CYS B 287 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   VAL B 289 " --> pdb=" O   ILE B 234 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ILE B 236 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   MET B 233 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   MET B 381 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   CYS B 235 " --> pdb=" O   MET B 381 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ARG B 461 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   GLY B 406 " --> pdb=" O   ARG B 461 " (cutoff:3.500A)
      removed outlier: 11.464A  pdb=" N   ILE B 405 " --> pdb=" O   TYR B 515 " (cutoff:3.500A)
      removed outlier: 14.829A  pdb=" N   LYS B 517 " --> pdb=" O   ILE B 405 " (cutoff:3.500A)
      removed outlier: 16.238A  pdb=" N   GLY B 407 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
      removed outlier: 12.629A  pdb=" N   ALA B 519 " --> pdb=" O   GLY B 407 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   CYS B 409 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   ALA B 521 " --> pdb=" O   CYS B 409 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   GLN B 411 " --> pdb=" O   ALA B 521 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   THR B 523 " --> pdb=" O   GLN B 411 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   THR B 413 " --> pdb=" O   THR B 523 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 387
      removed outlier: 11.464A  pdb=" N   ILE A 405 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 14.829A  pdb=" N   LYS A 517 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
      removed outlier: 16.238A  pdb=" N   GLY A 407 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 12.628A  pdb=" N   ALA A 519 " --> pdb=" O   GLY A 407 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   CYS A 409 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   ALA A 521 " --> pdb=" O   CYS A 409 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   GLN A 411 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   THR A 523 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   THR A 413 " --> pdb=" O   THR A 523 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   GLY A 406 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ARG A 461 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   MET A 233 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   MET A 381 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   CYS A 235 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU A 232 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   CYS A 287 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   ILE A 234 " --> pdb=" O   CYS A 287 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   VAL A 289 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ILE A 236 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   GLN A 346 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LYS A 352 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   THR A 332 " --> pdb=" O   ARG A 200 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   ARG A 200 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   HIS A 175 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   VAL A 174 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   SER B  55 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   LYS A 176 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337
    Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337

    834 hydrogen bonds defined for protein.
    2460 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: 2.15

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 2030
        1.29 -     1.42: 3786
        1.42 -     1.55: 7348
        1.55 -     1.68: 8
        1.68 -     1.81: 112
  Bond restraints: 13284
  Sorted by residual:
  bond pdb=" C25 BGI B1001 "
       pdb=" O26 BGI B1001 "
    ideal  model  delta    sigma   weight residual
    1.216  1.433 -0.217 2.00e-02 2.50e+03 1.18e+02
  bond pdb=" C25 BGI A1001 "
       pdb=" O26 BGI A1001 "
    ideal  model  delta    sigma   weight residual
    1.216  1.433 -0.217 2.00e-02 2.50e+03 1.18e+02
  bond pdb=" C17 BGI B1001 "
       pdb=" C18 BGI B1001 "
    ideal  model  delta    sigma   weight residual
    1.532  1.332  0.200 2.00e-02 2.50e+03 9.96e+01
  bond pdb=" C17 BGI A1001 "
       pdb=" C18 BGI A1001 "
    ideal  model  delta    sigma   weight residual
    1.532  1.333  0.199 2.00e-02 2.50e+03 9.88e+01
  bond pdb=" C17 BGI B1001 "
       pdb=" O21 BGI B1001 "
    ideal  model  delta    sigma   weight residual
    1.433  1.606 -0.173 2.00e-02 2.50e+03 7.46e+01
  ... (remaining 13279 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 17752
        1.69 -     3.38: 214
        3.38 -     5.06: 49
        5.06 -     6.75: 15
        6.75 -     8.44: 12
  Bond angle restraints: 18042
  Sorted by residual:
  angle pdb=" N   GLU B 463 "
        pdb=" CA  GLU B 463 "
        pdb=" C   GLU B 463 "
      ideal   model   delta    sigma   weight residual
     114.62  108.77    5.85 1.14e+00 7.69e-01 2.64e+01
  angle pdb=" N   GLU A 463 "
        pdb=" CA  GLU A 463 "
        pdb=" C   GLU A 463 "
      ideal   model   delta    sigma   weight residual
     114.62  108.78    5.84 1.14e+00 7.69e-01 2.63e+01
  angle pdb=" CA  GLU A 463 "
        pdb=" C   GLU A 463 "
        pdb=" N   ALA A 464 "
      ideal   model   delta    sigma   weight residual
     119.71  116.14    3.57 1.17e+00 7.31e-01 9.31e+00
  angle pdb=" CA  GLU B 463 "
        pdb=" C   GLU B 463 "
        pdb=" N   ALA B 464 "
      ideal   model   delta    sigma   weight residual
     119.71  116.18    3.53 1.17e+00 7.31e-01 9.09e+00
  angle pdb=" C18 BGI B1001 "
        pdb=" C19 BGI B1001 "
        pdb=" O30 BGI B1001 "
      ideal   model   delta    sigma   weight residual
     116.99  108.55    8.44 3.00e+00 1.11e-01 7.91e+00
  ... (remaining 18037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 7327
       17.32 -    34.63: 398
       34.63 -    51.95: 57
       51.95 -    69.27: 18
       69.27 -    86.58: 14
  Dihedral angle restraints: 7814
    sinusoidal: 3122
      harmonic: 4692
  Sorted by residual:
  dihedral pdb=" CA  TYR A 617 "
           pdb=" C   TYR A 617 "
           pdb=" N   SER A 618 "
           pdb=" CA  SER A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.72  -16.28     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  TYR B 617 "
           pdb=" C   TYR B 617 "
           pdb=" N   SER B 618 "
           pdb=" CA  SER B 618 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.75  -16.25     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CB  ARG B 797 "
           pdb=" CG  ARG B 797 "
           pdb=" CD  ARG B 797 "
           pdb=" NE  ARG B 797 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  123.01   56.99     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 7811 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1722
       0.056 -    0.112: 237
       0.112 -    0.168: 23
       0.168 -    0.223: 0
       0.223 -    0.279: 2
  Chirality restraints: 1984
  Sorted by residual:
  chirality pdb=" C18 BGI A1001 "
            pdb=" C17 BGI A1001 "
            pdb=" C19 BGI A1001 "
            pdb=" O31 BGI A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" C18 BGI B1001 "
            pdb=" C17 BGI B1001 "
            pdb=" C19 BGI B1001 "
            pdb=" O31 BGI B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" C19 BGI B1001 "
            pdb=" C18 BGI B1001 "
            pdb=" C20 BGI B1001 "
            pdb=" O30 BGI B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.63   -0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 1981 not shown)

  Planarity restraints: 2278
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 598 "    0.011 2.00e-02 2.50e+03   2.16e-02 4.65e+00
        pdb=" C   PHE B 598 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   PHE B 598 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ILE B 599 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 598 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.63e+00
        pdb=" C   PHE A 598 "    0.037 2.00e-02 2.50e+03
        pdb=" O   PHE A 598 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A 599 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 599 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.10e+00
        pdb=" C   ILE B 599 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ILE B 599 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL B 600 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2275 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1248
        2.74 -     3.28: 12232
        3.28 -     3.82: 20984
        3.82 -     4.36: 22611
        4.36 -     4.90: 43325
  Nonbonded interactions: 100400
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  88 "
            pdb=" OD1 ASP B 115 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" OE2 GLU B 225 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   LYS A 269 "
            pdb=" OH  TYR A 393 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   LYS B 269 "
            pdb=" OH  TYR B 393 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OE2 GLU A 225 "
            pdb=" OH  TYR B  52 "
     model   vdw
     2.284 3.040
  ... (remaining 100395 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.160
  Find NCS groups from input model:        0.060
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
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      :  0.006   0.217  13284  Z= 0.298
  Angle     :  0.554   8.440  18042  Z= 0.282
  Chirality :  0.040   0.279   1984
  Planarity :  0.004   0.031   2278
  Dihedral  : 11.696  86.583   4802
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.02 %
    Favored  : 93.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.22), residues: 1594
  helix:  2.59 (0.17), residues: 982
  sheet:  0.13 (0.43), residues: 170
  loop : -1.37 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 608 
 TYR   0.011   0.001   TYR A 365 
 PHE   0.016   0.001   PHE B 601 
 TRP   0.008   0.001   TRP B 804 
 HIS   0.005   0.001   HIS A 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (13284)
  covalent geometry    : angle       0.55368 (18042)
  hydrogen bonds       : bond        0.12284 (  834)
  hydrogen bonds       : angle       5.28296 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 230
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ARG cc_start: 0.7539 (mtt180) cc_final: 0.5958 (mtt90)
REVERT: A  264 MET cc_start: 0.7999 (tpp) cc_final: 0.7763 (ttt)
REVERT: A  552 TRP cc_start: 0.7187 (t-100) cc_final: 0.6802 (m-10)
REVERT: A  850 ILE cc_start: 0.8256 (tt) cc_final: 0.8026 (tt)
REVERT: B  187 ASP cc_start: 0.7188 (p0) cc_final: 0.6596 (p0)
REVERT: B  305 GLU cc_start: 0.7831 (tt0) cc_final: 0.7572 (tt0)
REVERT: B  645 LEU cc_start: 0.8575 (tp) cc_final: 0.8364 (tt)
REVERT: B  790 LYS cc_start: 0.7486 (mttt) cc_final: 0.7261 (mptt)
REVERT: B  820 SER cc_start: 0.7917 (m) cc_final: 0.7712 (p)
REVERT: B  850 ILE cc_start: 0.8487 (tt) cc_final: 0.8249 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 232
  average time/residue: 0.1462
  time to fit residues: 46.6948
Evaluate side-chains
  144 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain B residue  326 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 416 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.141088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.108972 restraints weight = 15437.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.95
r_work: 0.3119 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13284  Z= 0.193
  Angle     :  0.583   8.031  18042  Z= 0.310
  Chirality :  0.042   0.143   1984
  Planarity :  0.004   0.032   2278
  Dihedral  :  6.633  43.523   1852
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  9.43 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.52 (0.22), residues: 1594
  helix:  2.20 (0.17), residues: 990
  sheet: -0.16 (0.43), residues: 170
  loop : -1.38 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 497 
 TYR   0.023   0.002   TYR A 732 
 PHE   0.018   0.002   PHE A 601 
 TRP   0.008   0.001   TRP A 804 
 HIS   0.005   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (13284)
  covalent geometry    : angle       0.58343 (18042)
  hydrogen bonds       : bond        0.06104 (  834)
  hydrogen bonds       : angle       4.73750 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7941 (mp)
REVERT: A  238 MET cc_start: 0.8630 (ttm) cc_final: 0.8346 (ttm)
REVERT: A  403 HIS cc_start: 0.7474 (t-90) cc_final: 0.7063 (m170)
REVERT: A  552 TRP cc_start: 0.7861 (t-100) cc_final: 0.6954 (m-10)
REVERT: A  666 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7704 (ttm)
REVERT: A  730 THR cc_start: 0.8843 (m) cc_final: 0.8504 (p)
REVERT: A  850 ILE cc_start: 0.8392 (tt) cc_final: 0.8113 (tt)
REVERT: B  187 ASP cc_start: 0.7726 (p0) cc_final: 0.7309 (p0)
REVERT: B  195 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7810 (mm-30)
REVERT: B  305 GLU cc_start: 0.8421 (tt0) cc_final: 0.8113 (tt0)
REVERT: B  785 ARG cc_start: 0.7612 (mtt180) cc_final: 0.6810 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7341 (mt-10)
REVERT: B  820 SER cc_start: 0.8528 (m) cc_final: 0.8249 (p)
REVERT: B  850 ILE cc_start: 0.8615 (tt) cc_final: 0.8297 (tt)
  outliers start: 34
  outliers final: 15
  residues processed: 178
  average time/residue: 0.1297
  time to fit residues: 33.0743
Evaluate side-chains
  154 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  666 MET
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  527 HIS
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  816 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 121 optimal weight:    0.0270
   chunk 105 optimal weight:    0.0030
   chunk 111 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 126 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 132 optimal weight:    1.9990
   overall best weight:    0.7450

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.109851 restraints weight = 15555.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.11
r_work: 0.3137 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13284  Z= 0.133
  Angle     :  0.512   7.413  18042  Z= 0.272
  Chirality :  0.039   0.131   1984
  Planarity :  0.004   0.044   2278
  Dihedral  :  5.323  29.532   1851
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 10.81 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.64 (0.22), residues: 1594
  helix:  2.34 (0.17), residues: 980
  sheet: -0.26 (0.43), residues: 174
  loop : -1.30 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 220 
 TYR   0.013   0.001   TYR A 492 
 PHE   0.016   0.001   PHE B 601 
 TRP   0.006   0.001   TRP A 804 
 HIS   0.003   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (13284)
  covalent geometry    : angle       0.51225 (18042)
  hydrogen bonds       : bond        0.05509 (  834)
  hydrogen bonds       : angle       4.63464 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7825 (mp)
REVERT: A  199 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7682 (mtt-85)
REVERT: A  403 HIS cc_start: 0.7439 (t-90) cc_final: 0.7113 (m170)
REVERT: A  552 TRP cc_start: 0.7842 (t-100) cc_final: 0.6900 (m-10)
REVERT: A  730 THR cc_start: 0.8862 (m) cc_final: 0.8484 (p)
REVERT: A  850 ILE cc_start: 0.8360 (tt) cc_final: 0.8080 (tt)
REVERT: B  187 ASP cc_start: 0.7740 (p0) cc_final: 0.7331 (p0)
REVERT: B  195 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7718 (mm-30)
REVERT: B  305 GLU cc_start: 0.8441 (tt0) cc_final: 0.8132 (tt0)
REVERT: B  325 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7863 (mp10)
REVERT: B  736 ASN cc_start: 0.7458 (m110) cc_final: 0.6881 (m110)
REVERT: B  785 ARG cc_start: 0.7575 (mtt180) cc_final: 0.6814 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7345 (mt-10)
REVERT: B  820 SER cc_start: 0.8541 (m) cc_final: 0.8260 (p)
REVERT: B  850 ILE cc_start: 0.8544 (tt) cc_final: 0.8235 (tt)
  outliers start: 32
  outliers final: 19
  residues processed: 163
  average time/residue: 0.1273
  time to fit residues: 29.9128
Evaluate side-chains
  152 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 139 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 146 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 105 optimal weight:    0.6980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.137522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.104651 restraints weight = 15692.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.22
r_work: 0.3073 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  13284  Z= 0.231
  Angle     :  0.587   8.080  18042  Z= 0.312
  Chirality :  0.043   0.142   1984
  Planarity :  0.004   0.034   2278
  Dihedral  :  5.099  32.706   1850
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 11.39 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.32 (0.22), residues: 1594
  helix:  2.08 (0.17), residues: 978
  sheet: -0.53 (0.41), residues: 174
  loop : -1.32 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  86 
 TYR   0.018   0.002   TYR A 365 
 PHE   0.019   0.002   PHE B 601 
 TRP   0.009   0.001   TRP B 202 
 HIS   0.005   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 (13284)
  covalent geometry    : angle       0.58737 (18042)
  hydrogen bonds       : bond        0.06590 (  834)
  hydrogen bonds       : angle       4.77668 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7875 (mp)
REVERT: A  199 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7685 (mtt-85)
REVERT: A  552 TRP cc_start: 0.7948 (t-100) cc_final: 0.6989 (m-10)
REVERT: A  787 GLU cc_start: 0.7542 (tt0) cc_final: 0.7330 (tm-30)
REVERT: A  850 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8453 (tt)
REVERT: B   96 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8336 (pm20)
REVERT: B  187 ASP cc_start: 0.7805 (p0) cc_final: 0.7342 (p0)
REVERT: B  195 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7542 (mm-30)
REVERT: B  305 GLU cc_start: 0.8393 (tt0) cc_final: 0.8186 (tt0)
REVERT: B  325 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7902 (mp10)
REVERT: B  451 SER cc_start: 0.9158 (t) cc_final: 0.8728 (p)
REVERT: B  736 ASN cc_start: 0.7463 (m110) cc_final: 0.6962 (m110)
REVERT: B  785 ARG cc_start: 0.7613 (mtt180) cc_final: 0.6817 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7366 (mt-10)
REVERT: B  820 SER cc_start: 0.8575 (m) cc_final: 0.8298 (p)
REVERT: B  850 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8292 (tt)
  outliers start: 38
  outliers final: 24
  residues processed: 169
  average time/residue: 0.1337
  time to fit residues: 32.0821
Evaluate side-chains
  166 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  790 LYS
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain B residue   96 GLU
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  527 HIS
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   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 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.139281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.106688 restraints weight = 15703.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.13
r_work: 0.3091 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13284  Z= 0.176
  Angle     :  0.534   7.441  18042  Z= 0.285
  Chirality :  0.040   0.131   1984
  Planarity :  0.004   0.034   2278
  Dihedral  :  4.941  29.877   1850
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.84 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.36 (0.22), residues: 1594
  helix:  2.14 (0.17), residues: 978
  sheet: -0.63 (0.41), residues: 174
  loop : -1.33 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 567 
 TYR   0.014   0.001   TYR A 492 
 PHE   0.017   0.001   PHE A 601 
 TRP   0.008   0.001   TRP B 202 
 HIS   0.003   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (13284)
  covalent geometry    : angle       0.53422 (18042)
  hydrogen bonds       : bond        0.05999 (  834)
  hydrogen bonds       : angle       4.69633 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7837 (mp)
REVERT: A  238 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8601 (ttm)
REVERT: A  552 TRP cc_start: 0.7920 (t-100) cc_final: 0.6992 (m-10)
REVERT: A  787 GLU cc_start: 0.7541 (tt0) cc_final: 0.7314 (tm-30)
REVERT: A  850 ILE cc_start: 0.8499 (tt) cc_final: 0.8218 (tt)
REVERT: B   96 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8305 (pm20)
REVERT: B  187 ASP cc_start: 0.7834 (p0) cc_final: 0.7376 (p0)
REVERT: B  195 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7458 (mm-30)
REVERT: B  199 ARG cc_start: 0.8415 (mtt180) cc_final: 0.8002 (tpp80)
REVERT: B  451 SER cc_start: 0.9085 (t) cc_final: 0.8736 (p)
REVERT: B  785 ARG cc_start: 0.7611 (mtt180) cc_final: 0.6820 (ptp-170)
REVERT: B  820 SER cc_start: 0.8589 (m) cc_final: 0.8326 (p)
REVERT: B  850 ILE cc_start: 0.8577 (tt) cc_final: 0.8241 (tt)
  outliers start: 37
  outliers final: 25
  residues processed: 164
  average time/residue: 0.1343
  time to fit residues: 31.2417
Evaluate side-chains
  158 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  790 LYS
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   96 GLU
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  527 HIS
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  790 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 136 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 148 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.137489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.104598 restraints weight = 15624.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.22
r_work: 0.3056 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13284  Z= 0.209
  Angle     :  0.568   7.802  18042  Z= 0.302
  Chirality :  0.042   0.143   1984
  Planarity :  0.004   0.034   2278
  Dihedral  :  5.118  31.389   1850
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.21 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.19 (0.22), residues: 1594
  helix:  2.04 (0.17), residues: 974
  sheet: -0.76 (0.41), residues: 172
  loop : -1.42 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 199 
 TYR   0.016   0.002   TYR A 365 
 PHE   0.016   0.002   PHE B 601 
 TRP   0.009   0.001   TRP B 202 
 HIS   0.004   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (13284)
  covalent geometry    : angle       0.56824 (18042)
  hydrogen bonds       : bond        0.06402 (  834)
  hydrogen bonds       : angle       4.74362 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 133
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7854 (mp)
REVERT: A  199 ARG cc_start: 0.8232 (mtt90) cc_final: 0.8009 (mtp85)
REVERT: A  238 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8745 (ttm)
REVERT: A  787 GLU cc_start: 0.7577 (tt0) cc_final: 0.7314 (tm-30)
REVERT: A  850 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8409 (tt)
REVERT: B   75 MET cc_start: 0.2567 (mmt) cc_final: 0.2350 (mmt)
REVERT: B  187 ASP cc_start: 0.7834 (p0) cc_final: 0.7369 (p0)
REVERT: B  451 SER cc_start: 0.9096 (t) cc_final: 0.8738 (p)
REVERT: B  785 ARG cc_start: 0.7596 (mtt180) cc_final: 0.6855 (ptp-170)
REVERT: B  820 SER cc_start: 0.8597 (m) cc_final: 0.8328 (p)
REVERT: B  850 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8375 (tt)
  outliers start: 40
  outliers final: 29
  residues processed: 156
  average time/residue: 0.1331
  time to fit residues: 29.1986
Evaluate side-chains
  163 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  790 LYS
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  513 MET
Chi-restraints excluded: chain B residue  527 HIS
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  790 LYS
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 152 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.140347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.107629 restraints weight = 15467.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.17
r_work: 0.3114 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13284  Z= 0.141
  Angle     :  0.513   8.581  18042  Z= 0.273
  Chirality :  0.039   0.142   1984
  Planarity :  0.004   0.034   2278
  Dihedral  :  4.795  27.671   1850
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.79 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.43 (0.22), residues: 1594
  helix:  2.24 (0.17), residues: 974
  sheet: -0.66 (0.41), residues: 170
  loop : -1.36 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  86 
 TYR   0.018   0.001   TYR A 492 
 PHE   0.015   0.001   PHE B 601 
 TRP   0.007   0.001   TRP B 202 
 HIS   0.002   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (13284)
  covalent geometry    : angle       0.51345 (18042)
  hydrogen bonds       : bond        0.05565 (  834)
  hydrogen bonds       : angle       4.62535 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 133
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7827 (mp)
REVERT: A  199 ARG cc_start: 0.8188 (mtt90) cc_final: 0.7955 (mtp85)
REVERT: A  552 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.7050 (m-10)
REVERT: A  787 GLU cc_start: 0.7572 (tt0) cc_final: 0.7367 (tm-30)
REVERT: A  850 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8232 (tt)
REVERT: B   75 MET cc_start: 0.2669 (mmt) cc_final: 0.2415 (mmt)
REVERT: B  187 ASP cc_start: 0.7801 (p0) cc_final: 0.7319 (p0)
REVERT: B  451 SER cc_start: 0.9003 (t) cc_final: 0.8719 (p)
REVERT: B  538 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7523 (mtt-85)
REVERT: B  785 ARG cc_start: 0.7656 (mtt180) cc_final: 0.6954 (ptp-170)
REVERT: B  820 SER cc_start: 0.8573 (m) cc_final: 0.8344 (p)
REVERT: B  850 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8272 (tt)
  outliers start: 38
  outliers final: 27
  residues processed: 153
  average time/residue: 0.1308
  time to fit residues: 28.1111
Evaluate side-chains
  158 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  790 LYS
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  527 HIS
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  790 LYS
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 135 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 148 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.137817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.104949 restraints weight = 15539.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.17
r_work: 0.3051 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13284  Z= 0.209
  Angle     :  0.567   9.327  18042  Z= 0.300
  Chirality :  0.042   0.143   1984
  Planarity :  0.004   0.034   2278
  Dihedral  :  5.052  31.723   1850
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.51 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.25 (0.22), residues: 1594
  helix:  2.05 (0.17), residues: 986
  sheet: -0.61 (0.41), residues: 166
  loop : -1.42 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 789 
 TYR   0.017   0.001   TYR A 492 
 PHE   0.017   0.002   PHE B 601 
 TRP   0.009   0.001   TRP B 202 
 HIS   0.004   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (13284)
  covalent geometry    : angle       0.56684 (18042)
  hydrogen bonds       : bond        0.06272 (  834)
  hydrogen bonds       : angle       4.68767 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7804 (mp)
REVERT: A  787 GLU cc_start: 0.7562 (tt0) cc_final: 0.7309 (tm-30)
REVERT: A  850 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8436 (tt)
REVERT: B  187 ASP cc_start: 0.7975 (p0) cc_final: 0.7459 (p0)
REVERT: B  451 SER cc_start: 0.9063 (t) cc_final: 0.8729 (p)
REVERT: B  538 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7545 (mtt-85)
REVERT: B  785 ARG cc_start: 0.7636 (mtt180) cc_final: 0.6906 (ptp-170)
REVERT: B  820 SER cc_start: 0.8598 (m) cc_final: 0.8345 (p)
REVERT: B  850 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8380 (tt)
  outliers start: 38
  outliers final: 30
  residues processed: 154
  average time/residue: 0.1281
  time to fit residues: 27.8427
Evaluate side-chains
  164 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  790 LYS
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  513 MET
Chi-restraints excluded: chain B residue  527 HIS
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  712 PHE
Chi-restraints excluded: chain B residue  790 LYS
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 112 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 116 optimal weight:    0.6980
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.139802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.106975 restraints weight = 15643.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.17
r_work: 0.3092 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13284  Z= 0.149
  Angle     :  0.523   9.685  18042  Z= 0.276
  Chirality :  0.040   0.135   1984
  Planarity :  0.004   0.034   2278
  Dihedral  :  4.836  29.682   1850
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 14.37 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.39 (0.22), residues: 1594
  helix:  2.16 (0.17), residues: 986
  sheet: -0.59 (0.41), residues: 166
  loop : -1.37 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 199 
 TYR   0.018   0.001   TYR A 492 
 PHE   0.016   0.001   PHE B 601 
 TRP   0.007   0.001   TRP B 202 
 HIS   0.003   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (13284)
  covalent geometry    : angle       0.52324 (18042)
  hydrogen bonds       : bond        0.05643 (  834)
  hydrogen bonds       : angle       4.61084 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 133
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7775 (mp)
REVERT: A  199 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7893 (mtt-85)
REVERT: A  552 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7121 (m-10)
REVERT: A  787 GLU cc_start: 0.7539 (tt0) cc_final: 0.7304 (tm-30)
REVERT: A  850 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8221 (tt)
REVERT: B  187 ASP cc_start: 0.7934 (p0) cc_final: 0.7412 (p0)
REVERT: B  451 SER cc_start: 0.9024 (t) cc_final: 0.8740 (p)
REVERT: B  538 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7509 (mtt180)
REVERT: B  785 ARG cc_start: 0.7624 (mtt180) cc_final: 0.6905 (ptp-170)
REVERT: B  820 SER cc_start: 0.8598 (m) cc_final: 0.8367 (p)
REVERT: B  850 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8320 (tt)
  outliers start: 41
  outliers final: 30
  residues processed: 153
  average time/residue: 0.1261
  time to fit residues: 27.4517
Evaluate side-chains
  166 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  790 LYS
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  527 HIS
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  712 PHE
Chi-restraints excluded: chain B residue  790 LYS
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.139229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.106447 restraints weight = 15599.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.17
r_work: 0.3094 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13284  Z= 0.177
  Angle     :  0.557  10.638  18042  Z= 0.292
  Chirality :  0.041   0.137   1984
  Planarity :  0.004   0.033   2278
  Dihedral  :  4.954  30.508   1850
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.66 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.30 (0.22), residues: 1594
  helix:  2.09 (0.17), residues: 986
  sheet: -0.63 (0.41), residues: 166
  loop : -1.39 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 199 
 TYR   0.019   0.001   TYR A 492 
 PHE   0.019   0.001   PHE B 601 
 TRP   0.008   0.001   TRP A 202 
 HIS   0.003   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (13284)
  covalent geometry    : angle       0.55712 (18042)
  hydrogen bonds       : bond        0.05952 (  834)
  hydrogen bonds       : angle       4.63649 ( 2460)

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 132
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7819 (mp)
REVERT: A  199 ARG cc_start: 0.8245 (mtt90) cc_final: 0.8018 (mtp85)
REVERT: A  552 TRP cc_start: 0.8043 (OUTLIER) cc_final: 0.7118 (m-10)
REVERT: A  787 GLU cc_start: 0.7573 (tt0) cc_final: 0.7359 (tm-30)
REVERT: A  850 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8432 (tt)
REVERT: B  451 SER cc_start: 0.9005 (t) cc_final: 0.8734 (p)
REVERT: B  538 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7552 (mtt180)
REVERT: B  785 ARG cc_start: 0.7637 (mtt180) cc_final: 0.6956 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7113 (mt-10)
REVERT: B  820 SER cc_start: 0.8556 (m) cc_final: 0.8342 (p)
REVERT: B  850 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8376 (tt)
  outliers start: 39
  outliers final: 32
  residues processed: 151
  average time/residue: 0.1292
  time to fit residues: 27.5074
Evaluate side-chains
  166 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  552 TRP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  790 LYS
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  513 MET
Chi-restraints excluded: chain B residue  527 HIS
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  538 ARG
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  712 PHE
Chi-restraints excluded: chain B residue  790 LYS
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 96 optimal weight:    3.9990
   chunk 148 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.139160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.106522 restraints weight = 15436.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.17
r_work: 0.3094 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13284  Z= 0.178
  Angle     :  0.553  10.703  18042  Z= 0.292
  Chirality :  0.041   0.138   1984
  Planarity :  0.004   0.033   2278
  Dihedral  :  4.985  30.732   1850
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.59 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.29 (0.22), residues: 1594
  helix:  2.07 (0.17), residues: 986
  sheet: -0.65 (0.41), residues: 166
  loop : -1.37 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 199 
 TYR   0.021   0.001   TYR A 732 
 PHE   0.018   0.001   PHE B 601 
 TRP   0.008   0.001   TRP A 202 
 HIS   0.003   0.001   HIS B 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (13284)
  covalent geometry    : angle       0.55300 (18042)
  hydrogen bonds       : bond        0.05978 (  834)
  hydrogen bonds       : angle       4.64122 ( 2460)

===============================================================================
Job complete
usr+sys time: 3425.33 seconds
wall clock time: 59 minutes 21.07 seconds (3561.07 seconds total)