Starting phenix.real_space_refine
on Wed Jun 11 07:06:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wjo_32547/06_2025/7wjo_32547.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wjo_32547/06_2025/7wjo_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wjo_32547/06_2025/7wjo_32547.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wjo_32547/06_2025/7wjo_32547.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wjo_32547/06_2025/7wjo_32547.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wjo_32547/06_2025/7wjo_32547.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.80, per 1000 atoms: 1.14
  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: 3.39
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.42
  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: 4.62

  Time building geometry restraints manager: 3.97 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: 0.06
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:             1.890
  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:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     39.640
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.310
-------------------------------------------------------------------------------
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 : 4.21
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (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
 TRP   0.008   0.001   TRP B 804 
 HIS   0.005   0.001   HIS A 403 
 PHE   0.016   0.001   PHE B 601 
 TYR   0.011   0.001   TYR A 365 
 ARG   0.002   0.000   ARG B 608 

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

*********************** 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  : 1.540 
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: 0.3756
  time to fit residues: 119.3052
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  : 1.663 
-------------------------------------------------------------------------------
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 135 optimal weight:    1.9990
   chunk 121 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0170
   chunk 93 optimal weight:    4.9990
   chunk 145 optimal weight:    0.8980
   overall best weight:    0.7218

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.144659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.112220 restraints weight = 15305.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.17
r_work: 0.3170 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1379

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= 0.139
  Angle     :  0.520   7.046  18042  Z= 0.276
  Chirality :  0.040   0.176   1984
  Planarity :  0.004   0.031   2278
  Dihedral  :  6.670  46.465   1852
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  9.36 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.22), residues: 1594
  helix:  2.44 (0.17), residues: 998
  sheet: -0.00 (0.43), residues: 170
  loop : -1.34 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 804 
 HIS   0.003   0.001   HIS A 578 
 PHE   0.015   0.001   PHE A 601 
 TYR   0.018   0.001   TYR A 732 
 ARG   0.004   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05413 (  834)
  hydrogen bonds       : angle       4.65443 ( 2460)
  covalent geometry    : bond        0.00295 (13284)
  covalent geometry    : angle       0.51977 (18042)

*********************** 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
  181 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 1.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7818 (mp)
REVERT: A  193 MET cc_start: 0.7268 (mmm) cc_final: 0.6683 (mmm)
REVERT: A  238 MET cc_start: 0.8557 (ttm) cc_final: 0.8249 (ttm)
REVERT: A  403 HIS cc_start: 0.7273 (t-90) cc_final: 0.6815 (m170)
REVERT: A  552 TRP cc_start: 0.7793 (t-100) cc_final: 0.6983 (m-10)
REVERT: A  666 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7655 (ttm)
REVERT: A  730 THR cc_start: 0.8764 (m) cc_final: 0.8392 (p)
REVERT: A  850 ILE cc_start: 0.8246 (tt) cc_final: 0.7980 (tt)
REVERT: B  187 ASP cc_start: 0.7670 (p0) cc_final: 0.7245 (p0)
REVERT: B  305 GLU cc_start: 0.8461 (tt0) cc_final: 0.8161 (tt0)
REVERT: B  325 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7702 (mp10)
REVERT: B  403 HIS cc_start: 0.7556 (t-90) cc_final: 0.7264 (m-70)
REVERT: B  668 MET cc_start: 0.8153 (mmm) cc_final: 0.7941 (mmp)
REVERT: B  790 LYS cc_start: 0.7587 (mttt) cc_final: 0.7349 (mptt)
REVERT: B  794 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7132 (mt-10)
REVERT: B  820 SER cc_start: 0.8448 (m) cc_final: 0.8179 (p)
REVERT: B  850 ILE cc_start: 0.8568 (tt) cc_final: 0.8276 (tt)
  outliers start: 25
  outliers final: 13
  residues processed: 173
  average time/residue: 0.3314
  time to fit residues: 82.0552
Evaluate side-chains
  155 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
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  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  690 VAL
Chi-restraints excluded: chain B residue  452 VAL
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  684 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 136 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 84 optimal weight:    9.9990
   chunk 57 optimal weight:    0.4980
   chunk 157 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.144125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111679 restraints weight = 15447.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.17
r_work: 0.3164 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13284  Z= 0.131
  Angle     :  0.500   7.282  18042  Z= 0.266
  Chirality :  0.039   0.135   1984
  Planarity :  0.004   0.036   2278
  Dihedral  :  5.012  27.280   1850
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 10.60 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.22), residues: 1594
  helix:  2.46 (0.17), residues: 988
  sheet: -0.17 (0.43), residues: 174
  loop : -1.27 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 804 
 HIS   0.003   0.001   HIS A 578 
 PHE   0.016   0.001   PHE B 601 
 TYR   0.021   0.001   TYR A 732 
 ARG   0.006   0.000   ARG B 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05222 (  834)
  hydrogen bonds       : angle       4.57162 ( 2460)
  covalent geometry    : bond        0.00280 (13284)
  covalent geometry    : angle       0.49957 (18042)

*********************** 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
  176 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7800 (mp)
REVERT: A  199 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7754 (mtt-85)
REVERT: A  403 HIS cc_start: 0.7423 (t-90) cc_final: 0.7116 (m170)
REVERT: A  552 TRP cc_start: 0.7863 (t-100) cc_final: 0.7032 (m-10)
REVERT: A  730 THR cc_start: 0.8852 (m) cc_final: 0.8466 (p)
REVERT: A  850 ILE cc_start: 0.8307 (tt) cc_final: 0.8061 (tt)
REVERT: B  187 ASP cc_start: 0.7673 (p0) cc_final: 0.7260 (p0)
REVERT: B  195 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7902 (tp30)
REVERT: B  199 ARG cc_start: 0.8370 (tpp80) cc_final: 0.8012 (tpp80)
REVERT: B  305 GLU cc_start: 0.8397 (tt0) cc_final: 0.8081 (tt0)
REVERT: B  736 ASN cc_start: 0.7432 (m110) cc_final: 0.6916 (m110)
REVERT: B  785 ARG cc_start: 0.7540 (mtt180) cc_final: 0.6828 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7323 (mt-10)
REVERT: B  820 SER cc_start: 0.8436 (m) cc_final: 0.8162 (p)
REVERT: B  850 ILE cc_start: 0.8544 (tt) cc_final: 0.8249 (tt)
  outliers start: 29
  outliers final: 14
  residues processed: 167
  average time/residue: 0.2620
  time to fit residues: 62.7034
Evaluate side-chains
  153 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
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  670 SER
Chi-restraints excluded: chain A residue  690 VAL
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  816 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   chunk 133 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 150 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.138602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.106203 restraints weight = 15396.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.98
r_work: 0.3071 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13284  Z= 0.212
  Angle     :  0.575   8.467  18042  Z= 0.305
  Chirality :  0.042   0.138   1984
  Planarity :  0.004   0.032   2278
  Dihedral  :  5.061  32.316   1850
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 11.25 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.22), residues: 1594
  helix:  2.18 (0.17), residues: 974
  sheet: -0.44 (0.42), residues: 174
  loop : -1.27 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 202 
 HIS   0.005   0.001   HIS A 578 
 PHE   0.019   0.002   PHE B 601 
 TYR   0.019   0.002   TYR A 732 
 ARG   0.004   0.001   ARG A 839 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06446 (  834)
  hydrogen bonds       : angle       4.72636 ( 2460)
  covalent geometry    : bond        0.00504 (13284)
  covalent geometry    : angle       0.57544 (18042)

*********************** 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
  187 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 1.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7888 (mp)
REVERT: A  199 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7682 (mtt-85)
REVERT: A  238 MET cc_start: 0.8855 (ttm) cc_final: 0.8636 (ttm)
REVERT: A  552 TRP cc_start: 0.7942 (t-100) cc_final: 0.7010 (m-10)
REVERT: A  787 GLU cc_start: 0.7605 (tt0) cc_final: 0.7395 (tm-30)
REVERT: A  816 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8578 (p)
REVERT: A  850 ILE cc_start: 0.8590 (tt) cc_final: 0.8307 (tt)
REVERT: B  187 ASP cc_start: 0.7772 (p0) cc_final: 0.7297 (p0)
REVERT: B  305 GLU cc_start: 0.8399 (tt0) cc_final: 0.8175 (tt0)
REVERT: B  451 SER cc_start: 0.9157 (t) cc_final: 0.8725 (p)
REVERT: B  785 ARG cc_start: 0.7642 (mtt180) cc_final: 0.6854 (ptp-170)
REVERT: B  820 SER cc_start: 0.8555 (m) cc_final: 0.8285 (p)
REVERT: B  850 ILE cc_start: 0.8630 (tt) cc_final: 0.8276 (tt)
  outliers start: 38
  outliers final: 25
  residues processed: 176
  average time/residue: 0.2783
  time to fit residues: 70.2166
Evaluate side-chains
  161 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
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  530 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  326 CYS
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  530 VAL
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  648 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 158 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3651 r_free = 0.3651 target = 0.139854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.107071 restraints weight = 15518.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.15
r_work: 0.3098 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2553

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= 0.165
  Angle     :  0.534   7.425  18042  Z= 0.284
  Chirality :  0.040   0.132   1984
  Planarity :  0.004   0.032   2278
  Dihedral  :  4.860  29.405   1850
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.19 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.22), residues: 1594
  helix:  2.23 (0.17), residues: 978
  sheet: -0.53 (0.42), residues: 174
  loop : -1.29 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 202 
 HIS   0.003   0.001   HIS A 578 
 PHE   0.017   0.001   PHE A 601 
 TYR   0.018   0.001   TYR A 732 
 ARG   0.003   0.000   ARG B 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05853 (  834)
  hydrogen bonds       : angle       4.65116 ( 2460)
  covalent geometry    : bond        0.00379 (13284)
  covalent geometry    : angle       0.53408 (18042)

*********************** 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
  183 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 144
  time to evaluate  : 1.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7872 (mp)
REVERT: A  199 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7620 (mtt-85)
REVERT: A  238 MET cc_start: 0.8867 (ttm) cc_final: 0.8606 (ttm)
REVERT: A  552 TRP cc_start: 0.7932 (t-100) cc_final: 0.6989 (m-10)
REVERT: A  850 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8305 (tt)
REVERT: B  187 ASP cc_start: 0.7775 (p0) cc_final: 0.7289 (p0)
REVERT: B  195 GLU cc_start: 0.8155 (tp30) cc_final: 0.7280 (tp30)
REVERT: B  199 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7926 (tpp80)
REVERT: B  451 SER cc_start: 0.9072 (t) cc_final: 0.8719 (p)
REVERT: B  785 ARG cc_start: 0.7600 (mtt180) cc_final: 0.6867 (ptp-170)
REVERT: B  820 SER cc_start: 0.8554 (m) cc_final: 0.8297 (p)
REVERT: B  850 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8273 (tt)
  outliers start: 39
  outliers final: 24
  residues processed: 167
  average time/residue: 0.2849
  time to fit residues: 67.8615
Evaluate side-chains
  160 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
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  564 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  790 LYS
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  852 THR
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  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  850 ILE
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 157 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 116 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 137 optimal weight:    3.9990
   chunk 131 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 736 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.140198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.107121 restraints weight = 15646.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.25
r_work: 0.3104 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13284  Z= 0.159
  Angle     :  0.527   7.653  18042  Z= 0.279
  Chirality :  0.040   0.129   1984
  Planarity :  0.004   0.032   2278
  Dihedral  :  4.813  28.391   1850
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.13 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.22), residues: 1594
  helix:  2.26 (0.17), residues: 978
  sheet: -0.63 (0.41), residues: 174
  loop : -1.32 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 202 
 HIS   0.003   0.001   HIS B 578 
 PHE   0.016   0.001   PHE A 601 
 TYR   0.018   0.001   TYR A 732 
 ARG   0.003   0.000   ARG B 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05729 (  834)
  hydrogen bonds       : angle       4.62536 ( 2460)
  covalent geometry    : bond        0.00362 (13284)
  covalent geometry    : angle       0.52685 (18042)

*********************** 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
  178 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 1.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7789 (mp)
REVERT: A  238 MET cc_start: 0.8871 (ttm) cc_final: 0.8590 (ttm)
REVERT: A  552 TRP cc_start: 0.7894 (t-100) cc_final: 0.6926 (m-10)
REVERT: A  650 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8263 (mmmt)
REVERT: A  850 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8220 (tt)
REVERT: B  187 ASP cc_start: 0.7819 (p0) cc_final: 0.7343 (p0)
REVERT: B  451 SER cc_start: 0.9060 (t) cc_final: 0.8719 (p)
REVERT: B  785 ARG cc_start: 0.7581 (mtt180) cc_final: 0.6812 (ptp-170)
REVERT: B  820 SER cc_start: 0.8559 (m) cc_final: 0.8285 (p)
REVERT: B  850 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8226 (tt)
  outliers start: 37
  outliers final: 27
  residues processed: 162
  average time/residue: 0.2966
  time to fit residues: 67.8713
Evaluate side-chains
  166 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
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  564 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  816 VAL
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  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  712 PHE
Chi-restraints excluded: chain B residue  850 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 94 optimal weight:    0.2980
   chunk 48 optimal weight:    3.9990
   chunk 152 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 147 optimal weight:    2.9990
   chunk 82 optimal weight:    9.9990
   chunk 132 optimal weight:    0.0670
   chunk 61 optimal weight:    0.1980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.9122

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.140848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.108099 restraints weight = 15508.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.21
r_work: 0.3113 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2779

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= 0.146
  Angle     :  0.519   8.468  18042  Z= 0.275
  Chirality :  0.039   0.134   1984
  Planarity :  0.004   0.033   2278
  Dihedral  :  4.718  27.165   1850
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.64 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.22), residues: 1594
  helix:  2.30 (0.17), residues: 978
  sheet: -0.69 (0.41), residues: 174
  loop : -1.31 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 202 
 HIS   0.003   0.001   HIS B 578 
 PHE   0.017   0.001   PHE A 601 
 TYR   0.017   0.001   TYR A 732 
 ARG   0.003   0.000   ARG B 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05527 (  834)
  hydrogen bonds       : angle       4.59223 ( 2460)
  covalent geometry    : bond        0.00327 (13284)
  covalent geometry    : angle       0.51922 (18042)

*********************** 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
  179 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 1.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7826 (mp)
REVERT: A  199 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7809 (mtt-85)
REVERT: A  552 TRP cc_start: 0.7932 (t-100) cc_final: 0.7026 (m-10)
REVERT: A  850 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8225 (tt)
REVERT: B  187 ASP cc_start: 0.7787 (p0) cc_final: 0.7300 (p0)
REVERT: B  199 ARG cc_start: 0.8292 (tpp80) cc_final: 0.8089 (tpp80)
REVERT: B  451 SER cc_start: 0.9032 (t) cc_final: 0.8719 (p)
REVERT: B  785 ARG cc_start: 0.7663 (mtt180) cc_final: 0.6914 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7202 (mt-10)
REVERT: B  820 SER cc_start: 0.8549 (m) cc_final: 0.8304 (p)
REVERT: B  850 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8244 (tt)
  outliers start: 39
  outliers final: 27
  residues processed: 164
  average time/residue: 0.2946
  time to fit residues: 68.0501
Evaluate side-chains
  164 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
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  564 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  690 VAL
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  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 40 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 15 optimal weight:    0.3980
   chunk 89 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   chunk 117 optimal weight:    0.0970
   chunk 110 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.5978

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.143028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.110497 restraints weight = 15532.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.15
r_work: 0.3140 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  13284  Z= 0.120
  Angle     :  0.494   8.843  18042  Z= 0.261
  Chirality :  0.038   0.125   1984
  Planarity :  0.004   0.033   2278
  Dihedral  :  4.536  26.391   1850
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.72 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.22), residues: 1594
  helix:  2.44 (0.17), residues: 974
  sheet: -0.58 (0.42), residues: 172
  loop : -1.30 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 539 
 HIS   0.002   0.001   HIS B 578 
 PHE   0.015   0.001   PHE A 545 
 TYR   0.017   0.001   TYR A 732 
 ARG   0.005   0.000   ARG A 797 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05006 (  834)
  hydrogen bonds       : angle       4.52475 ( 2460)
  covalent geometry    : bond        0.00251 (13284)
  covalent geometry    : angle       0.49388 (18042)

*********************** 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
  186 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 1.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7731 (mp)
REVERT: A  162 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7176 (mm-30)
REVERT: A  199 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7809 (mtt-85)
REVERT: A  552 TRP cc_start: 0.7919 (OUTLIER) cc_final: 0.6962 (m-10)
REVERT: A  850 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8156 (tt)
REVERT: B  187 ASP cc_start: 0.7711 (p0) cc_final: 0.7195 (p0)
REVERT: B  199 ARG cc_start: 0.8268 (tpp80) cc_final: 0.8057 (tpp80)
REVERT: B  371 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8141 (mm-30)
REVERT: B  451 SER cc_start: 0.8983 (t) cc_final: 0.8682 (p)
REVERT: B  785 ARG cc_start: 0.7683 (mtt180) cc_final: 0.6926 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7273 (tt0)
REVERT: B  820 SER cc_start: 0.8559 (m) cc_final: 0.8328 (p)
REVERT: B  850 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8228 (tt)
  outliers start: 38
  outliers final: 25
  residues processed: 170
  average time/residue: 0.2844
  time to fit residues: 68.7160
Evaluate side-chains
  168 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
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  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  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  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  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  645 LEU
Chi-restraints excluded: chain B residue  648 ASN
Chi-restraints excluded: chain B residue  712 PHE
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 109 optimal weight:    0.9980
   chunk 150 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 152 optimal weight:    2.9990
   chunk 136 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 157 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 736 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.142330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.109840 restraints weight = 15428.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.13
r_work: 0.3128 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13284  Z= 0.130
  Angle     :  0.508  10.094  18042  Z= 0.267
  Chirality :  0.039   0.191   1984
  Planarity :  0.004   0.034   2278
  Dihedral  :  4.526  26.500   1850
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.08 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.22), residues: 1594
  helix:  2.40 (0.17), residues: 978
  sheet: -0.60 (0.41), residues: 172
  loop : -1.29 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 202 
 HIS   0.002   0.001   HIS B 578 
 PHE   0.017   0.001   PHE B 601 
 TYR   0.018   0.001   TYR A 732 
 ARG   0.004   0.000   ARG A 797 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05139 (  834)
  hydrogen bonds       : angle       4.50799 ( 2460)
  covalent geometry    : bond        0.00285 (13284)
  covalent geometry    : angle       0.50844 (18042)

*********************** 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
  176 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7763 (mp)
REVERT: A  199 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7766 (mtt-85)
REVERT: A  552 TRP cc_start: 0.7941 (OUTLIER) cc_final: 0.6978 (m-10)
REVERT: A  850 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8207 (tt)
REVERT: B  187 ASP cc_start: 0.7748 (p0) cc_final: 0.7235 (p0)
REVERT: B  371 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8163 (mm-30)
REVERT: B  451 SER cc_start: 0.8987 (t) cc_final: 0.8686 (p)
REVERT: B  785 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7000 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7481 (tt0)
REVERT: B  820 SER cc_start: 0.8538 (m) cc_final: 0.8306 (p)
REVERT: B  850 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8262 (tt)
  outliers start: 36
  outliers final: 29
  residues processed: 161
  average time/residue: 0.2907
  time to fit residues: 66.6391
Evaluate side-chains
  168 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 135
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
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  206 VAL
Chi-restraints excluded: chain A residue  238 MET
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  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  670 SER
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  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  645 LEU
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 139 optimal weight:    1.9990
   chunk 146 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   chunk 131 optimal weight:    0.6980
   chunk 80 optimal weight:    0.0370
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.1464

-------------------------------------------------------------------------------
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 736 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.140314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.107649 restraints weight = 15509.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.17
r_work: 0.3106 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2967

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= 0.166
  Angle     :  0.534  10.340  18042  Z= 0.281
  Chirality :  0.040   0.177   1984
  Planarity :  0.004   0.033   2278
  Dihedral  :  4.748  28.952   1850
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.08 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.22), residues: 1594
  helix:  2.30 (0.17), residues: 978
  sheet: -0.69 (0.41), residues: 172
  loop : -1.30 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 202 
 HIS   0.004   0.001   HIS B 578 
 PHE   0.019   0.001   PHE B 601 
 TYR   0.015   0.001   TYR A 492 
 ARG   0.003   0.000   ARG A 797 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05666 (  834)
  hydrogen bonds       : angle       4.56975 ( 2460)
  covalent geometry    : bond        0.00384 (13284)
  covalent geometry    : angle       0.53395 (18042)

********************** 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
  174 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 138
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7798 (mp)
REVERT: A  199 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7830 (mtt-85)
REVERT: A  552 TRP cc_start: 0.7964 (OUTLIER) cc_final: 0.7054 (m-10)
REVERT: A  850 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8273 (tt)
REVERT: B  371 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8167 (mm-30)
REVERT: B  451 SER cc_start: 0.9028 (t) cc_final: 0.8732 (p)
REVERT: B  785 ARG cc_start: 0.7691 (mtt180) cc_final: 0.6933 (ptp-170)
REVERT: B  794 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7365 (mt-10)
REVERT: B  820 SER cc_start: 0.8514 (m) cc_final: 0.8273 (p)
REVERT: B  850 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8338 (tt)
  outliers start: 36
  outliers final: 28
  residues processed: 158
  average time/residue: 0.2925
  time to fit residues: 65.5609
Evaluate side-chains
  165 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
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  206 VAL
Chi-restraints excluded: chain A residue  238 MET
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  670 SER
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  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  645 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 108 optimal weight:    4.9990
   chunk 139 optimal weight:    0.8980
   chunk 131 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 736 ASN
** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.139665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.106971 restraints weight = 15527.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.22
r_work: 0.3099 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3036

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= 0.179
  Angle     :  0.552  10.132  18042  Z= 0.291
  Chirality :  0.041   0.174   1984
  Planarity :  0.004   0.033   2278
  Dihedral  :  4.900  30.141   1850
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.08 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.22), residues: 1594
  helix:  2.23 (0.17), residues: 978
  sheet: -0.78 (0.41), residues: 174
  loop : -1.31 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 202 
 HIS   0.004   0.001   HIS B 578 
 PHE   0.019   0.001   PHE B 601 
 TYR   0.015   0.001   TYR A 492 
 ARG   0.003   0.000   ARG A 797 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05863 (  834)
  hydrogen bonds       : angle       4.61308 ( 2460)
  covalent geometry    : bond        0.00421 (13284)
  covalent geometry    : angle       0.55232 (18042)

===============================================================================
Job complete
usr+sys time: 7203.08 seconds
wall clock time: 126 minutes 1.05 seconds (7561.05 seconds total)