Starting phenix.real_space_refine
on Wed Sep 17 15:36:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n5a_24184/09_2025/7n5a_24184.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n5a_24184/09_2025/7n5a_24184.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n5a_24184/09_2025/7n5a_24184.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n5a_24184/09_2025/7n5a_24184.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n5a_24184/09_2025/7n5a_24184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n5a_24184/09_2025/7n5a_24184.map"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.072
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: 7
    Type Number    sf(0)   Gaussians
     V       2      8.30       5
     P       4      5.49       5
     Mg      2      5.21       5
     S      34      5.16       5
     C    5886      2.51       5
     N    1586      2.21       5
     O    1740      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9254
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4594
          Classifications: {'peptide': 589}
          Link IDs: {'PTRANS': 13, 'TRANS': 575}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.05, per 1000 atoms: 0.33
  Number of scatterers: 9254
  At special positions: 0
  Unit cell: (76.26, 92.66, 139.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     V       2     22.97
     S      34     16.00
     P       4     15.00
     Mg      2     11.99
     O    1740      8.00
     N    1586      7.00
     C    5886      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: 0.92
  Conformation dependent library (CDL) restraints added in 276.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2204

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 6 sheets defined
      66.8% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 117 through 132
    Processing helix  chain 'A' and resid 136 through 175
      removed outlier: 3.965A  pdb=" N   ARG A 140 " --> pdb=" O   ASN A 136 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
      removed outlier: 4.053A  pdb=" N   LEU A 166 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 243
      removed outlier: 4.195A  pdb=" N   VAL A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG A 209 " --> pdb=" O   TYR A 205 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   THR A 220 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA A 221 " --> pdb=" O   GLU A 217 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LYS A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   VAL A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS A 243 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 251
    Processing helix  chain 'A' and resid 257 through 279
      removed outlier: 3.726A  pdb=" N   ASN A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 293
      removed outlier: 3.772A  pdb=" N   ILE A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU A 285 " --> pdb=" O   VAL A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 297
    Processing helix  chain 'A' and resid 301 through 348
      removed outlier: 4.792A  pdb=" N   ALA A 330 " --> pdb=" O   LYS A 326 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   MET A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP A 337 " --> pdb=" O   LYS A 333 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 338 " --> pdb=" O   ALA A 334 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 356
    Processing helix  chain 'A' and resid 357 through 408
      removed outlier: 3.687A  pdb=" N   GLU A 361 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER A 382 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ASN A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY A 408 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 414
      removed outlier: 3.587A  pdb=" N   GLN A 413 " --> pdb=" O   MET A 410 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   MET A 414 " --> pdb=" O   ASN A 411 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 410 through 414'
    Processing helix  chain 'A' and resid 417 through 429
      removed outlier: 3.623A  pdb=" N   LEU A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE A 427 " --> pdb=" O   ASN A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 439
      removed outlier: 3.681A  pdb=" N   ASN A 434 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE A 435 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 456
      removed outlier: 3.659A  pdb=" N   GLN A 445 " --> pdb=" O   ARG A 441 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   VAL A 448 " --> pdb=" O   ILE A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 459
      No H-bonds generated for 'chain 'A' and resid 457 through 459'
    Processing helix  chain 'A' and resid 547 through 553
    Processing helix  chain 'A' and resid 568 through 575
    Processing helix  chain 'A' and resid 581 through 592
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 617 through 633
      removed outlier: 3.521A  pdb=" N   ALA A 625 " --> pdb=" O   LYS A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 661
      removed outlier: 3.762A  pdb=" N   LEU A 661 " --> pdb=" O   ALA A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 703
      removed outlier: 3.908A  pdb=" N   GLY A 702 " --> pdb=" O   ASP A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 716
      removed outlier: 3.507A  pdb=" N   GLN A 713 " --> pdb=" O   GLN A 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 132
    Processing helix  chain 'B' and resid 136 through 175
      removed outlier: 3.966A  pdb=" N   ARG B 140 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
      Proline residue:  B 161  - end of helix
      removed outlier: 4.053A  pdb=" N   LEU B 166 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 243
      removed outlier: 4.196A  pdb=" N   VAL B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG B 209 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   THR B 220 " --> pdb=" O   ASN B 216 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 221 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LYS B 225 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   VAL B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS B 243 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 251
    Processing helix  chain 'B' and resid 257 through 279
      removed outlier: 3.725A  pdb=" N   ASN B 270 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 293
      removed outlier: 3.772A  pdb=" N   ILE B 284 " --> pdb=" O   VAL B 280 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B 285 " --> pdb=" O   VAL B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 297
    Processing helix  chain 'B' and resid 301 through 348
      removed outlier: 4.792A  pdb=" N   ALA B 330 " --> pdb=" O   LYS B 326 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   MET B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASP B 337 " --> pdb=" O   LYS B 333 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA B 338 " --> pdb=" O   ALA B 334 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER B 339 " --> pdb=" O   ASP B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 356
    Processing helix  chain 'B' and resid 357 through 408
      removed outlier: 3.688A  pdb=" N   GLU B 361 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER B 382 " --> pdb=" O   GLN B 378 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ASN B 387 " --> pdb=" O   LEU B 383 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLY B 408 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 414
      removed outlier: 3.588A  pdb=" N   GLN B 413 " --> pdb=" O   MET B 410 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   MET B 414 " --> pdb=" O   ASN B 411 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 410 through 414'
    Processing helix  chain 'B' and resid 417 through 429
      removed outlier: 3.624A  pdb=" N   LEU B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE B 427 " --> pdb=" O   ASN B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 439
      removed outlier: 3.681A  pdb=" N   ASN B 434 " --> pdb=" O   SER B 430 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   PHE B 435 " --> pdb=" O   LEU B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 456
      removed outlier: 3.660A  pdb=" N   GLN B 445 " --> pdb=" O   ARG B 441 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   VAL B 448 " --> pdb=" O   ILE B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 459
      No H-bonds generated for 'chain 'B' and resid 457 through 459'
    Processing helix  chain 'B' and resid 547 through 553
    Processing helix  chain 'B' and resid 568 through 575
    Processing helix  chain 'B' and resid 581 through 592
    Processing helix  chain 'B' and resid 594 through 599
    Processing helix  chain 'B' and resid 617 through 633
      removed outlier: 3.522A  pdb=" N   ALA B 625 " --> pdb=" O   LYS B 621 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 661
      removed outlier: 3.762A  pdb=" N   LEU B 661 " --> pdb=" O   ALA B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 703
      removed outlier: 3.906A  pdb=" N   GLY B 702 " --> pdb=" O   ASP B 698 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 716
      removed outlier: 3.507A  pdb=" N   GLN B 713 " --> pdb=" O   GLN B 709 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 496
      removed outlier: 3.861A  pdb=" N   LEU A 495 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   PHE A 486 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496
      removed outlier: 3.861A  pdb=" N   LEU A 495 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   PHE A 486 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   VAL A 484 " --> pdb=" O   SER A 533 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   SER A 533 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 558
      removed outlier: 6.917A  pdb=" N   ILE A 683 " --> pdb=" O   GLN A 694 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   GLN A 694 " --> pdb=" O   ILE A 683 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL A 685 " --> pdb=" O   VAL A 692 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 495 through 496
      removed outlier: 3.861A  pdb=" N   LEU B 495 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   PHE B 486 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 495 through 496
      removed outlier: 3.861A  pdb=" N   LEU B 495 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   PHE B 486 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   VAL B 484 " --> pdb=" O   SER B 533 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   SER B 533 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 558
      removed outlier: 6.917A  pdb=" N   ILE B 683 " --> pdb=" O   GLN B 694 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLN B 694 " --> pdb=" O   ILE B 683 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   VAL B 685 " --> pdb=" O   VAL B 692 " (cutoff:3.500A)

    583 hydrogen bonds defined for protein.
    1719 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: 1.25

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 3044
        1.36 -     1.50: 2362
        1.50 -     1.64: 3938
        1.64 -     1.77: 0
        1.77 -     1.91: 70
  Bond restraints: 9414
  Sorted by residual:
  bond pdb=" CA  SER B 633 "
       pdb=" CB  SER B 633 "
    ideal  model  delta    sigma   weight residual
    1.522  1.531 -0.008 7.00e-03 2.04e+04 1.45e+00
  bond pdb=" CA  SER A 633 "
       pdb=" CB  SER A 633 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.27e+00
  bond pdb=" C4  ADP B 802 "
       pdb=" C5  ADP B 802 "
    ideal  model  delta    sigma   weight residual
    1.490  1.469  0.021 2.00e-02 2.50e+03 1.06e+00
  bond pdb=" C4  ADP A 801 "
       pdb=" C5  ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 1.04e+00
  bond pdb=" C   LYS A 632 "
       pdb=" N   SER A 633 "
    ideal  model  delta    sigma   weight residual
    1.329  1.340 -0.011 1.12e-02 7.97e+03 9.64e-01
  ... (remaining 9409 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 12393
        1.57 -     3.14: 273
        3.14 -     4.71: 58
        4.71 -     6.28: 20
        6.28 -     7.85: 2
  Bond angle restraints: 12746
  Sorted by residual:
  angle pdb=" C   PRO B 559 "
        pdb=" N   GLN B 560 "
        pdb=" CA  GLN B 560 "
      ideal   model   delta    sigma   weight residual
     120.44  123.99   -3.55 1.30e+00 5.92e-01 7.46e+00
  angle pdb=" C   PRO A 559 "
        pdb=" N   GLN A 560 "
        pdb=" CA  GLN A 560 "
      ideal   model   delta    sigma   weight residual
     120.44  123.92   -3.48 1.30e+00 5.92e-01 7.15e+00
  angle pdb=" N   VAL A 692 "
        pdb=" CA  VAL A 692 "
        pdb=" C   VAL A 692 "
      ideal   model   delta    sigma   weight residual
     110.74  113.07   -2.33 9.10e-01 1.21e+00 6.56e+00
  angle pdb=" N   VAL B 692 "
        pdb=" CA  VAL B 692 "
        pdb=" C   VAL B 692 "
      ideal   model   delta    sigma   weight residual
     110.74  113.06   -2.32 9.10e-01 1.21e+00 6.51e+00
  angle pdb=" C   VAL B 609 "
        pdb=" CA  VAL B 609 "
        pdb=" CB  VAL B 609 "
      ideal   model   delta    sigma   weight residual
     111.88  108.80    3.08 1.37e+00 5.33e-01 5.05e+00
  ... (remaining 12741 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.63: 5299
       24.63 -    49.26: 299
       49.26 -    73.89: 20
       73.89 -    98.53: 2
       98.53 -   123.16: 2
  Dihedral angle restraints: 5622
    sinusoidal: 2212
      harmonic: 3410
  Sorted by residual:
  dihedral pdb=" O1B ADP B 802 "
           pdb=" O3A ADP B 802 "
           pdb=" PB  ADP B 802 "
           pdb=" PA  ADP B 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   63.15 -123.16     1      2.00e+01 2.50e-03 3.71e+01
  dihedral pdb=" O1B ADP A 801 "
           pdb=" O3A ADP A 801 "
           pdb=" PB  ADP A 801 "
           pdb=" PA  ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   63.13 -123.14     1      2.00e+01 2.50e-03 3.71e+01
  dihedral pdb=" CA  VAL B 691 "
           pdb=" C   VAL B 691 "
           pdb=" N   VAL B 692 "
           pdb=" CA  VAL B 692 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.21  -17.79     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 5619 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 937
       0.029 -    0.058: 371
       0.058 -    0.087: 110
       0.087 -    0.117: 60
       0.117 -    0.146: 12
  Chirality restraints: 1490
  Sorted by residual:
  chirality pdb=" CG  LEU B 456 "
            pdb=" CB  LEU B 456 "
            pdb=" CD1 LEU B 456 "
            pdb=" CD2 LEU B 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CG  LEU A 456 "
            pdb=" CB  LEU A 456 "
            pdb=" CD1 LEU A 456 "
            pdb=" CD2 LEU A 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 5.11e-01
  chirality pdb=" CA  GLN B 413 "
            pdb=" N   GLN B 413 "
            pdb=" C   GLN B 413 "
            pdb=" CB  GLN B 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.78e-01
  ... (remaining 1487 not shown)

  Planarity restraints: 1606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 427 "    0.015 2.00e-02 2.50e+03   1.28e-02 2.85e+00
        pdb=" CG  PHE B 427 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 427 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 427 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 427 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 427 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 427 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 427 "    0.015 2.00e-02 2.50e+03   1.25e-02 2.74e+00
        pdb=" CG  PHE A 427 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 427 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 427 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 427 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 427 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 427 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 489 "   -0.020 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO B 490 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 490 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 490 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1603 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 114
        2.62 -     3.19: 8974
        3.19 -     3.76: 14774
        3.76 -     4.33: 19539
        4.33 -     4.90: 31527
  Nonbonded interactions: 74928
  Sorted by model distance:
  nonbonded pdb="MG    MG A 803 "
            pdb=" O4  VO4 B 803 "
     model   vdw
     2.045 2.170
  nonbonded pdb=" O4  VO4 A 802 "
            pdb="MG    MG B 801 "
     model   vdw
     2.045 2.170
  nonbonded pdb="MG    MG A 803 "
            pdb=" O3B ADP B 802 "
     model   vdw
     2.066 2.170
  nonbonded pdb=" O3B ADP A 801 "
            pdb="MG    MG B 801 "
     model   vdw
     2.067 2.170
  nonbonded pdb=" OG  SER A 487 "
            pdb=" O   ARG A 492 "
     model   vdw
     2.133 3.040
  ... (remaining 74923 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 117 through 716)
  selection = (chain 'B' and resid 117 through 716)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.390
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.090
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
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      :  0.003   0.029   9414  Z= 0.128
  Angle     :  0.613   7.847  12746  Z= 0.318
  Chirality :  0.039   0.146   1490
  Planarity :  0.003   0.031   1606
  Dihedral  : 14.007 123.157   3418
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.80 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.25), residues: 1170
  helix:  1.49 (0.20), residues: 722
  sheet:  0.68 (0.61), residues: 90
  loop : -1.20 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 590 
 TYR   0.008   0.001   TYR A 349 
 PHE   0.028   0.001   PHE B 427 
 TRP   0.010   0.001   TRP B 304 
 HIS   0.009   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9414)
  covalent geometry    : angle       0.61341 (12746)
  hydrogen bonds       : bond        0.19778 (  583)
  hydrogen bonds       : angle       6.12994 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  253 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7030 (tpt90)
REVERT: A  276 MET cc_start: 0.9332 (mmm) cc_final: 0.8855 (mmm)
REVERT: B  253 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.7065 (tpt90)
  outliers start: 2
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0827
  time to fit residues: 9.9001
Evaluate side-chains
  61 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 560 GLN
A 622 GLN
A 672 HIS
B 390 GLN
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 560 GLN
B 622 GLN
B 672 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.102394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.076975 restraints weight = 24963.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.077537 restraints weight = 18918.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.078565 restraints weight = 14509.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.078721 restraints weight = 11863.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.078868 restraints weight = 11675.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9414  Z= 0.176
  Angle     :  0.658   6.859  12746  Z= 0.340
  Chirality :  0.042   0.155   1490
  Planarity :  0.004   0.032   1606
  Dihedral  :  7.380 115.332   1296
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  8.23 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.25), residues: 1170
  helix:  1.53 (0.19), residues: 720
  sheet:  1.39 (0.65), residues: 86
  loop : -1.06 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 236 
 TYR   0.020   0.002   TYR B 205 
 PHE   0.022   0.002   PHE A 302 
 TRP   0.006   0.001   TRP B 132 
 HIS   0.007   0.002   HIS B 697 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9414)
  covalent geometry    : angle       0.65798 (12746)
  hydrogen bonds       : bond        0.06035 (  583)
  hydrogen bonds       : angle       4.69027 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.7977 (ttt) cc_final: 0.6380 (mmp)
REVERT: A  421 MET cc_start: 0.9048 (mpp) cc_final: 0.8540 (mpp)
REVERT: B  276 MET cc_start: 0.8919 (mmp) cc_final: 0.8610 (mmm)
REVERT: B  421 MET cc_start: 0.9115 (mpp) cc_final: 0.8602 (mpp)
REVERT: B  434 ASN cc_start: 0.8658 (t0) cc_final: 0.8395 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 75
  average time/residue: 0.0815
  time to fit residues: 9.0585
Evaluate side-chains
  63 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  429 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
B 250 HIS
** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.099112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.075232 restraints weight = 25280.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.075170 restraints weight = 21613.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.076301 restraints weight = 15966.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.076483 restraints weight = 13006.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.076777 restraints weight = 12963.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   9414  Z= 0.271
  Angle     :  0.749   8.288  12746  Z= 0.384
  Chirality :  0.046   0.176   1490
  Planarity :  0.005   0.049   1606
  Dihedral  :  7.741 123.767   1296
  Min Nonbonded Distance : 1.777

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.05 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.24), residues: 1170
  helix:  1.27 (0.18), residues: 734
  sheet:  1.17 (0.64), residues: 88
  loop : -1.48 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 253 
 TYR   0.018   0.003   TYR A 205 
 PHE   0.029   0.002   PHE A 302 
 TRP   0.008   0.001   TRP A 132 
 HIS   0.015   0.003   HIS A 672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 ( 9414)
  covalent geometry    : angle       0.74873 (12746)
  hydrogen bonds       : bond        0.05847 (  583)
  hydrogen bonds       : angle       4.82310 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8931 (mpp) cc_final: 0.8445 (mpp)
REVERT: B  276 MET cc_start: 0.8763 (mmp) cc_final: 0.8529 (mmm)
REVERT: B  421 MET cc_start: 0.9022 (mpp) cc_final: 0.8476 (mpp)
  outliers start: 15
  outliers final: 7
  residues processed: 76
  average time/residue: 0.0700
  time to fit residues: 8.2368
Evaluate side-chains
  66 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  629 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 113 optimal weight:    0.5980
   chunk 75 optimal weight:    8.9990
   chunk 96 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0170
   chunk 92 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.6820

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.102975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.077327 restraints weight = 25250.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.079052 restraints weight = 16539.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.080180 restraints weight = 12450.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.080722 restraints weight = 10391.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.081276 restraints weight = 9389.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9414  Z= 0.129
  Angle     :  0.617  11.122  12746  Z= 0.308
  Chirality :  0.039   0.157   1490
  Planarity :  0.003   0.033   1606
  Dihedral  :  7.302 120.221   1296
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 14.96 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.25), residues: 1170
  helix:  1.57 (0.19), residues: 742
  sheet:  0.95 (0.64), residues: 88
  loop : -0.83 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 236 
 TYR   0.021   0.001   TYR A 205 
 PHE   0.021   0.001   PHE A 164 
 TRP   0.006   0.001   TRP A 132 
 HIS   0.003   0.001   HIS A 672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9414)
  covalent geometry    : angle       0.61681 (12746)
  hydrogen bonds       : bond        0.05016 (  583)
  hydrogen bonds       : angle       4.33150 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  402 MET cc_start: 0.7879 (mmm) cc_final: 0.7599 (mmm)
REVERT: A  421 MET cc_start: 0.9137 (mpp) cc_final: 0.8783 (mpp)
REVERT: B  402 MET cc_start: 0.7906 (mmm) cc_final: 0.7604 (mmm)
REVERT: B  426 LEU cc_start: 0.9080 (mp) cc_final: 0.8749 (mt)
REVERT: B  429 LEU cc_start: 0.9318 (tt) cc_final: 0.9030 (pp)
  outliers start: 6
  outliers final: 2
  residues processed: 70
  average time/residue: 0.0641
  time to fit residues: 7.3800
Evaluate side-chains
  65 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  284 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
A 259 ASN
A 434 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 HIS
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 ASN
B 390 GLN
B 434 ASN
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 595 HIS
** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.099105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.074909 restraints weight = 25670.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.074765 restraints weight = 21591.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.076058 restraints weight = 15833.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.076174 restraints weight = 12903.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.076403 restraints weight = 12691.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   9414  Z= 0.265
  Angle     :  0.729  10.135  12746  Z= 0.369
  Chirality :  0.047   0.413   1490
  Planarity :  0.005   0.042   1606
  Dihedral  :  7.600 124.304   1296
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.27 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.24), residues: 1170
  helix:  1.37 (0.18), residues: 742
  sheet:  0.99 (0.61), residues: 88
  loop : -1.36 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 341 
 TYR   0.033   0.003   TYR A 360 
 PHE   0.021   0.002   PHE B 630 
 TRP   0.007   0.001   TRP B 132 
 HIS   0.013   0.003   HIS A 672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 ( 9414)
  covalent geometry    : angle       0.72887 (12746)
  hydrogen bonds       : bond        0.05382 (  583)
  hydrogen bonds       : angle       4.56065 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 MET cc_start: 0.7819 (mmm) cc_final: 0.7474 (mmm)
REVERT: A  434 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8342 (t0)
REVERT: B  402 MET cc_start: 0.7898 (mmm) cc_final: 0.7552 (mmm)
REVERT: B  434 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8278 (t0)
  outliers start: 15
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0631
  time to fit residues: 7.3201
Evaluate side-chains
  67 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  434 ASN
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  434 ASN
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  568 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0030
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.3998

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 ASN
B 259 ASN
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 664 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.101372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.078054 restraints weight = 25264.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.076267 restraints weight = 20417.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.077806 restraints weight = 16640.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.078189 restraints weight = 13179.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.078359 restraints weight = 12389.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9414  Z= 0.142
  Angle     :  0.643  11.323  12746  Z= 0.317
  Chirality :  0.042   0.339   1490
  Planarity :  0.003   0.034   1606
  Dihedral  :  7.442 122.956   1296
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 17.27 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.25), residues: 1170
  helix:  1.53 (0.19), residues: 740
  sheet:  0.85 (0.63), residues: 88
  loop : -1.04 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 236 
 TYR   0.034   0.002   TYR A 360 
 PHE   0.014   0.001   PHE A 486 
 TRP   0.007   0.001   TRP B 132 
 HIS   0.006   0.001   HIS A 672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9414)
  covalent geometry    : angle       0.64312 (12746)
  hydrogen bonds       : bond        0.04977 (  583)
  hydrogen bonds       : angle       4.33829 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 MET cc_start: 0.7923 (mmm) cc_final: 0.7669 (mmm)
REVERT: A  664 ASN cc_start: 0.5481 (OUTLIER) cc_final: 0.5096 (m-40)
REVERT: B  402 MET cc_start: 0.7977 (mmm) cc_final: 0.7672 (mmm)
REVERT: B  664 ASN cc_start: 0.5315 (OUTLIER) cc_final: 0.4915 (m-40)
  outliers start: 19
  outliers final: 5
  residues processed: 81
  average time/residue: 0.0599
  time to fit residues: 7.9410
Evaluate side-chains
  67 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  664 ASN
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  664 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:   10.0000
   chunk 60 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 HIS
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 595 HIS
** B 664 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 = 0.4044 r_free = 0.4044 target = 0.100416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.075981 restraints weight = 25439.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.075701 restraints weight = 19754.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.076911 restraints weight = 16478.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.077553 restraints weight = 12755.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.077512 restraints weight = 12399.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9414  Z= 0.175
  Angle     :  0.671  13.030  12746  Z= 0.331
  Chirality :  0.044   0.343   1490
  Planarity :  0.004   0.035   1606
  Dihedral  :  7.417 122.845   1296
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.27 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.25), residues: 1170
  helix:  1.52 (0.19), residues: 740
  sheet:  0.91 (0.63), residues: 88
  loop : -1.10 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 236 
 TYR   0.025   0.002   TYR A 360 
 PHE   0.014   0.001   PHE A 630 
 TRP   0.007   0.001   TRP B 132 
 HIS   0.008   0.002   HIS B 672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9414)
  covalent geometry    : angle       0.67084 (12746)
  hydrogen bonds       : bond        0.04961 (  583)
  hydrogen bonds       : angle       4.37179 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 MET cc_start: 0.8136 (mmm) cc_final: 0.7867 (mmm)
REVERT: A  421 MET cc_start: 0.7805 (mmt) cc_final: 0.7522 (mpp)
REVERT: B  402 MET cc_start: 0.8205 (mmm) cc_final: 0.7897 (mmm)
  outliers start: 21
  outliers final: 7
  residues processed: 81
  average time/residue: 0.0576
  time to fit residues: 7.5732
Evaluate side-chains
  65 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  568 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 111 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 66 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 86 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 59 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 6 optimal weight:    0.3980
   overall best weight:    3.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 HIS
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 595 HIS
** B 664 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 = 0.4021 r_free = 0.4021 target = 0.099116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.075989 restraints weight = 25148.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.074977 restraints weight = 20841.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.076045 restraints weight = 17329.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.076426 restraints weight = 13177.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.076492 restraints weight = 12792.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   9414  Z= 0.221
  Angle     :  0.717  13.183  12746  Z= 0.355
  Chirality :  0.046   0.354   1490
  Planarity :  0.004   0.035   1606
  Dihedral  :  7.608 125.650   1296
  Min Nonbonded Distance : 1.803

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.18 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1170
  helix:  1.40 (0.18), residues: 740
  sheet:  1.04 (0.63), residues: 88
  loop : -1.33 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 577 
 TYR   0.026   0.002   TYR B 205 
 PHE   0.031   0.002   PHE B 302 
 TRP   0.009   0.001   TRP B 132 
 HIS   0.011   0.003   HIS A 672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 9414)
  covalent geometry    : angle       0.71707 (12746)
  hydrogen bonds       : bond        0.05116 (  583)
  hydrogen bonds       : angle       4.46517 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 MET cc_start: 0.8081 (mmm) cc_final: 0.7776 (mmm)
REVERT: B  431 LEU cc_start: 0.9286 (mm) cc_final: 0.8876 (pp)
  outliers start: 14
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0664
  time to fit residues: 7.7150
Evaluate side-chains
  65 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  568 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 106 optimal weight:    0.0670
   chunk 2 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 64 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   overall best weight:    3.0124

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 HIS
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 664 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 = 0.4027 r_free = 0.4027 target = 0.099570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.074841 restraints weight = 25018.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.075726 restraints weight = 19040.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.076379 restraints weight = 14118.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.077046 restraints weight = 12281.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.077030 restraints weight = 10880.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9414  Z= 0.191
  Angle     :  0.709  13.352  12746  Z= 0.349
  Chirality :  0.045   0.341   1490
  Planarity :  0.004   0.035   1606
  Dihedral  :  7.570 125.737   1296
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.18 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.25), residues: 1170
  helix:  1.33 (0.18), residues: 758
  sheet:  1.04 (0.63), residues: 88
  loop : -1.46 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 253 
 TYR   0.027   0.002   TYR B 205 
 PHE   0.028   0.001   PHE B 302 
 TRP   0.008   0.001   TRP B 132 
 HIS   0.008   0.002   HIS B 672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 9414)
  covalent geometry    : angle       0.70867 (12746)
  hydrogen bonds       : bond        0.05009 (  583)
  hydrogen bonds       : angle       4.44090 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: B  402 MET cc_start: 0.8030 (mmm) cc_final: 0.7383 (mmm)
REVERT: B  421 MET cc_start: 0.8084 (mmt) cc_final: 0.7623 (mpp)
REVERT: B  431 LEU cc_start: 0.9329 (mm) cc_final: 0.9092 (pp)
  outliers start: 16
  outliers final: 14
  residues processed: 74
  average time/residue: 0.0606
  time to fit residues: 7.1320
Evaluate side-chains
  70 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  629 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 47 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 105 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 88 optimal weight:    0.0030
   chunk 65 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.3794

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 664 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 = 0.4061 r_free = 0.4061 target = 0.101493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.075412 restraints weight = 25059.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.077104 restraints weight = 16890.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.078250 restraints weight = 12791.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.078993 restraints weight = 10683.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.079396 restraints weight = 9458.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9414  Z= 0.140
  Angle     :  0.694  14.376  12746  Z= 0.335
  Chirality :  0.043   0.296   1490
  Planarity :  0.003   0.035   1606
  Dihedral  :  7.363 122.805   1296
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 19.58 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.25), residues: 1170
  helix:  1.42 (0.19), residues: 758
  sheet:  1.03 (0.63), residues: 88
  loop : -1.28 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 324 
 TYR   0.028   0.001   TYR B 205 
 PHE   0.024   0.001   PHE B 302 
 TRP   0.007   0.001   TRP B 132 
 HIS   0.007   0.001   HIS A 697 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9414)
  covalent geometry    : angle       0.69428 (12746)
  hydrogen bonds       : bond        0.04738 (  583)
  hydrogen bonds       : angle       4.30519 ( 1719)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 MET cc_start: 0.8133 (mmm) cc_final: 0.7521 (mmm)
REVERT: A  421 MET cc_start: 0.8969 (mpp) cc_final: 0.8671 (mpp)
REVERT: B  402 MET cc_start: 0.8249 (mmm) cc_final: 0.7684 (mmm)
REVERT: B  421 MET cc_start: 0.8127 (mmt) cc_final: 0.7800 (mpp)
REVERT: B  431 LEU cc_start: 0.9354 (mm) cc_final: 0.9075 (pp)
  outliers start: 11
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0599
  time to fit residues: 7.0759
Evaluate side-chains
  65 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  568 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0770
   chunk 83 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 108 optimal weight:    0.4980
   chunk 74 optimal weight:    0.0570
   chunk 58 optimal weight:   20.0000
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.3260

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.101813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.076531 restraints weight = 24874.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.077326 restraints weight = 19535.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.078220 restraints weight = 14730.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.078574 restraints weight = 12363.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.078734 restraints weight = 11482.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9414  Z= 0.141
  Angle     :  0.704  14.194  12746  Z= 0.337
  Chirality :  0.043   0.280   1490
  Planarity :  0.003   0.035   1606
  Dihedral  :  7.247 120.190   1296
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 20.18 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.25), residues: 1170
  helix:  1.45 (0.19), residues: 756
  sheet:  1.15 (0.62), residues: 88
  loop : -1.25 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 324 
 TYR   0.028   0.001   TYR B 205 
 PHE   0.026   0.001   PHE B 302 
 TRP   0.007   0.001   TRP B 132 
 HIS   0.010   0.002   HIS A 697 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9414)
  covalent geometry    : angle       0.70416 (12746)
  hydrogen bonds       : bond        0.04708 (  583)
  hydrogen bonds       : angle       4.27411 ( 1719)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1419.05 seconds
wall clock time: 25 minutes 22.61 seconds (1522.61 seconds total)