Starting phenix.real_space_refine
on Thu Feb 13 22:13:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n5a_24184/02_2025/7n5a_24184.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n5a_24184/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n5a_24184/02_2025/7n5a_24184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n5a_24184/02_2025/7n5a_24184.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n5a_24184/02_2025/7n5a_24184.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n5a_24184/02_2025/7n5a_24184.cif"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 9.31, per 1000 atoms: 1.01
  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: 2.61
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.93
  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: 2.87

  Time building geometry restraints manager: 2.97 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: 0.05
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:             1.570
  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:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.500
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.020
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.870
-------------------------------------------------------------------------------
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= 0.170
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (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
 TRP   0.010   0.001   TRP B 304 
 HIS   0.009   0.001   HIS A 595 
 PHE   0.028   0.001   PHE B 427 
 TYR   0.008   0.001   TYR A 349 
 ARG   0.005   0.001   ARG A 590 

*********************** 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  : 1.132 
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: 0.2154
  time to fit residues: 25.9232
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  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 55 optimal weight:    8.9990
   chunk 67 optimal weight:    9.9990
   chunk 105 optimal weight:    4.9990
   overall best weight:    2.4586

-------------------------------------------------------------------------------
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 = 0.4085 r_free = 0.4085 target = 0.101938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.075765 restraints weight = 24741.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.077336 restraints weight = 16739.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.078411 restraints weight = 12839.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9414  Z= 0.263
  Angle     :  0.668   6.941  12746  Z= 0.346
  Chirality :  0.042   0.157   1490
  Planarity :  0.004   0.037   1606
  Dihedral  :  7.398 115.831   1296
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  8.03 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.25), residues: 1170
  helix:  1.52 (0.19), residues: 720
  sheet:  1.38 (0.65), residues: 86
  loop : -1.12 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 132 
 HIS   0.007   0.002   HIS B 697 
 PHE   0.021   0.002   PHE A 302 
 TYR   0.020   0.002   TYR A 205 
 ARG   0.003   0.001   ARG B 142 

*********************** 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  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.7975 (ttt) cc_final: 0.6376 (mmp)
REVERT: A  421 MET cc_start: 0.9099 (mpp) cc_final: 0.8592 (mpp)
REVERT: B  276 MET cc_start: 0.8873 (mmp) cc_final: 0.8565 (mmm)
REVERT: B  289 MET cc_start: 0.7298 (mpp) cc_final: 0.7074 (mpp)
REVERT: B  421 MET cc_start: 0.9157 (mpp) cc_final: 0.8677 (mpp)
REVERT: B  434 ASN cc_start: 0.8677 (t0) cc_final: 0.8407 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 75
  average time/residue: 0.2058
  time to fit residues: 22.5973
Evaluate side-chains
  62 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 14 optimal weight:    7.9990
   chunk 84 optimal weight:   20.0000
   chunk 86 optimal weight:    0.0170
   chunk 90 optimal weight:    0.9990
   chunk 115 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0030
   chunk 37 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    0.5232

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.105604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.079247 restraints weight = 24773.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.081111 restraints weight = 16050.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.082403 restraints weight = 11901.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9414  Z= 0.166
  Angle     :  0.619   9.567  12746  Z= 0.309
  Chirality :  0.039   0.158   1490
  Planarity :  0.004   0.043   1606
  Dihedral  :  7.107 114.472   1296
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 10.24 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.25), residues: 1170
  helix:  1.61 (0.19), residues: 722
  sheet:  1.25 (0.64), residues: 86
  loop : -0.68 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 132 
 HIS   0.004   0.001   HIS B 697 
 PHE   0.026   0.001   PHE A 302 
 TYR   0.022   0.002   TYR A 205 
 ARG   0.004   0.000   ARG B 236 

*********************** 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
  83 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 LEU cc_start: 0.9005 (mp) cc_final: 0.8801 (mp)
REVERT: A  429 LEU cc_start: 0.9236 (tt) cc_final: 0.8955 (pp)
REVERT: B  429 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8996 (tp)
  outliers start: 6
  outliers final: 1
  residues processed: 82
  average time/residue: 0.1921
  time to fit residues: 23.5168
Evaluate side-chains
  67 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain B residue  429 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 102 optimal weight:    3.9990
   chunk 58 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** 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 250 HIS
B 390 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.101363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.075756 restraints weight = 24669.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.076505 restraints weight = 18292.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.077529 restraints weight = 14284.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9414  Z= 0.305
  Angle     :  0.678  10.365  12746  Z= 0.341
  Chirality :  0.044   0.338   1490
  Planarity :  0.004   0.033   1606
  Dihedral  :  7.225 118.257   1296
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.25 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.25), residues: 1170
  helix:  1.58 (0.18), residues: 734
  sheet:  1.01 (0.64), residues: 88
  loop : -1.11 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 132 
 HIS   0.010   0.002   HIS A 672 
 PHE   0.032   0.002   PHE A 302 
 TYR   0.018   0.002   TYR B 205 
 ARG   0.003   0.000   ARG B 341 

*********************** 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
  77 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.8909 (mmt) cc_final: 0.8579 (mmm)
REVERT: A  429 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9024 (pp)
  outliers start: 12
  outliers final: 6
  residues processed: 71
  average time/residue: 0.1656
  time to fit residues: 18.8526
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  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  538 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.104164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.080518 restraints weight = 25092.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.080434 restraints weight = 17326.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.081353 restraints weight = 14256.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9414  Z= 0.164
  Angle     :  0.621  11.857  12746  Z= 0.303
  Chirality :  0.040   0.287   1490
  Planarity :  0.003   0.034   1606
  Dihedral  :  7.001 115.564   1296
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 14.46 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.25), residues: 1170
  helix:  1.55 (0.18), residues: 748
  sheet:  1.00 (0.63), residues: 88
  loop : -0.84 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 132 
 HIS   0.003   0.001   HIS A 672 
 PHE   0.029   0.001   PHE A 302 
 TYR   0.020   0.002   TYR B 205 
 ARG   0.004   0.000   ARG B 236 

*********************** 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
  78 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.7907 (mmt) cc_final: 0.7440 (mpp)
REVERT: B  289 MET cc_start: 0.8132 (mpt) cc_final: 0.7842 (mpt)
REVERT: B  421 MET cc_start: 0.8037 (mmt) cc_final: 0.7458 (mpp)
REVERT: B  426 LEU cc_start: 0.8827 (mt) cc_final: 0.8615 (mp)
REVERT: B  429 LEU cc_start: 0.9232 (tt) cc_final: 0.8945 (pp)
  outliers start: 10
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1563
  time to fit residues: 18.7646
Evaluate side-chains
  66 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  416 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 104 optimal weight:    7.9990
   chunk 39 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 78 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 664 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.101238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.076956 restraints weight = 24986.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.077303 restraints weight = 19260.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.077752 restraints weight = 15775.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9414  Z= 0.277
  Angle     :  0.656  10.026  12746  Z= 0.329
  Chirality :  0.043   0.314   1490
  Planarity :  0.004   0.035   1606
  Dihedral  :  7.170 119.827   1296
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.87 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.25), residues: 1170
  helix:  1.54 (0.18), residues: 748
  sheet:  1.01 (0.63), residues: 88
  loop : -1.11 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.009   0.002   HIS A 672 
 PHE   0.032   0.001   PHE A 302 
 TYR   0.017   0.002   TYR B 205 
 ARG   0.002   0.000   ARG B 236 

*********************** 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
  71 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8018 (mmt) cc_final: 0.7557 (mpp)
REVERT: B  289 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7837 (mpt)
REVERT: B  421 MET cc_start: 0.8126 (mmt) cc_final: 0.7551 (mpp)
REVERT: B  426 LEU cc_start: 0.8768 (mt) cc_final: 0.8443 (mt)
REVERT: B  429 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8928 (pp)
REVERT: B  664 ASN cc_start: 0.5159 (OUTLIER) cc_final: 0.4831 (m-40)
  outliers start: 16
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1649
  time to fit residues: 17.9946
Evaluate side-chains
  65 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  629 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 2 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 57 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 87 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   overall best weight:    3.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
** 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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.099994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.075081 restraints weight = 24947.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.075870 restraints weight = 20583.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.076107 restraints weight = 14988.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9414  Z= 0.345
  Angle     :  0.707  11.599  12746  Z= 0.355
  Chirality :  0.046   0.324   1490
  Planarity :  0.004   0.036   1606
  Dihedral  :  7.434 123.691   1296
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.24), residues: 1170
  helix:  1.35 (0.18), residues: 748
  sheet:  1.10 (0.64), residues: 88
  loop : -1.41 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.012   0.002   HIS A 672 
 PHE   0.030   0.002   PHE A 302 
 TYR   0.018   0.002   TYR B 575 
 ARG   0.004   0.001   ARG B 665 

*********************** 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
  73 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8051 (mmt) cc_final: 0.7729 (mpp)
REVERT: B  289 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7898 (mpt)
REVERT: B  421 MET cc_start: 0.8181 (mmt) cc_final: 0.7610 (mpp)
REVERT: B  426 LEU cc_start: 0.8881 (mt) cc_final: 0.8546 (mt)
REVERT: B  429 LEU cc_start: 0.9181 (tt) cc_final: 0.8965 (pp)
  outliers start: 15
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1823
  time to fit residues: 19.6358
Evaluate side-chains
  61 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  629 THR
Chi-restraints excluded: chain B residue  289 MET
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
Chi-restraints excluded: chain B residue  629 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 111 optimal weight:    0.0070
   chunk 14 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 92 optimal weight:    0.2980
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.0604

-------------------------------------------------------------------------------
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 595 HIS
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 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 = 0.4085 r_free = 0.4085 target = 0.102651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.077493 restraints weight = 25092.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.078278 restraints weight = 16627.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.079390 restraints weight = 13395.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9414  Z= 0.177
  Angle     :  0.654  13.506  12746  Z= 0.316
  Chirality :  0.042   0.285   1490
  Planarity :  0.003   0.035   1606
  Dihedral  :  7.125 118.516   1296
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 17.97 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.25), residues: 1170
  helix:  1.57 (0.18), residues: 750
  sheet:  1.03 (0.64), residues: 88
  loop : -1.08 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.004   0.001   HIS B 672 
 PHE   0.025   0.001   PHE A 302 
 TYR   0.022   0.001   TYR B 205 
 ARG   0.004   0.000   ARG B 236 

*********************** 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
  68 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8079 (mmt) cc_final: 0.7668 (mpp)
REVERT: B  289 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7911 (mpt)
REVERT: B  402 MET cc_start: 0.8213 (mmm) cc_final: 0.7573 (mmm)
  outliers start: 10
  outliers final: 4
  residues processed: 64
  average time/residue: 0.1775
  time to fit residues: 17.7867
Evaluate side-chains
  57 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  524 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 107 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 111 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    1.9984

-------------------------------------------------------------------------------
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 595 HIS
** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 595 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.101863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.076985 restraints weight = 24939.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.077419 restraints weight = 18060.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.078340 restraints weight = 14353.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9414  Z= 0.222
  Angle     :  0.667  12.937  12746  Z= 0.324
  Chirality :  0.043   0.281   1490
  Planarity :  0.004   0.036   1606
  Dihedral  :  7.113 118.369   1296
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 18.57 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.25), residues: 1170
  helix:  1.55 (0.18), residues: 750
  sheet:  1.03 (0.64), residues: 88
  loop : -1.15 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.006   0.002   HIS A 672 
 PHE   0.025   0.001   PHE A 302 
 TYR   0.022   0.002   TYR B 205 
 ARG   0.004   0.000   ARG A 253 

*********************** 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
  65 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8137 (mmt) cc_final: 0.7704 (mpp)
REVERT: B  289 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7922 (mpt)
REVERT: B  421 MET cc_start: 0.8220 (mmt) cc_final: 0.7741 (mpp)
  outliers start: 10
  outliers final: 6
  residues processed: 61
  average time/residue: 0.1647
  time to fit residues: 16.5930
Evaluate side-chains
  60 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  289 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  538 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0050
   chunk 58 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0670
   chunk 59 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.8136

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.103848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.079131 restraints weight = 24980.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.079709 restraints weight = 15256.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.080413 restraints weight = 12711.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9414  Z= 0.164
  Angle     :  0.665  13.175  12746  Z= 0.315
  Chirality :  0.041   0.252   1490
  Planarity :  0.003   0.035   1606
  Dihedral  :  6.849 112.460   1296
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 18.37 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.25), residues: 1170
  helix:  1.59 (0.18), residues: 754
  sheet:  1.00 (0.63), residues: 88
  loop : -0.96 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 697 
 PHE   0.026   0.001   PHE A 302 
 TYR   0.024   0.001   TYR B 205 
 ARG   0.004   0.000   ARG B 236 

********************** 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
  67 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 MET cc_start: 0.7873 (mmm) cc_final: 0.7256 (mmm)
REVERT: A  421 MET cc_start: 0.8153 (mmt) cc_final: 0.7861 (mpp)
REVERT: B  289 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7938 (mpt)
REVERT: B  402 MET cc_start: 0.7967 (mmm) cc_final: 0.7244 (mmm)
REVERT: B  421 MET cc_start: 0.8191 (mmt) cc_final: 0.7856 (mpp)
  outliers start: 9
  outliers final: 6
  residues processed: 63
  average time/residue: 0.1688
  time to fit residues: 17.2505
Evaluate side-chains
  61 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain B residue  250 HIS
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  524 MET
Chi-restraints excluded: chain B residue  538 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    0.0060
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    0.1980
   chunk 28 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 56 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 664 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.104996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.079103 restraints weight = 24870.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.081003 restraints weight = 16141.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.082316 restraints weight = 11912.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9414  Z= 0.158
  Angle     :  0.649  13.536  12746  Z= 0.308
  Chirality :  0.040   0.226   1490
  Planarity :  0.003   0.036   1606
  Dihedral  :  6.630 107.508   1296
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 18.27 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.25), residues: 1170
  helix:  1.67 (0.18), residues: 754
  sheet:  0.94 (0.63), residues: 88
  loop : -0.88 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 304 
 HIS   0.003   0.001   HIS A 697 
 PHE   0.023   0.001   PHE B 302 
 TYR   0.023   0.001   TYR B 205 
 ARG   0.004   0.000   ARG B 236 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2711.91 seconds
wall clock time: 49 minutes 54.97 seconds (2994.97 seconds total)