Starting phenix.real_space_refine
on Sun Dec 29 00:40:03 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n5a_24184/12_2024/7n5a_24184.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n5a_24184/12_2024/7n5a_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_24184/12_2024/7n5a_24184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n5a_24184/12_2024/7n5a_24184.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n5a_24184/12_2024/7n5a_24184.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n5a_24184/12_2024/7n5a_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.99, per 1000 atoms: 0.97
  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: 2.48
  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: 1.14
  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: 3.71

  Time building geometry restraints manager: 2.84 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: 0.00
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:             2.960
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     28.260
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.160
-------------------------------------------------------------------------------
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  : 1.034 
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: 0.2166
  time to fit residues: 26.1252
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  : 1.222 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
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  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.7978 (ttt) cc_final: 0.6380 (mmp)
REVERT: A  253 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.7076 (tpt90)
REVERT: A  421 MET cc_start: 0.9105 (mpp) cc_final: 0.8628 (mpp)
REVERT: B  253 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.7151 (tpt90)
REVERT: B  276 MET cc_start: 0.9049 (mmp) cc_final: 0.8742 (mmm)
REVERT: B  421 MET cc_start: 0.9163 (mpp) cc_final: 0.8722 (mpp)
REVERT: B  434 ASN cc_start: 0.8969 (t0) cc_final: 0.8722 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 75
  average time/residue: 0.2114
  time to fit residues: 23.6443
Evaluate side-chains
  64 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
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 58 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 87 optimal weight:    9.9990
   chunk 71 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 105 optimal weight:    0.3980
   chunk 114 optimal weight:    5.9990
   chunk 93 optimal weight:    0.5980
   chunk 104 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 84 optimal weight:   20.0000
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1600

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= 0.175
  Angle     :  0.616   8.940  12746  Z= 0.308
  Chirality :  0.040   0.158   1490
  Planarity :  0.003   0.032   1606
  Dihedral  :  7.174 115.623   1296
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.14 %
    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:  1.19 (0.25), residues: 1170
  helix:  1.53 (0.19), residues: 734
  sheet:  1.30 (0.64), residues: 86
  loop : -0.91 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 132 
 HIS   0.005   0.001   HIS B 697 
 PHE   0.026   0.001   PHE A 302 
 TYR   0.021   0.002   TYR A 205 
 ARG   0.003   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
  79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7137 (tpt90)
REVERT: A  429 LEU cc_start: 0.9334 (tt) cc_final: 0.9006 (pp)
REVERT: B  253 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.7183 (tpt90)
  outliers start: 7
  outliers final: 3
  residues processed: 77
  average time/residue: 0.1893
  time to fit residues: 21.9526
Evaluate side-chains
  69 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain B residue  284 ILE
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 104 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 50 optimal weight:    0.2980
   chunk 70 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9990
   chunk 112 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9414  Z= 0.193
  Angle     :  0.625  10.686  12746  Z= 0.309
  Chirality :  0.041   0.257   1490
  Planarity :  0.003   0.033   1606
  Dihedral  :  7.064 115.133   1296
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.05 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.62 (0.19), residues: 742
  sheet:  1.05 (0.64), residues: 88
  loop : -0.81 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 132 
 HIS   0.006   0.001   HIS A 672 
 PHE   0.015   0.001   PHE A 164 
 TYR   0.020   0.001   TYR B 205 
 ARG   0.003   0.000   ARG B 236 

*********************** 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
  82 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7446 (mtm-85) cc_final: 0.7175 (tpt90)
REVERT: A  421 MET cc_start: 0.9096 (mpp) cc_final: 0.8678 (mpp)
REVERT: B  253 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7235 (tpt90)
  outliers start: 11
  outliers final: 5
  residues processed: 75
  average time/residue: 0.1942
  time to fit residues: 21.9648
Evaluate side-chains
  72 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
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 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 93 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0020
   chunk 77 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    4.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 250 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 243 HIS
B 250 HIS
** 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: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9414  Z= 0.381
  Angle     :  0.729  10.285  12746  Z= 0.369
  Chirality :  0.046   0.351   1490
  Planarity :  0.005   0.043   1606
  Dihedral  :  7.574 125.456   1296
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.06 %
    Favored  : 83.23 %
  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:  0.94 (0.24), residues: 1170
  helix:  1.40 (0.18), residues: 742
  sheet:  1.15 (0.63), residues: 88
  loop : -1.24 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.014   0.003   HIS B 672 
 PHE   0.021   0.002   PHE B 630 
 TYR   0.017   0.003   TYR B 575 
 ARG   0.004   0.001   ARG A 341 

*********************** 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: 17
    poor density    : 61
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7266 (tpt90)
REVERT: A  410 MET cc_start: 0.7897 (ppp) cc_final: 0.7625 (ppp)
REVERT: B  253 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7246 (tpt90)
REVERT: B  289 MET cc_start: 0.7912 (mpt) cc_final: 0.7501 (mpt)
REVERT: B  421 MET cc_start: 0.8211 (mmt) cc_final: 0.7812 (mpp)
  outliers start: 17
  outliers final: 10
  residues processed: 72
  average time/residue: 0.1975
  time to fit residues: 21.5251
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  : 1.070 
-------------------------------------------------------------------------------
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  429 LEU
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  294 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 100 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 112 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   chunk 108 optimal weight:    0.9980
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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
B 434 ASN
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 664 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9414  Z= 0.172
  Angle     :  0.626  11.998  12746  Z= 0.307
  Chirality :  0.041   0.303   1490
  Planarity :  0.003   0.036   1606
  Dihedral  :  7.200 120.010   1296
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 16.77 %
    Favored  : 81.83 %
  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:  1.23 (0.25), residues: 1170
  helix:  1.56 (0.18), residues: 752
  sheet:  1.02 (0.64), residues: 88
  loop : -0.96 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.004   0.001   HIS B 672 
 PHE   0.015   0.001   PHE B 486 
 TYR   0.021   0.001   TYR B 205 
 ARG   0.003   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
  78 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7473 (mtm-85) cc_final: 0.7226 (tpt90)
REVERT: A  664 ASN cc_start: 0.5488 (OUTLIER) cc_final: 0.5050 (m-40)
REVERT: B  253 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7272 (tpt90)
REVERT: B  289 MET cc_start: 0.7892 (mpt) cc_final: 0.7478 (mpt)
REVERT: B  421 MET cc_start: 0.8157 (mmt) cc_final: 0.7777 (mpp)
REVERT: B  431 LEU cc_start: 0.9612 (mt) cc_final: 0.9378 (mt)
REVERT: B  664 ASN cc_start: 0.5321 (OUTLIER) cc_final: 0.4899 (m-40)
  outliers start: 14
  outliers final: 4
  residues processed: 74
  average time/residue: 0.1853
  time to fit residues: 20.9154
Evaluate side-chains
  63 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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  664 ASN
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  416 VAL
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 12 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 111 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 68 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    2.1984

-------------------------------------------------------------------------------
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
** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9414  Z= 0.228
  Angle     :  0.649  12.470  12746  Z= 0.319
  Chirality :  0.043   0.306   1490
  Planarity :  0.004   0.036   1606
  Dihedral  :  7.188 119.795   1296
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 17.07 %
    Favored  : 81.63 %
  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:  1.23 (0.25), residues: 1170
  helix:  1.58 (0.18), residues: 752
  sheet:  1.01 (0.63), residues: 88
  loop : -1.00 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.006   0.001   HIS B 672 
 PHE   0.039   0.001   PHE B 302 
 TYR   0.019   0.002   TYR B 205 
 ARG   0.003   0.000   ARG B 236 

*********************** 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
  74 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7240 (tpt90)
REVERT: B  253 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7322 (tpt90)
REVERT: B  289 MET cc_start: 0.7941 (mpt) cc_final: 0.7539 (mpt)
REVERT: B  421 MET cc_start: 0.8234 (mmt) cc_final: 0.7827 (mpp)
  outliers start: 13
  outliers final: 9
  residues processed: 70
  average time/residue: 0.2119
  time to fit residues: 22.6027
Evaluate side-chains
  66 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
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  568 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  416 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 76 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 87 optimal weight:    3.9990
   chunk 101 optimal weight:    0.2980
   chunk 107 optimal weight:    0.5980
   chunk 97 optimal weight:    0.3980
   chunk 104 optimal weight:    8.9990
   overall best weight:    1.0182

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2441

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= 0.169
  Angle     :  0.664  18.590  12746  Z= 0.313
  Chirality :  0.041   0.284   1490
  Planarity :  0.003   0.036   1606
  Dihedral  :  7.006 116.596   1296
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 17.57 %
    Favored  : 81.33 %
  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:  1.33 (0.25), residues: 1170
  helix:  1.59 (0.18), residues: 758
  sheet:  1.00 (0.63), residues: 88
  loop : -0.82 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.003   0.001   HIS B 672 
 PHE   0.032   0.001   PHE B 302 
 TYR   0.030   0.001   TYR B 205 
 ARG   0.003   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
  75 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.7233 (tpt90)
REVERT: A  431 LEU cc_start: 0.9609 (pp) cc_final: 0.9379 (mp)
REVERT: B  253 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.7282 (tpt90)
REVERT: B  289 MET cc_start: 0.8030 (mpt) cc_final: 0.7663 (mpt)
REVERT: B  402 MET cc_start: 0.8348 (mmm) cc_final: 0.7843 (mmm)
REVERT: B  421 MET cc_start: 0.8184 (mmt) cc_final: 0.7641 (mpp)
  outliers start: 11
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1872
  time to fit residues: 20.3841
Evaluate side-chains
  65 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
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  538 ILE
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 107 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 595 HIS
** B 465 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: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9414  Z= 0.222
  Angle     :  0.668  14.631  12746  Z= 0.321
  Chirality :  0.043   0.290   1490
  Planarity :  0.004   0.037   1606
  Dihedral  :  7.036 117.572   1296
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 17.67 %
    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:  1.26 (0.25), residues: 1170
  helix:  1.59 (0.18), residues: 756
  sheet:  1.01 (0.64), residues: 88
  loop : -0.98 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 132 
 HIS   0.006   0.001   HIS B 672 
 PHE   0.034   0.001   PHE A 394 
 TYR   0.027   0.002   TYR B 205 
 ARG   0.003   0.000   ARG B 236 

*********************** 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
  74 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.7255 (tpt90)
REVERT: A  276 MET cc_start: 0.8954 (mmt) cc_final: 0.8675 (mmm)
REVERT: A  431 LEU cc_start: 0.9609 (pp) cc_final: 0.9100 (mp)
REVERT: B  253 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7311 (tpt90)
REVERT: B  289 MET cc_start: 0.8081 (mpt) cc_final: 0.7715 (mpt)
REVERT: B  402 MET cc_start: 0.8390 (mmm) cc_final: 0.7860 (mmm)
REVERT: B  421 MET cc_start: 0.8192 (mmt) cc_final: 0.7741 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1953
  time to fit residues: 21.0865
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  : 1.025 
-------------------------------------------------------------------------------
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  538 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain B residue  250 HIS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 115 optimal weight:   10.0000
   chunk 106 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 9 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0770
   chunk 73 optimal weight:    0.0040
   chunk 98 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   overall best weight:    0.9152

-------------------------------------------------------------------------------
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**
** B 465 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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2618

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= 0.167
  Angle     :  0.669  15.019  12746  Z= 0.314
  Chirality :  0.042   0.265   1490
  Planarity :  0.003   0.036   1606
  Dihedral  :  6.882 113.770   1296
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 17.97 %
    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:  1.24 (0.25), residues: 1170
  helix:  1.56 (0.18), residues: 752
  sheet:  1.00 (0.63), residues: 88
  loop : -0.90 (0.37), residues: 330

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 B 302 
 TYR   0.029   0.001   TYR B 205 
 ARG   0.003   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
  71 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7491 (mtm-85) cc_final: 0.7246 (tpt90)
REVERT: A  431 LEU cc_start: 0.9532 (pp) cc_final: 0.9314 (mp)
REVERT: B  253 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.7273 (tpt90)
REVERT: B  289 MET cc_start: 0.8072 (mpt) cc_final: 0.7692 (mpt)
REVERT: B  402 MET cc_start: 0.8327 (mmm) cc_final: 0.7792 (mmm)
REVERT: B  421 MET cc_start: 0.8185 (mmt) cc_final: 0.7823 (mpp)
  outliers start: 12
  outliers final: 11
  residues processed: 68
  average time/residue: 0.2012
  time to fit residues: 20.8891
Evaluate side-chains
  70 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 LEU
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  250 HIS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 92 optimal weight:    0.1980
   chunk 38 optimal weight:    8.9990
   chunk 94 optimal weight:    0.0030
   chunk 11 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 80 optimal weight:    0.6980
   chunk 5 optimal weight:   20.0000
   chunk 66 optimal weight:    7.9990
   overall best weight:    3.5794

-------------------------------------------------------------------------------
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 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 = 0.4037 r_free = 0.4037 target = 0.099955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.075619 restraints weight = 25078.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.075337 restraints weight = 19934.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.076293 restraints weight = 15736.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2734

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= 0.330
  Angle     :  0.735  13.936  12746  Z= 0.358
  Chirality :  0.045   0.297   1490
  Planarity :  0.004   0.037   1606
  Dihedral  :  7.294 122.123   1296
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.67 %
    Favored  : 80.92 %
  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:  1.39 (0.18), residues: 752
  sheet:  1.06 (0.64), residues: 88
  loop : -1.31 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.012   0.002   HIS B 672 
 PHE   0.034   0.002   PHE B 302 
 TYR   0.025   0.002   TYR B 205 
 ARG   0.004   0.000   ARG B 341 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1647.95 seconds
wall clock time: 31 minutes 31.07 seconds (1891.07 seconds total)