Starting phenix.real_space_refine
on Fri Mar 14 01:54:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n5a_24184/03_2025/7n5a_24184.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n5a_24184/03_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_24184/03_2025/7n5a_24184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n5a_24184/03_2025/7n5a_24184.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n5a_24184/03_2025/7n5a_24184.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n5a_24184/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 9.15, per 1000 atoms: 0.99
  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: 2.51
  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: 1.13
  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: 2.76

  Time building geometry restraints manager: 2.94 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: 0.04
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:             2.630
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.550
  Find NCS groups from input model:        0.450
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.980
-------------------------------------------------------------------------------
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  : 1.281 
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: 0.2362
  time to fit residues: 28.3563
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  : 1.074 
-------------------------------------------------------------------------------
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 = 49)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.075783 restraints weight = 24741.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.077339 restraints weight = 16690.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.078397 restraints weight = 12873.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
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  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.7973 (ttt) cc_final: 0.6375 (mmp)
REVERT: A  421 MET cc_start: 0.9098 (mpp) cc_final: 0.8593 (mpp)
REVERT: B  276 MET cc_start: 0.8874 (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: 0.2367
  time to fit residues: 25.9283
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  : 1.048 
-------------------------------------------------------------------------------
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:    0.0050
   chunk 90 optimal weight:    0.9990
   chunk 115 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0040
   chunk 37 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    0.4808

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.105392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.079024 restraints weight = 24781.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.080885 restraints weight = 15854.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.082132 restraints weight = 11854.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9414  Z= 0.173
  Angle     :  0.620   9.174  12746  Z= 0.309
  Chirality :  0.039   0.158   1490
  Planarity :  0.003   0.032   1606
  Dihedral  :  7.125 114.483   1296
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  9.94 %
    Favored  : 89.46 %
  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:  1.31 (0.25), residues: 1170
  helix:  1.61 (0.19), residues: 722
  sheet:  1.27 (0.64), residues: 86
  loop : -0.70 (0.35), residues: 362

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   0.025   0.001   PHE A 302 
 TYR   0.021   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
  81 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 LEU cc_start: 0.9021 (mp) cc_final: 0.8802 (mp)
REVERT: A  429 LEU cc_start: 0.9256 (tt) cc_final: 0.8964 (pp)
REVERT: B  429 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8988 (tp)
  outliers start: 6
  outliers final: 1
  residues processed: 80
  average time/residue: 0.2025
  time to fit residues: 23.8707
Evaluate side-chains
  66 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 102 optimal weight:    3.9990
   chunk 58 optimal weight:   20.0000
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 111 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0570
   overall best weight:    1.8106

-------------------------------------------------------------------------------
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 = 0.4102 r_free = 0.4102 target = 0.103499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.077804 restraints weight = 24606.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.078603 restraints weight = 18306.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.079860 restraints weight = 13650.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1937

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= 0.208
  Angle     :  0.629  10.525  12746  Z= 0.313
  Chirality :  0.041   0.306   1490
  Planarity :  0.003   0.033   1606
  Dihedral  :  7.040 114.750   1296
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.95 %
    Favored  : 87.15 %
  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:  1.63 (0.19), residues: 742
  sheet:  1.04 (0.63), residues: 88
  loop : -0.78 (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   0.027   0.001   PHE A 164 
 TYR   0.019   0.002   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
  76 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 4
  residues processed: 70
  average time/residue: 0.1591
  time to fit residues: 18.1859
Evaluate side-chains
  67 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
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  294 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    2.1386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.102368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.078575 restraints weight = 25009.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.078329 restraints weight = 17651.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.078983 restraints weight = 14519.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2128

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= 0.221
  Angle     :  0.633  11.351  12746  Z= 0.312
  Chirality :  0.042   0.305   1490
  Planarity :  0.004   0.034   1606
  Dihedral  :  7.059 116.995   1296
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.96 %
    Favored  : 84.64 %
  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:  1.30 (0.25), residues: 1170
  helix:  1.60 (0.18), residues: 752
  sheet:  1.06 (0.64), residues: 88
  loop : -0.87 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.007   0.002   HIS A 672 
 PHE   0.016   0.001   PHE A 164 
 TYR   0.020   0.002   TYR A 360 
 ARG   0.003   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
  79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8105 (mmt) cc_final: 0.7477 (mpp)
REVERT: B  289 MET cc_start: 0.8155 (mpt) cc_final: 0.7886 (mpt)
REVERT: B  421 MET cc_start: 0.8063 (mmt) cc_final: 0.7491 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1557
  time to fit residues: 18.7114
Evaluate side-chains
  70 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
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  429 LEU
Chi-restraints excluded: chain A residue  538 ILE
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 101 optimal weight:    0.0000
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 78 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.3590

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.103068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.078580 restraints weight = 24849.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.078849 restraints weight = 17857.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.080197 restraints weight = 14249.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9414  Z= 0.181
  Angle     :  0.616  11.573  12746  Z= 0.302
  Chirality :  0.041   0.301   1490
  Planarity :  0.003   0.035   1606
  Dihedral  :  6.953 115.631   1296
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.96 %
    Favored  : 82.83 %
  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:  1.39 (0.25), residues: 1170
  helix:  1.62 (0.18), residues: 754
  sheet:  1.10 (0.64), residues: 88
  loop : -0.74 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.004   0.001   HIS A 672 
 PHE   0.013   0.001   PHE B 435 
 TYR   0.020   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
  79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  289 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7807 (mpt)
REVERT: B  421 MET cc_start: 0.8088 (mmt) cc_final: 0.7571 (mpp)
REVERT: B  664 ASN cc_start: 0.5018 (OUTLIER) cc_final: 0.4640 (m-40)
  outliers start: 12
  outliers final: 7
  residues processed: 76
  average time/residue: 0.1494
  time to fit residues: 18.4592
Evaluate side-chains
  70 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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  242 LEU
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  664 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 19 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 95 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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 250 HIS
** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 595 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.097405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.074598 restraints weight = 25629.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.074691 restraints weight = 21256.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.075537 restraints weight = 17844.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056   9414  Z= 0.542
  Angle     :  0.863  11.313  12746  Z= 0.436
  Chirality :  0.051   0.355   1490
  Planarity :  0.006   0.055   1606
  Dihedral  :  7.898 129.962   1296
  Min Nonbonded Distance : 1.751

Molprobity Statistics.
  All-atom Clashscore : 18.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.17 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.47 (0.24), residues: 1170
  helix:  1.04 (0.18), residues: 742
  sheet:  1.13 (0.64), residues: 88
  loop : -1.51 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 132 
 HIS   0.020   0.004   HIS B 672 
 PHE   0.019   0.002   PHE A 529 
 TYR   0.024   0.003   TYR B 575 
 ARG   0.007   0.001   ARG B 577 

*********************** 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: 16
    poor density    : 57
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8040 (mmt) cc_final: 0.7607 (mpp)
REVERT: B  289 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7949 (mpt)
REVERT: B  421 MET cc_start: 0.8106 (mmt) cc_final: 0.7582 (mpp)
  outliers start: 16
  outliers final: 10
  residues processed: 68
  average time/residue: 0.2915
  time to fit residues: 30.8572
Evaluate side-chains
  62 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
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  302 PHE
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  289 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0060
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.9400

-------------------------------------------------------------------------------
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 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 = 0.4075 r_free = 0.4075 target = 0.102343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.077123 restraints weight = 25166.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.077362 restraints weight = 18735.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.078600 restraints weight = 14587.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2561

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= 0.186
  Angle     :  0.670  13.310  12746  Z= 0.326
  Chirality :  0.042   0.301   1490
  Planarity :  0.003   0.036   1606
  Dihedral  :  7.394 123.332   1296
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.57 %
    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:  1.10 (0.25), residues: 1170
  helix:  1.47 (0.18), residues: 758
  sheet:  1.01 (0.64), residues: 88
  loop : -1.10 (0.36), residues: 324

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   0.016   0.001   PHE B 486 
 TYR   0.020   0.001   TYR B 205 
 ARG   0.004   0.000   ARG A 324 

*********************** 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
  73 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ARG cc_start: 0.7820 (tpt90) cc_final: 0.7614 (tpt90)
REVERT: A  421 MET cc_start: 0.8108 (mmt) cc_final: 0.7550 (mpp)
REVERT: B  289 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7917 (mpt)
REVERT: B  421 MET cc_start: 0.8200 (mmt) cc_final: 0.7586 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1772
  time to fit residues: 18.6409
Evaluate side-chains
  63 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  538 ILE
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  524 MET
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 63 optimal weight:   30.0000
   chunk 90 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 51 optimal weight:    0.2980
   chunk 53 optimal weight:    4.9990
   chunk 111 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   overall best weight:    4.0588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.099128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.076281 restraints weight = 25248.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.076053 restraints weight = 20254.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.076957 restraints weight = 17003.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9414  Z= 0.353
  Angle     :  0.756  17.258  12746  Z= 0.369
  Chirality :  0.046   0.319   1490
  Planarity :  0.004   0.037   1606
  Dihedral  :  7.588 125.543   1296
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.67 %
    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:  0.78 (0.25), residues: 1170
  helix:  1.27 (0.18), residues: 758
  sheet:  1.15 (0.63), residues: 88
  loop : -1.44 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.012   0.003   HIS B 672 
 PHE   0.013   0.002   PHE A 529 
 TYR   0.028   0.003   TYR B 205 
 ARG   0.003   0.001   ARG A 341 

*********************** 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
  72 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  421 MET cc_start: 0.8051 (mmt) cc_final: 0.7599 (mpp)
REVERT: A  431 LEU cc_start: 0.9259 (pp) cc_final: 0.8963 (mp)
REVERT: B  289 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7996 (mpt)
REVERT: B  421 MET cc_start: 0.8177 (mmt) cc_final: 0.7605 (mpp)
  outliers start: 16
  outliers final: 10
  residues processed: 67
  average time/residue: 0.2131
  time to fit residues: 21.9230
Evaluate side-chains
  63 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
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 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  524 MET
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  629 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 74 optimal weight:    0.0070
   chunk 7 optimal weight:    0.0270
   chunk 58 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 105 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   chunk 109 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0070
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.4089 r_free = 0.4089 target = 0.103241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.078055 restraints weight = 25086.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.078633 restraints weight = 20237.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.079636 restraints weight = 14531.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2757

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     :  0.695  15.616  12746  Z= 0.329
  Chirality :  0.042   0.263   1490
  Planarity :  0.003   0.035   1606
  Dihedral  :  7.231 119.303   1296
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 18.17 %
    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:  1.13 (0.25), residues: 1170
  helix:  1.52 (0.19), residues: 756
  sheet:  1.07 (0.64), residues: 88
  loop : -1.15 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.007   0.001   HIS B 697 
 PHE   0.015   0.001   PHE B 302 
 TYR   0.030   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: 10
    poor density    : 61
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.9076 (mmm) cc_final: 0.8864 (mmt)
REVERT: A  421 MET cc_start: 0.8066 (mmt) cc_final: 0.7758 (mpp)
REVERT: A  431 LEU cc_start: 0.9490 (pp) cc_final: 0.9262 (mp)
REVERT: B  289 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7995 (mpt)
REVERT: B  402 MET cc_start: 0.7993 (mmm) cc_final: 0.7264 (mmm)
REVERT: B  421 MET cc_start: 0.8169 (mmt) cc_final: 0.7821 (mpp)
  outliers start: 10
  outliers final: 6
  residues processed: 67
  average time/residue: 0.1612
  time to fit residues: 17.4216
Evaluate side-chains
  62 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  538 ILE
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
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 94 optimal weight:    0.0570
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0050
   chunk 22 optimal weight:    0.6980
   chunk 58 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5514

-------------------------------------------------------------------------------
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 595 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.104095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.078146 restraints weight = 24811.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.079955 restraints weight = 16089.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.081201 restraints weight = 12063.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2891

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= 0.167
  Angle     :  0.698  16.256  12746  Z= 0.327
  Chirality :  0.042   0.248   1490
  Planarity :  0.003   0.036   1606
  Dihedral  :  7.003 114.508   1296
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 18.88 %
    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:  1.23 (0.25), residues: 1170
  helix:  1.55 (0.19), residues: 758
  sheet:  1.29 (0.62), residues: 86
  loop : -1.03 (0.36), residues: 326

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   0.015   0.001   PHE B 302 
 TYR   0.030   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: 3000.12 seconds
wall clock time: 55 minutes 1.23 seconds (3301.23 seconds total)