Starting phenix.real_space_refine
on Thu Mar 13 21:33:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n5b_24185/03_2025/7n5b_24185.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n5b_24185/03_2025/7n5b_24185.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n5b_24185/03_2025/7n5b_24185.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n5b_24185/03_2025/7n5b_24185.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n5b_24185/03_2025/7n5b_24185.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n5b_24185/03_2025/7n5b_24185.cif"
  }
  resolution = 3.8
  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=   0.001 sd=   0.019
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    5802      2.51       5
     N    1566      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 9122
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4528
          Classifications: {'peptide': 580}
          Link IDs: {'PTRANS': 12, 'TRANS': 567}
          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}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.53, per 1000 atoms: 0.94
  Number of scatterers: 9122
  At special positions: 0
  Unit cell: (84.645, 76.095, 137.655, 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    1712      8.00
     N    1566      7.00
     C    5802      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: 2.32
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2168

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      71.1% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 117 through 132
      removed outlier: 3.515A  pdb=" N   TYR A 130 " --> pdb=" O   THR A 126 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 174
      removed outlier: 4.127A  pdb=" N   ARG A 140 " --> pdb=" O   ASN A 136 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
    Processing helix  chain 'A' and resid 196 through 245
      removed outlier: 3.575A  pdb=" N   THR A 220 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ALA A 221 " --> pdb=" O   GLU A 217 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 279
      removed outlier: 4.190A  pdb=" N   ASN A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   PHE A 271 " --> pdb=" O   ARG A 267 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   PHE A 278 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 296
      removed outlier: 3.523A  pdb=" N   THR A 283 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 348
      removed outlier: 4.113A  pdb=" N   LYS A 326 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   PHE A 327 " --> pdb=" O   TRP A 323 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 355
    Processing helix  chain 'A' and resid 358 through 408
      removed outlier: 3.746A  pdb=" N   ALA A 362 " --> pdb=" O   GLU A 358 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ARG A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE A 394 " --> pdb=" O   GLN A 390 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLY A 408 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 458
      removed outlier: 3.857A  pdb=" N   LEU A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL A 420 " --> pdb=" O   VAL A 416 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASN A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      Proline residue:  A 432  - end of helix
      removed outlier: 3.583A  pdb=" N   VAL A 448 " --> pdb=" O   ILE A 444 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ASP A 449 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   SER A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   MET A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A 454 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 517
      removed outlier: 4.015A  pdb=" N   GLY A 517 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 526
      removed outlier: 4.170A  pdb=" N   LEU A 522 " --> pdb=" O   LYS A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 554
      removed outlier: 3.683A  pdb=" N   SER A 553 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 575
    Processing helix  chain 'A' and resid 581 through 592
      removed outlier: 3.521A  pdb=" N   ARG A 591 " --> pdb=" O   GLU A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 600
      removed outlier: 3.596A  pdb=" N   ASN A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 614
    Processing helix  chain 'A' and resid 617 through 633
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.505A  pdb=" N   ALA A 652 " --> pdb=" O   SER A 648 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   GLU A 653 " --> pdb=" O   THR A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 679
      removed outlier: 4.062A  pdb=" N   ALA A 677 " --> pdb=" O   ARG A 673 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLN A 679 " --> pdb=" O   THR A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 704
      removed outlier: 3.661A  pdb=" N   SER A 704 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 716
    Processing helix  chain 'B' and resid 118 through 132
      removed outlier: 3.515A  pdb=" N   TYR B 130 " --> pdb=" O   THR B 126 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 174
      removed outlier: 4.127A  pdb=" N   ARG B 140 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
      Proline residue:  B 161  - end of helix
    Processing helix  chain 'B' and resid 196 through 245
      removed outlier: 3.574A  pdb=" N   THR B 220 " --> pdb=" O   ASN B 216 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA B 221 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   VAL B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE B 223 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 279
      removed outlier: 4.189A  pdb=" N   ASN B 270 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   PHE B 271 " --> pdb=" O   ARG B 267 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   VAL B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 296
      removed outlier: 3.523A  pdb=" N   THR B 283 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 348
      removed outlier: 4.113A  pdb=" N   LYS B 326 " --> pdb=" O   GLN B 322 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   PHE B 327 " --> pdb=" O   TRP B 323 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS B 329 " --> pdb=" O   THR B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 355
    Processing helix  chain 'B' and resid 358 through 408
      removed outlier: 3.746A  pdb=" N   ALA B 362 " --> pdb=" O   GLU B 358 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR B 379 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE B 394 " --> pdb=" O   GLN B 390 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY B 408 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 458
      removed outlier: 3.857A  pdb=" N   LEU B 419 " --> pdb=" O   THR B 415 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL B 420 " --> pdb=" O   VAL B 416 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASN B 423 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      Proline residue:  B 432  - end of helix
      removed outlier: 3.583A  pdb=" N   VAL B 448 " --> pdb=" O   ILE B 444 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ASP B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   SER B 452 " --> pdb=" O   VAL B 448 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   MET B 453 " --> pdb=" O   ASP B 449 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B 454 " --> pdb=" O   MET B 450 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B 456 " --> pdb=" O   SER B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 517
      removed outlier: 4.015A  pdb=" N   GLY B 517 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 526
      removed outlier: 4.170A  pdb=" N   LEU B 522 " --> pdb=" O   LYS B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 554
      removed outlier: 3.682A  pdb=" N   SER B 553 " --> pdb=" O   ASP B 549 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER B 554 " --> pdb=" O   SER B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 575
    Processing helix  chain 'B' and resid 581 through 592
      removed outlier: 3.522A  pdb=" N   ARG B 591 " --> pdb=" O   GLU B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 600
      removed outlier: 3.596A  pdb=" N   ASN B 600 " --> pdb=" O   GLU B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 614
    Processing helix  chain 'B' and resid 617 through 633
    Processing helix  chain 'B' and resid 647 through 662
      removed outlier: 3.504A  pdb=" N   ALA B 652 " --> pdb=" O   SER B 648 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLU B 653 " --> pdb=" O   THR B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 673 through 679
      removed outlier: 4.061A  pdb=" N   ALA B 677 " --> pdb=" O   ARG B 673 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLN B 679 " --> pdb=" O   THR B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 704
      removed outlier: 3.661A  pdb=" N   SER B 704 " --> pdb=" O   LEU B 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 716
    Processing sheet with id=AA1, first strand: chain 'A' and resid 501 through 502
    Processing sheet with id=AA2, first strand: chain 'A' and resid 484 through 486
      removed outlier: 6.057A  pdb=" N   VAL A 484 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY A 497 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE A 486 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 558
      removed outlier: 6.534A  pdb=" N   LEU A 637 " --> pdb=" O   ILE A 668 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   ILE A 670 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   CYS A 639 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 510 " --> pdb=" O   PHE A 669 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   SER A 507 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 684 " --> pdb=" O   SER A 507 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ALA A 509 " --> pdb=" O   VAL A 684 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LEU A 686 " --> pdb=" O   ALA A 509 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL A 511 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ILE A 683 " --> pdb=" O   GLN A 694 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   GLN A 694 " --> pdb=" O   ILE A 683 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL A 685 " --> pdb=" O   VAL A 692 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 502
    Processing sheet with id=AA5, first strand: chain 'B' and resid 484 through 486
      removed outlier: 6.057A  pdb=" N   VAL B 484 " --> pdb=" O   GLY B 497 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY B 497 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE B 486 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 558
      removed outlier: 6.534A  pdb=" N   LEU B 637 " --> pdb=" O   ILE B 668 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   ILE B 670 " --> pdb=" O   LEU B 637 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   CYS B 639 " --> pdb=" O   ILE B 670 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE B 510 " --> pdb=" O   PHE B 669 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   SER B 507 " --> pdb=" O   GLU B 682 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   VAL B 684 " --> pdb=" O   SER B 507 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ALA B 509 " --> pdb=" O   VAL B 684 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LEU B 686 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   VAL B 511 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ILE B 683 " --> pdb=" O   GLN B 694 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   GLN B 694 " --> pdb=" O   ILE B 683 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL B 685 " --> pdb=" O   VAL B 692 " (cutoff:3.500A)

    605 hydrogen bonds defined for protein.
    1767 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: 2.75

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.36: 3010
        1.36 -     1.50: 2337
        1.50 -     1.64: 3863
        1.64 -     1.77: 0
        1.77 -     1.91: 70
  Bond restraints: 9280
  Sorted by residual:
  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=" C4  ADP B 801 "
       pdb=" C5  ADP B 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 1.00e+00
  bond pdb=" CA  LYS B 470 "
       pdb=" CB  LYS B 470 "
    ideal  model  delta    sigma   weight residual
    1.526  1.539 -0.013 1.51e-02 4.39e+03 7.00e-01
  bond pdb=" CA  LYS A 470 "
       pdb=" CB  LYS A 470 "
    ideal  model  delta    sigma   weight residual
    1.526  1.539 -0.012 1.51e-02 4.39e+03 6.79e-01
  bond pdb=" CG  GLU B 458 "
       pdb=" CD  GLU B 458 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.52e-01
  ... (remaining 9275 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 12339
        1.42 -     2.84: 153
        2.84 -     4.25: 36
        4.25 -     5.67: 26
        5.67 -     7.09: 2
  Bond angle restraints: 12556
  Sorted by residual:
  angle pdb=" CB  MET B 453 "
        pdb=" CG  MET B 453 "
        pdb=" SD  MET B 453 "
      ideal   model   delta    sigma   weight residual
     112.70  105.61    7.09 3.00e+00 1.11e-01 5.59e+00
  angle pdb=" CB  MET A 453 "
        pdb=" CG  MET A 453 "
        pdb=" SD  MET A 453 "
      ideal   model   delta    sigma   weight residual
     112.70  105.62    7.08 3.00e+00 1.11e-01 5.57e+00
  angle pdb=" CB  GLU B 458 "
        pdb=" CG  GLU B 458 "
        pdb=" CD  GLU B 458 "
      ideal   model   delta    sigma   weight residual
     112.60  116.34   -3.74 1.70e+00 3.46e-01 4.85e+00
  angle pdb=" CB  GLU A 458 "
        pdb=" CG  GLU A 458 "
        pdb=" CD  GLU A 458 "
      ideal   model   delta    sigma   weight residual
     112.60  116.31   -3.71 1.70e+00 3.46e-01 4.77e+00
  angle pdb=" CA  LYS B 297 "
        pdb=" CB  LYS B 297 "
        pdb=" CG  LYS B 297 "
      ideal   model   delta    sigma   weight residual
     114.10  118.38   -4.28 2.00e+00 2.50e-01 4.58e+00
  ... (remaining 12551 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.16: 5122
       21.16 -    42.32: 364
       42.32 -    63.48: 38
       63.48 -    84.64: 8
       84.64 -   105.80: 8
  Dihedral angle restraints: 5540
    sinusoidal: 2184
      harmonic: 3356
  Sorted by residual:
  dihedral pdb=" C5' ADP B 801 "
           pdb=" O5' ADP B 801 "
           pdb=" PA  ADP B 801 "
           pdb=" O2A ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   45.80 -105.80     1      2.00e+01 2.50e-03 3.05e+01
  dihedral pdb=" C5' ADP A 801 "
           pdb=" O5' ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" O2A ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   45.73 -105.73     1      2.00e+01 2.50e-03 3.05e+01
  dihedral pdb=" O1B ADP B 801 "
           pdb=" O3A ADP B 801 "
           pdb=" PB  ADP B 801 "
           pdb=" PA  ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -150.08   90.08     1      2.00e+01 2.50e-03 2.40e+01
  ... (remaining 5537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1069
       0.031 -    0.063: 268
       0.063 -    0.094: 87
       0.094 -    0.126: 31
       0.126 -    0.157: 3
  Chirality restraints: 1458
  Sorted by residual:
  chirality pdb=" CB  ILE B 538 "
            pdb=" CA  ILE B 538 "
            pdb=" CG1 ILE B 538 "
            pdb=" CG2 ILE B 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.16e-01
  chirality pdb=" CB  ILE A 538 "
            pdb=" CA  ILE A 538 "
            pdb=" CG1 ILE A 538 "
            pdb=" CG2 ILE A 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.12e-01
  chirality pdb=" CA  ILE B 683 "
            pdb=" N   ILE B 683 "
            pdb=" C   ILE B 683 "
            pdb=" CB  ILE B 683 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 1455 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 239 "    0.010 2.00e-02 2.50e+03   7.39e-03 9.57e-01
        pdb=" CG  PHE A 239 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 239 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 239 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 239 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 239 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 239 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 239 "   -0.010 2.00e-02 2.50e+03   7.32e-03 9.37e-01
        pdb=" CG  PHE B 239 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 239 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 239 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 239 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 239 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 239 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 510 "   -0.004 2.00e-02 2.50e+03   8.48e-03 7.19e-01
        pdb=" C   ILE B 510 "    0.015 2.00e-02 2.50e+03
        pdb=" O   ILE B 510 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   VAL B 511 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 38
        2.50 -     3.10: 6719
        3.10 -     3.70: 13441
        3.70 -     4.30: 18400
        4.30 -     4.90: 29859
  Nonbonded interactions: 68457
  Sorted by model distance:
  nonbonded pdb=" V   VO4 A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     1.903 2.180
  nonbonded pdb=" V   VO4 B 802 "
            pdb="MG    MG B 803 "
     model   vdw
     1.903 2.180
  nonbonded pdb=" O1  VO4 A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.115 2.170
  nonbonded pdb=" O1  VO4 B 802 "
            pdb="MG    MG B 803 "
     model   vdw
     2.116 2.170
  nonbonded pdb=" O2  VO4 A 802 "
            pdb="MG    MG A 803 "
     model   vdw
     2.127 2.170
  ... (remaining 68452 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.130
  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:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.470
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
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      :  0.002   0.024   9280  Z= 0.110
  Angle     :  0.482   7.092  12556  Z= 0.240
  Chirality :  0.035   0.157   1458
  Planarity :  0.002   0.024   1584
  Dihedral  : 14.243 105.795   3372
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.41 %
    Favored  : 99.39 %
  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:  2.06 (0.24), residues: 1152
  helix:  2.03 (0.18), residues: 754
  sheet:  2.83 (0.61), residues: 74
  loop : -0.60 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 323 
 HIS   0.001   0.000   HIS B 243 
 PHE   0.016   0.001   PHE A 239 
 TYR   0.014   0.001   TYR B 205 
 ARG   0.006   0.000   ARG A 665 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A  276 MET cc_start: 0.7701 (ttp) cc_final: 0.7463 (tmm)
REVERT: A  498 ILE cc_start: 0.7578 (mt) cc_final: 0.7334 (mm)
REVERT: B  498 ILE cc_start: 0.7584 (mt) cc_final: 0.7323 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1622
  time to fit residues: 30.4131
Evaluate side-chains
  94 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0270
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   overall best weight:    1.0180

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
A 243 HIS
B 159 GLN
B 243 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.155856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.118708 restraints weight = 13842.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.122291 restraints weight = 8171.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.124783 restraints weight = 5721.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9280  Z= 0.196
  Angle     :  0.567   8.396  12556  Z= 0.290
  Chirality :  0.038   0.129   1458
  Planarity :  0.003   0.035   1584
  Dihedral  :  6.931 124.305   1278
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  7.26 %
    Favored  : 91.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.24), residues: 1152
  helix:  2.72 (0.19), residues: 766
  sheet:  2.71 (0.61), residues: 74
  loop : -0.61 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 711 
 HIS   0.004   0.001   HIS B 250 
 PHE   0.016   0.001   PHE A 149 
 TYR   0.010   0.001   TYR A 440 
 ARG   0.004   0.000   ARG B 665 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A  276 MET cc_start: 0.7950 (ttp) cc_final: 0.7439 (tmm)
REVERT: A  450 MET cc_start: 0.7024 (tpp) cc_final: 0.6809 (tpp)
  outliers start: 14
  outliers final: 6
  residues processed: 124
  average time/residue: 0.1934
  time to fit residues: 35.1021
Evaluate side-chains
  97 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0370
   chunk 44 optimal weight:    0.3980
   chunk 100 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 91 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    1.0662

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
A 357 ASN
B 243 HIS
B 357 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.154358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.117085 restraints weight = 14123.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.120646 restraints weight = 8286.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.123101 restraints weight = 5774.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9280  Z= 0.194
  Angle     :  0.551   7.580  12556  Z= 0.279
  Chirality :  0.038   0.126   1458
  Planarity :  0.003   0.025   1584
  Dihedral  :  7.091 132.109   1278
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 10.63 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.25), residues: 1152
  helix:  2.78 (0.19), residues: 758
  sheet:  2.60 (0.62), residues: 74
  loop : -0.65 (0.30), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.010   0.001   HIS A 243 
 PHE   0.012   0.001   PHE A 454 
 TYR   0.015   0.001   TYR B 205 
 ARG   0.005   0.000   ARG B 665 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A  410 MET cc_start: 0.7795 (pmm) cc_final: 0.7404 (ppp)
REVERT: A  450 MET cc_start: 0.7127 (tpp) cc_final: 0.6916 (tpp)
REVERT: A  646 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8234 (mp)
  outliers start: 18
  outliers final: 10
  residues processed: 99
  average time/residue: 0.1773
  time to fit residues: 27.0868
Evaluate side-chains
  90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  567 ASP
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  678 MET
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  567 ASP
Chi-restraints excluded: chain B residue  701 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 93 optimal weight:    0.0670
   chunk 78 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0070
   chunk 16 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 104 optimal weight:    0.2980
   chunk 55 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.4338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.158231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.120919 restraints weight = 13878.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.124507 restraints weight = 8144.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.126960 restraints weight = 5682.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9280  Z= 0.135
  Angle     :  0.504   7.402  12556  Z= 0.255
  Chirality :  0.036   0.134   1458
  Planarity :  0.002   0.024   1584
  Dihedral  :  7.157 138.384   1278
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.47 %
    Favored  : 86.61 %
  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:  2.97 (0.25), residues: 1152
  helix:  2.93 (0.19), residues: 758
  sheet:  2.40 (0.63), residues: 74
  loop : -0.63 (0.30), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 132 
 HIS   0.006   0.001   HIS A 243 
 PHE   0.012   0.001   PHE A 454 
 TYR   0.013   0.001   TYR B 205 
 ARG   0.004   0.000   ARG A 665 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 1.052 
Fit side-chains
REVERT: A  324 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7717 (mtp85)
  outliers start: 9
  outliers final: 8
  residues processed: 93
  average time/residue: 0.1566
  time to fit residues: 23.0583
Evaluate side-chains
  87 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  567 ASP
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  423 ASN
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  567 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 113 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.152218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.114826 restraints weight = 14063.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.118281 restraints weight = 8365.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.120643 restraints weight = 5870.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9280  Z= 0.236
  Angle     :  0.565   7.925  12556  Z= 0.284
  Chirality :  0.039   0.236   1458
  Planarity :  0.003   0.021   1584
  Dihedral  :  7.305 141.468   1278
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.29 %
    Favored  : 84.56 %
  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:  2.78 (0.25), residues: 1152
  helix:  2.87 (0.19), residues: 754
  sheet:  1.69 (0.56), residues: 86
  loop : -0.84 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 132 
 HIS   0.006   0.001   HIS B 250 
 PHE   0.013   0.001   PHE A 271 
 TYR   0.010   0.001   TYR B 205 
 ARG   0.004   0.000   ARG B 665 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A  450 MET cc_start: 0.7237 (tpp) cc_final: 0.7029 (tpp)
REVERT: A  646 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8215 (mp)
REVERT: B  646 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8248 (mp)
  outliers start: 21
  outliers final: 12
  residues processed: 101
  average time/residue: 0.1589
  time to fit residues: 25.2062
Evaluate side-chains
  89 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  567 ASP
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  678 MET
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  567 ASP
Chi-restraints excluded: chain B residue  614 LEU
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  683 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 102 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 112 optimal weight:    0.1980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.155560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.117848 restraints weight = 13856.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.121406 restraints weight = 8202.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.123859 restraints weight = 5723.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9280  Z= 0.151
  Angle     :  0.525   8.914  12556  Z= 0.261
  Chirality :  0.036   0.132   1458
  Planarity :  0.003   0.023   1584
  Dihedral  :  7.411 146.637   1278
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 15.64 %
    Favored  : 82.82 %
  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:  2.91 (0.25), residues: 1152
  helix:  2.98 (0.19), residues: 754
  sheet:  1.65 (0.56), residues: 86
  loop : -0.79 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.002   0.001   HIS A 250 
 PHE   0.010   0.001   PHE B 271 
 TYR   0.023   0.001   TYR A 354 
 ARG   0.005   0.000   ARG A 324 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A  450 MET cc_start: 0.7152 (tpp) cc_final: 0.6932 (tpp)
  outliers start: 15
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1513
  time to fit residues: 22.9406
Evaluate side-chains
  86 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  567 ASP
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  567 ASP
Chi-restraints excluded: chain B residue  614 LEU
Chi-restraints excluded: chain B residue  683 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0470
   chunk 7 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.6880

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.155450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.117485 restraints weight = 14140.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.121066 restraints weight = 8344.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.123533 restraints weight = 5809.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9280  Z= 0.153
  Angle     :  0.523   8.786  12556  Z= 0.259
  Chirality :  0.036   0.130   1458
  Planarity :  0.003   0.023   1584
  Dihedral  :  7.405 147.835   1278
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.67 %
    Favored  : 82.00 %
  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:  2.92 (0.25), residues: 1152
  helix:  3.01 (0.19), residues: 756
  sheet:  1.55 (0.56), residues: 86
  loop : -0.85 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 132 
 HIS   0.003   0.001   HIS A 250 
 PHE   0.014   0.001   PHE A 271 
 TYR   0.018   0.001   TYR A 354 
 ARG   0.004   0.000   ARG A 324 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A  450 MET cc_start: 0.7070 (tpp) cc_final: 0.6864 (tpp)
  outliers start: 13
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1503
  time to fit residues: 21.5643
Evaluate side-chains
  87 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  567 ASP
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  567 ASP
Chi-restraints excluded: chain B residue  614 LEU
Chi-restraints excluded: chain B residue  683 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 93 optimal weight:    0.1980
   chunk 36 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 112 optimal weight:    2.9990
   overall best weight:    3.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 348 ASN
B 348 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.142731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.105146 restraints weight = 14919.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.108314 restraints weight = 9026.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.110507 restraints weight = 6451.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   9280  Z= 0.482
  Angle     :  0.764   8.524  12556  Z= 0.393
  Chirality :  0.044   0.189   1458
  Planarity :  0.004   0.038   1584
  Dihedral  :  8.366 167.460   1278
  Min Nonbonded Distance : 1.818

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 17.08 %
    Favored  : 81.29 %
  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:  1.95 (0.25), residues: 1152
  helix:  2.34 (0.19), residues: 752
  sheet:  0.93 (0.55), residues: 88
  loop : -1.34 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 323 
 HIS   0.011   0.003   HIS B 250 
 PHE   0.022   0.002   PHE A 271 
 TYR   0.042   0.002   TYR A 354 
 ARG   0.007   0.001   ARG B 623 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 1.116 
Fit side-chains
REVERT: A  228 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7704 (mp)
REVERT: A  435 PHE cc_start: 0.7878 (t80) cc_final: 0.7626 (t80)
REVERT: A  646 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8313 (mp)
REVERT: B  450 MET cc_start: 0.7414 (tpp) cc_final: 0.7129 (tpp)
REVERT: B  646 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8319 (mp)
  outliers start: 16
  outliers final: 13
  residues processed: 95
  average time/residue: 0.1806
  time to fit residues: 25.8327
Evaluate side-chains
  94 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  567 ASP
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  423 ASN
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  567 ASP
Chi-restraints excluded: chain B residue  614 LEU
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  683 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.149307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.110745 restraints weight = 14269.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.114181 restraints weight = 8536.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.116548 restraints weight = 6047.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9280  Z= 0.197
  Angle     :  0.570   9.231  12556  Z= 0.290
  Chirality :  0.038   0.180   1458
  Planarity :  0.003   0.025   1584
  Dihedral  :  8.119 165.425   1278
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.69 %
    Favored  : 80.47 %
  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:  2.44 (0.25), residues: 1152
  helix:  2.75 (0.19), residues: 752
  sheet:  0.92 (0.54), residues: 86
  loop : -1.13 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 132 
 HIS   0.005   0.001   HIS A 250 
 PHE   0.016   0.001   PHE A 271 
 TYR   0.028   0.001   TYR A 354 
 ARG   0.004   0.000   ARG A 324 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7292 (mp)
REVERT: B  345 SER cc_start: 0.8559 (t) cc_final: 0.8260 (p)
  outliers start: 18
  outliers final: 16
  residues processed: 96
  average time/residue: 0.1621
  time to fit residues: 23.9753
Evaluate side-chains
  96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  567 ASP
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  567 ASP
Chi-restraints excluded: chain B residue  614 LEU
Chi-restraints excluded: chain B residue  683 ILE
Chi-restraints excluded: chain B residue  701 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0870
   chunk 40 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0270
   chunk 11 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 85 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.0222

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.150675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.111969 restraints weight = 14483.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.115411 restraints weight = 8658.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.117753 restraints weight = 6114.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9280  Z= 0.191
  Angle     :  0.565   9.895  12556  Z= 0.284
  Chirality :  0.038   0.189   1458
  Planarity :  0.003   0.025   1584
  Dihedral  :  7.950 163.044   1278
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 18.40 %
    Favored  : 79.96 %
  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:  2.54 (0.25), residues: 1152
  helix:  2.79 (0.19), residues: 752
  sheet:  1.01 (0.54), residues: 86
  loop : -1.03 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.004   0.001   HIS A 250 
 PHE   0.014   0.001   PHE A 215 
 TYR   0.025   0.001   TYR A 354 
 ARG   0.003   0.000   ARG A 665 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 PHE cc_start: 0.8039 (t80) cc_final: 0.7768 (t80)
REVERT: A  345 SER cc_start: 0.8453 (t) cc_final: 0.8088 (p)
REVERT: B  217 GLU cc_start: 0.7953 (mm-30) cc_final: 0.6979 (mt-10)
REVERT: B  228 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7280 (mp)
REVERT: B  345 SER cc_start: 0.8505 (t) cc_final: 0.8166 (p)
  outliers start: 16
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1666
  time to fit residues: 24.2462
Evaluate side-chains
  93 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  567 ASP
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  423 ASN
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  567 ASP
Chi-restraints excluded: chain B residue  607 THR
Chi-restraints excluded: chain B residue  614 LEU
Chi-restraints excluded: chain B residue  683 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 103 optimal weight:    0.3980
   chunk 64 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0570
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.0904

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.150858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.112393 restraints weight = 14260.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.115814 restraints weight = 8589.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.118146 restraints weight = 6095.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9280  Z= 0.194
  Angle     :  0.562  10.178  12556  Z= 0.284
  Chirality :  0.037   0.185   1458
  Planarity :  0.003   0.025   1584
  Dihedral  :  7.941 162.943   1278
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 18.71 %
    Favored  : 79.55 %
  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:  2.55 (0.25), residues: 1152
  helix:  2.78 (0.19), residues: 754
  sheet:  0.98 (0.54), residues: 86
  loop : -0.99 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 132 
 HIS   0.005   0.001   HIS A 250 
 PHE   0.016   0.001   PHE A 215 
 TYR   0.027   0.001   TYR A 354 
 ARG   0.003   0.000   ARG A 665 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2834.85 seconds
wall clock time: 51 minutes 13.19 seconds (3073.19 seconds total)