Starting phenix.real_space_refine
on Thu May 15 15:34:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w7j_37339/05_2025/8w7j_37339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w7j_37339/05_2025/8w7j_37339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w7j_37339/05_2025/8w7j_37339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w7j_37339/05_2025/8w7j_37339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w7j_37339/05_2025/8w7j_37339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w7j_37339/05_2025/8w7j_37339.cif"
  }
  resolution = 3.98
  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=   0.003 sd=   0.047
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      30      5.16       5
     C    8689      2.51       5
     N    2207      2.21       5
     O    2507      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13437
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 857, 7020
          Classifications: {'peptide': 857}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 28, 'TRANS': 828}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 70
          Classifications: {'peptide': 14}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'TRANS': 13}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'UNK:plan-1': 14}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 6310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 770, 6310
          Classifications: {'peptide': 770}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 748}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'GTP': 1, 'PO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.65, per 1000 atoms: 0.57
  Number of scatterers: 13437
  At special positions: 0
  Unit cell: (106.392, 112.398, 135.564, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       4     15.00
     O    2507      8.00
     N    2207      7.00
     C    8689      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: 3.02
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3072

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 9 sheets defined
      40.3% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 76
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 92 through 100
      removed outlier: 3.616A  pdb=" N   PHE A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 131
      removed outlier: 3.799A  pdb=" N   ARG A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 206
      removed outlier: 3.736A  pdb=" N   ASP A 206 " --> pdb=" O   ASN A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 274
      removed outlier: 3.759A  pdb=" N   ALA A 266 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   SER A 267 " --> pdb=" O   GLU A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 325 through 340
      removed outlier: 3.603A  pdb=" N   ARG A 329 " --> pdb=" O   ASP A 325 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ILE A 333 " --> pdb=" O   ARG A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 346
      removed outlier: 3.545A  pdb=" N   SER A 346 " --> pdb=" O   ASN A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 417
    Processing helix  chain 'A' and resid 429 through 443
      removed outlier: 3.874A  pdb=" N   THR A 433 " --> pdb=" O   TYR A 429 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   LYS A 438 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   LYS A 439 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 462
      removed outlier: 4.119A  pdb=" N   ILE A 451 " --> pdb=" O   THR A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 512
      removed outlier: 3.993A  pdb=" N   ILE A 492 " --> pdb=" O   SER A 488 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS A 512 " --> pdb=" O   GLY A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 548
      removed outlier: 3.624A  pdb=" N   LEU A 540 " --> pdb=" O   ASP A 536 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A 548 " --> pdb=" O   GLN A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 568
    Processing helix  chain 'A' and resid 586 through 595
    Processing helix  chain 'A' and resid 601 through 614
      removed outlier: 5.958A  pdb=" N   ILE A 610 " --> pdb=" O   THR A 606 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   GLU A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 639
      removed outlier: 4.097A  pdb=" N   ILE A 628 " --> pdb=" O   GLY A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 663
      removed outlier: 3.538A  pdb=" N   LEU A 650 " --> pdb=" O   GLY A 646 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   GLU A 655 " --> pdb=" O   ILE A 651 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   LEU A 658 " --> pdb=" O   ARG A 654 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR A 660 " --> pdb=" O   TYR A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 705
      removed outlier: 4.098A  pdb=" N   LEU A 697 " --> pdb=" O   GLY A 693 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE A 698 " --> pdb=" O   VAL A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 722
      removed outlier: 3.904A  pdb=" N   LYS A 711 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 722 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 759
      removed outlier: 3.804A  pdb=" N   LEU A 753 " --> pdb=" O   SER A 749 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 754 " --> pdb=" O   ALA A 750 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU A 755 " --> pdb=" O   GLY A 751 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASN A 759 " --> pdb=" O   LEU A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 769
      No H-bonds generated for 'chain 'A' and resid 767 through 769'
    Processing helix  chain 'A' and resid 770 through 778
      removed outlier: 3.977A  pdb=" N   ARG A 776 " --> pdb=" O   THR A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 823
      removed outlier: 4.440A  pdb=" N   GLY A 811 " --> pdb=" O   ASP A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 861
      removed outlier: 3.548A  pdb=" N   VAL A 851 " --> pdb=" O   GLY A 847 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   MET A 859 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 81
      removed outlier: 3.729A  pdb=" N   LEU B  72 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 100
    Processing helix  chain 'B' and resid 124 through 129
    Processing helix  chain 'B' and resid 267 through 274
    Processing helix  chain 'B' and resid 305 through 314
    Processing helix  chain 'B' and resid 325 through 345
      removed outlier: 3.555A  pdb=" N   ARG B 329 " --> pdb=" O   ASP B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 414
      removed outlier: 4.127A  pdb=" N   ASP B 404 " --> pdb=" O   PRO B 400 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   TYR B 406 " --> pdb=" O   GLU B 402 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLY B 407 " --> pdb=" O   ILE B 403 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ALA B 412 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 445
      removed outlier: 3.799A  pdb=" N   ARG B 434 " --> pdb=" O   VAL B 430 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE B 435 " --> pdb=" O   SER B 431 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS B 439 " --> pdb=" O   ILE B 435 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   LEU B 440 " --> pdb=" O   GLU B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 463
    Processing helix  chain 'B' and resid 473 through 477
      removed outlier: 3.729A  pdb=" N   VAL B 476 " --> pdb=" O   ARG B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 509
      removed outlier: 3.784A  pdb=" N   ILE B 492 " --> pdb=" O   SER B 488 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG B 501 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLY B 502 " --> pdb=" O   LYS B 498 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE B 503 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 514
      removed outlier: 4.346A  pdb=" N   GLU B 513 " --> pdb=" O   GLN B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 550
      removed outlier: 4.090A  pdb=" N   TRP B 541 " --> pdb=" O   LEU B 537 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   SER B 542 " --> pdb=" O   ALA B 538 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL B 550 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 572
      removed outlier: 4.724A  pdb=" N   GLU B 568 " --> pdb=" O   GLN B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 575
      No H-bonds generated for 'chain 'B' and resid 573 through 575'
    Processing helix  chain 'B' and resid 586 through 595
    Processing helix  chain 'B' and resid 598 through 614
      removed outlier: 6.129A  pdb=" N   ILE B 610 " --> pdb=" O   THR B 606 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   GLU B 611 " --> pdb=" O   THR B 607 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU B 614 " --> pdb=" O   ILE B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 626
      No H-bonds generated for 'chain 'B' and resid 625 through 626'
    Processing helix  chain 'B' and resid 628 through 628
      No H-bonds generated for 'chain 'B' and resid 628 through 628'
    Processing helix  chain 'B' and resid 629 through 639
      removed outlier: 3.955A  pdb=" N   LYS B 638 " --> pdb=" O   TYR B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 663
    Processing helix  chain 'B' and resid 690 through 692
      No H-bonds generated for 'chain 'B' and resid 690 through 692'
    Processing helix  chain 'B' and resid 693 through 705
      removed outlier: 4.305A  pdb=" N   LEU B 697 " --> pdb=" O   GLY B 693 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   THR B 705 " --> pdb=" O   ALA B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 722
    Processing helix  chain 'B' and resid 748 through 757
      removed outlier: 3.580A  pdb=" N   LEU B 752 " --> pdb=" O   GLY B 748 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 771 through 778
    Processing helix  chain 'B' and resid 791 through 800
      removed outlier: 3.675A  pdb=" N   LEU B 795 " --> pdb=" O   GLY B 791 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ASN B 800 " --> pdb=" O   GLU B 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 808 through 820
    Processing helix  chain 'B' and resid 847 through 860
      removed outlier: 3.765A  pdb=" N   VAL B 851 " --> pdb=" O   GLY B 847 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46
      removed outlier: 3.734A  pdb=" N   HIS A  89 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   CYS A 115 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ILE A  60 " --> pdb=" O   CYS A 115 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 221
      removed outlier: 3.526A  pdb=" N   ASP A 220 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ASN A 233 " --> pdb=" O   ASP A 220 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A 230 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A 243 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   GLY A 297 " --> pdb=" O   TYR A 285 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 305
    Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 351
      removed outlier: 3.543A  pdb=" N   VAL A 376 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 725 through 727
      removed outlier: 3.708A  pdb=" N   TYR A 735 " --> pdb=" O   LEU A 742 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 824 through 826
      removed outlier: 3.563A  pdb=" N   CYS A 824 " --> pdb=" O   VAL A 831 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ILE A 826 " --> pdb=" O   GLY A 829 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 38
      removed outlier: 3.601A  pdb=" N   TYR B  47 " --> pdb=" O   HIS B  35 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL B  44 " --> pdb=" O   HIS B  89 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR B 114 " --> pdb=" O   LYS B  88 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS B 115 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE B  60 " --> pdb=" O   CYS B 115 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 725 through 727
    Processing sheet with id=AA9, first strand: chain 'B' and resid 823 through 826
      removed outlier: 3.807A  pdb=" N   CYS B 824 " --> pdb=" O   VAL B 831 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B 831 " --> pdb=" O   CYS B 824 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY B 829 " --> pdb=" O   ILE B 826 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1239 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: 4.09

  Time building geometry restraints manager: 3.55 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2394
        1.32 -     1.45: 3710
        1.45 -     1.57: 7602
        1.57 -     1.69: 9
        1.69 -     1.81: 44
  Bond restraints: 13759
  Sorted by residual:
  bond pdb=" C5  GTP A 901 "
       pdb=" C6  GTP A 901 "
    ideal  model  delta    sigma   weight residual
    1.390  1.476 -0.086 2.00e-02 2.50e+03 1.86e+01
  bond pdb=" C4  GTP A 901 "
       pdb=" C5  GTP A 901 "
    ideal  model  delta    sigma   weight residual
    1.390  1.463 -0.073 2.00e-02 2.50e+03 1.33e+01
  bond pdb=" CA  LYS B 464 "
       pdb=" C   LYS B 464 "
    ideal  model  delta    sigma   weight residual
    1.526  1.487  0.039 1.22e-02 6.72e+03 1.00e+01
  bond pdb=" O4  PO4 A 902 "
       pdb=" P   PO4 A 902 "
    ideal  model  delta    sigma   weight residual
    1.568  1.509  0.059 2.00e-02 2.50e+03 8.75e+00
  bond pdb=" O3  PO4 A 902 "
       pdb=" P   PO4 A 902 "
    ideal  model  delta    sigma   weight residual
    1.569  1.510  0.059 2.00e-02 2.50e+03 8.63e+00
  ... (remaining 13754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.99: 18094
        2.99 -     5.99: 434
        5.99 -     8.98: 73
        8.98 -    11.97: 12
       11.97 -    14.96: 5
  Bond angle restraints: 18618
  Sorted by residual:
  angle pdb=" N   LYS B 464 "
        pdb=" CA  LYS B 464 "
        pdb=" C   LYS B 464 "
      ideal   model   delta    sigma   weight residual
     107.57   92.61   14.96 1.94e+00 2.66e-01 5.95e+01
  angle pdb=" C   LYS A 324 "
        pdb=" N   ASP A 325 "
        pdb=" CA  ASP A 325 "
      ideal   model   delta    sigma   weight residual
     122.08  132.35  -10.27 1.47e+00 4.63e-01 4.88e+01
  angle pdb=" C   GLU A 827 "
        pdb=" CA  GLU A 827 "
        pdb=" CB  GLU A 827 "
      ideal   model   delta    sigma   weight residual
     117.23  109.81    7.42 1.36e+00 5.41e-01 2.97e+01
  angle pdb=" N   GLU B 715 "
        pdb=" CA  GLU B 715 "
        pdb=" CB  GLU B 715 "
      ideal   model   delta    sigma   weight residual
     110.16  118.05   -7.89 1.48e+00 4.57e-01 2.84e+01
  angle pdb=" C   ARG A 654 "
        pdb=" N   GLU A 655 "
        pdb=" CA  GLU A 655 "
      ideal   model   delta    sigma   weight residual
     121.54  131.63  -10.09 1.91e+00 2.74e-01 2.79e+01
  ... (remaining 18613 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.87: 7477
       23.87 -    47.74: 563
       47.74 -    71.62: 40
       71.62 -    95.49: 15
       95.49 -   119.36: 3
  Dihedral angle restraints: 8098
    sinusoidal: 3303
      harmonic: 4795
  Sorted by residual:
  dihedral pdb=" O2G GTP A 901 "
           pdb=" O3B GTP A 901 "
           pdb=" PG  GTP A 901 "
           pdb=" PB  GTP A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30  -63.34 -119.36     1      2.00e+01 2.50e-03 3.58e+01
  dihedral pdb=" C8  GTP A 901 "
           pdb=" C1' GTP A 901 "
           pdb=" N9  GTP A 901 "
           pdb=" O4' GTP A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59 -137.48 -117.93     1      2.00e+01 2.50e-03 3.52e+01
  dihedral pdb=" CA  GLU A 796 "
           pdb=" C   GLU A 796 "
           pdb=" N   VAL A 797 "
           pdb=" CA  VAL A 797 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.43   27.57     0      5.00e+00 4.00e-02 3.04e+01
  ... (remaining 8095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1775
       0.092 -    0.184: 209
       0.184 -    0.276: 14
       0.276 -    0.368: 6
       0.368 -    0.460: 2
  Chirality restraints: 2006
  Sorted by residual:
  chirality pdb=" CB  ILE B 532 "
            pdb=" CA  ILE B 532 "
            pdb=" CG1 ILE B 532 "
            pdb=" CG2 ILE B 532 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CB  ILE A 641 "
            pdb=" CA  ILE A 641 "
            pdb=" CG1 ILE A 641 "
            pdb=" CG2 ILE A 641 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.61e+00
  chirality pdb=" CB  ILE A 175 "
            pdb=" CA  ILE A 175 "
            pdb=" CG1 ILE A 175 "
            pdb=" CG2 ILE A 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.99   -0.35 2.00e-01 2.50e+01 3.04e+00
  ... (remaining 2003 not shown)

  Planarity restraints: 2359
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 465 "   -0.057 5.00e-02 4.00e+02   8.72e-02 1.22e+01
        pdb=" N   PRO B 466 "    0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO B 466 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B 466 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 473 "    0.015 2.00e-02 2.50e+03   2.94e-02 8.64e+00
        pdb=" C   ARG A 473 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ARG A 473 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LYS A 474 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 655 "    0.015 2.00e-02 2.50e+03   2.92e-02 8.50e+00
        pdb=" C   GLU A 655 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLU A 655 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TYR A 656 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2356 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3776
        2.81 -     3.33: 12137
        3.33 -     3.86: 21477
        3.86 -     4.38: 23419
        4.38 -     4.90: 39654
  Nonbonded interactions: 100463
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 524 "
            pdb=" OD1 ASP B 679 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" N   UNK C   0 "
            pdb=" O   UNK C   0 "
     model   vdw
     2.303 2.496
  nonbonded pdb=" O   CYS B 783 "
            pdb=" OH  TYR B 822 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   LEU B 337 "
            pdb=" OG1 THR B 341 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   PRO B 139 "
            pdb=" OH  TYR B 153 "
     model   vdw
     2.332 3.040
  ... (remaining 100458 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 4 through 83 or (resid 84 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 85 through 141 or resid 145 through 157 or res \ 
id 231 or resid 242 through 248 or resid 251 through 264 or resid 266 through 28 \ 
9 or resid 293 through 595 or resid 597 through 626 or resid 628 through 670 or  \ 
resid 673 through 869))
  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:             1.180
  Set stop_for_unknowns flag:              0.010
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.610
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.060
  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:3.080
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   36.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
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      :  0.005   0.086  13759  Z= 0.250
  Angle     :  1.102  14.964  18618  Z= 0.567
  Chirality :  0.062   0.460   2006
  Planarity :  0.007   0.087   2359
  Dihedral  : 15.739 119.359   5026
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  : 11.37 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.41 %
    Favored  : 99.38 %
  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: -3.79 (0.17), residues: 1601
  helix: -1.93 (0.17), residues: 597
  sheet: -1.12 (0.63), residues: 74
  loop : -3.19 (0.17), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 395 
 HIS   0.015   0.002   HIS A   9 
 PHE   0.048   0.002   PHE A 573 
 TYR   0.035   0.002   TYR B 656 
 ARG   0.013   0.001   ARG A  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16731 (  426)
  hydrogen bonds       : angle       6.92841 ( 1239)
  covalent geometry    : bond        0.00494 (13759)
  covalent geometry    : angle       1.10159 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 215
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 CYS cc_start: 0.8375 (p) cc_final: 0.8157 (p)
REVERT: A  469 GLU cc_start: 0.6118 (mp0) cc_final: 0.5862 (mp0)
REVERT: A  507 TYR cc_start: 0.8051 (t80) cc_final: 0.7709 (t80)
REVERT: A  747 THR cc_start: 0.8580 (p) cc_final: 0.8280 (p)
REVERT: B   26 TYR cc_start: 0.6761 (m-10) cc_final: 0.6472 (m-80)
REVERT: B   80 CYS cc_start: 0.8725 (m) cc_final: 0.8386 (m)
REVERT: B   83 MET cc_start: 0.8300 (pmm) cc_final: 0.8002 (pmm)
REVERT: B  744 TYR cc_start: 0.7014 (m-80) cc_final: 0.6702 (m-10)
  outliers start: 3
  outliers final: 2
  residues processed: 218
  average time/residue: 0.2203
  time to fit residues: 73.7211
Evaluate side-chains
  158 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 156
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  464 LYS
Chi-restraints excluded: chain B residue  465 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:    2.9990
   chunk 123 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 83 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 127 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 95 optimal weight:   20.0000
   chunk 148 optimal weight:   20.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 ASN
A 432 GLN
A 737 GLN
** B  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 450 HIS
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 GLN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.139275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.113568 restraints weight = 34265.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.114964 restraints weight = 20190.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.116825 restraints weight = 14185.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  13759  Z= 0.201
  Angle     :  0.729   9.445  18618  Z= 0.385
  Chirality :  0.046   0.202   2006
  Planarity :  0.005   0.059   2359
  Dihedral  :  7.740 116.042   1803
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.93 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.84 %
    Favored  : 86.30 %
  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: -2.88 (0.19), residues: 1601
  helix: -0.56 (0.21), residues: 608
  sheet: -1.55 (0.62), residues: 74
  loop : -3.07 (0.18), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 395 
 HIS   0.008   0.001   HIS B   9 
 PHE   0.017   0.002   PHE A 503 
 TYR   0.037   0.002   TYR B 656 
 ARG   0.005   0.001   ARG B 652 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04666 (  426)
  hydrogen bonds       : angle       5.22554 ( 1239)
  covalent geometry    : bond        0.00442 (13759)
  covalent geometry    : angle       0.72922 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 1.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 TYR cc_start: 0.8446 (m-10) cc_final: 0.8193 (m-80)
REVERT: A  568 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7215 (pm20)
REVERT: A  593 TYR cc_start: 0.8577 (t80) cc_final: 0.8332 (t80)
REVERT: A  747 THR cc_start: 0.8639 (p) cc_final: 0.8397 (p)
REVERT: B   80 CYS cc_start: 0.9014 (m) cc_final: 0.8715 (m)
REVERT: B  324 LYS cc_start: 0.5323 (mmtt) cc_final: 0.4861 (mmtp)
REVERT: B  678 ASN cc_start: 0.7253 (t0) cc_final: 0.6987 (t0)
REVERT: B  744 TYR cc_start: 0.7334 (m-80) cc_final: 0.6799 (m-10)
  outliers start: 27
  outliers final: 17
  residues processed: 178
  average time/residue: 0.2047
  time to fit residues: 56.8641
Evaluate side-chains
  158 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  568 GLU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  465 CYS
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain B residue  668 CYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  702 TYR
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  840 ILE
Chi-restraints excluded: chain B residue  855 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 131 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 159 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 100 optimal weight:   40.0000
   chunk 68 optimal weight:    6.9990
   chunk 157 optimal weight:    2.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 ASN
B   9 HIS
B  33 ASN
B  46 GLN
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 GLN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.143504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.116648 restraints weight = 37017.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.119578 restraints weight = 21550.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.121524 restraints weight = 14967.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  13759  Z= 0.143
  Angle     :  0.647   8.166  18618  Z= 0.340
  Chirality :  0.044   0.198   2006
  Planarity :  0.004   0.053   2359
  Dihedral  :  7.346 117.465   1799
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.06 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.49 %
    Favored  : 82.31 %
  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: -2.55 (0.20), residues: 1601
  helix: -0.13 (0.21), residues: 607
  sheet: -1.47 (0.62), residues: 72
  loop : -2.98 (0.18), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 395 
 HIS   0.006   0.001   HIS A   9 
 PHE   0.028   0.001   PHE A 573 
 TYR   0.019   0.001   TYR B 414 
 ARG   0.003   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  426)
  hydrogen bonds       : angle       4.88849 ( 1239)
  covalent geometry    : bond        0.00319 (13759)
  covalent geometry    : angle       0.64690 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 2.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 TYR cc_start: 0.8204 (m-10) cc_final: 0.7977 (m-80)
REVERT: A  363 ASP cc_start: 0.7675 (t0) cc_final: 0.7339 (t0)
REVERT: A  568 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7319 (pm20)
REVERT: A  593 TYR cc_start: 0.8408 (t80) cc_final: 0.8158 (t80)
REVERT: A  747 THR cc_start: 0.8449 (p) cc_final: 0.8226 (p)
REVERT: B   80 CYS cc_start: 0.8920 (m) cc_final: 0.8609 (m)
REVERT: B  154 LEU cc_start: 0.7534 (pt) cc_final: 0.7014 (tp)
REVERT: B  559 TYR cc_start: 0.8820 (m-80) cc_final: 0.8616 (m-80)
REVERT: B  744 TYR cc_start: 0.7284 (m-80) cc_final: 0.6798 (m-80)
  outliers start: 32
  outliers final: 20
  residues processed: 174
  average time/residue: 0.2122
  time to fit residues: 59.2608
Evaluate side-chains
  151 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  568 GLU
Chi-restraints excluded: chain A residue  820 TYR
Chi-restraints excluded: chain B residue    9 HIS
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  537 LEU
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain B residue  647 GLU
Chi-restraints excluded: chain B residue  668 CYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  840 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 65 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 141 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   chunk 137 optimal weight:    9.9990
   chunk 129 optimal weight:    9.9990
   chunk 159 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 481 HIS
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.140392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.115383 restraints weight = 33290.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.117165 restraints weight = 19912.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.118427 restraints weight = 13501.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  13759  Z= 0.157
  Angle     :  0.661  11.054  18618  Z= 0.342
  Chirality :  0.044   0.198   2006
  Planarity :  0.004   0.054   2359
  Dihedral  :  7.215 116.495   1798
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.12 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.55 %
    Favored  : 79.70 %
  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: -2.48 (0.20), residues: 1601
  helix:  0.04 (0.22), residues: 606
  sheet: -1.72 (0.62), residues: 74
  loop : -3.00 (0.18), residues: 921

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 395 
 HIS   0.008   0.001   HIS B   9 
 PHE   0.020   0.001   PHE A 189 
 TYR   0.043   0.002   TYR B 656 
 ARG   0.005   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  426)
  hydrogen bonds       : angle       4.86161 ( 1239)
  covalent geometry    : bond        0.00352 (13759)
  covalent geometry    : angle       0.66138 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 TYR cc_start: 0.8316 (m-10) cc_final: 0.8104 (m-80)
REVERT: A  363 ASP cc_start: 0.7725 (t0) cc_final: 0.7419 (t0)
REVERT: A  593 TYR cc_start: 0.8605 (t80) cc_final: 0.8264 (t80)
REVERT: A  747 THR cc_start: 0.8570 (p) cc_final: 0.8348 (p)
REVERT: B   80 CYS cc_start: 0.8982 (m) cc_final: 0.8649 (m)
REVERT: B  154 LEU cc_start: 0.7621 (pt) cc_final: 0.7157 (tp)
REVERT: B  559 TYR cc_start: 0.8776 (m-80) cc_final: 0.8576 (m-80)
REVERT: B  636 LEU cc_start: 0.8421 (pp) cc_final: 0.8187 (tp)
REVERT: B  744 TYR cc_start: 0.7210 (m-10) cc_final: 0.6682 (m-80)
  outliers start: 40
  outliers final: 23
  residues processed: 167
  average time/residue: 0.2084
  time to fit residues: 54.8608
Evaluate side-chains
  153 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  820 TYR
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  537 LEU
Chi-restraints excluded: chain B residue  668 CYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  840 ILE
Chi-restraints excluded: chain B residue  853 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 2 optimal weight:    0.0870
   chunk 119 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 124 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    0.5980
   chunk 150 optimal weight:    0.1980
   chunk 77 optimal weight:    0.8980
   chunk 114 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   overall best weight:    0.5560

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

Flipped N/Q/H residues before XYZ refinement:
A 481 HIS
B   9 HIS
B 564 GLN
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 ASN
B 812 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.146628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.120331 restraints weight = 36941.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.123445 restraints weight = 21235.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.125493 restraints weight = 14620.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  13759  Z= 0.105
  Angle     :  0.608   8.430  18618  Z= 0.313
  Chirality :  0.043   0.234   2006
  Planarity :  0.004   0.050   2359
  Dihedral  :  6.857 116.112   1798
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.49 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.06 %
    Favored  : 79.08 %
  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: -2.21 (0.20), residues: 1601
  helix:  0.22 (0.22), residues: 604
  sheet: -1.27 (0.64), residues: 72
  loop : -2.82 (0.19), residues: 925

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 510 
 HIS   0.005   0.001   HIS A   9 
 PHE   0.033   0.001   PHE A 573 
 TYR   0.035   0.001   TYR B 656 
 ARG   0.003   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03300 (  426)
  hydrogen bonds       : angle       4.51135 ( 1239)
  covalent geometry    : bond        0.00223 (13759)
  covalent geometry    : angle       0.60763 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 1.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.7550 (ppp) cc_final: 0.7259 (ppp)
REVERT: A  115 CYS cc_start: 0.8216 (p) cc_final: 0.7820 (p)
REVERT: A  363 ASP cc_start: 0.7807 (t0) cc_final: 0.7538 (t0)
REVERT: A  593 TYR cc_start: 0.8460 (t80) cc_final: 0.8170 (t80)
REVERT: A  747 THR cc_start: 0.8258 (p) cc_final: 0.7979 (p)
REVERT: A  749 SER cc_start: 0.8624 (p) cc_final: 0.8195 (t)
REVERT: B   12 PHE cc_start: 0.5126 (OUTLIER) cc_final: 0.4643 (t80)
REVERT: B   80 CYS cc_start: 0.8919 (m) cc_final: 0.8581 (m)
REVERT: B  154 LEU cc_start: 0.7619 (pt) cc_final: 0.7088 (tp)
REVERT: B  510 TRP cc_start: 0.6927 (t-100) cc_final: 0.6402 (t-100)
REVERT: B  568 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.9004 (pm20)
REVERT: B  744 TYR cc_start: 0.7039 (m-10) cc_final: 0.6531 (m-80)
  outliers start: 27
  outliers final: 15
  residues processed: 180
  average time/residue: 0.2010
  time to fit residues: 56.7557
Evaluate side-chains
  150 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  641 ILE
Chi-restraints excluded: chain A residue  662 GLU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  820 TYR
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain B residue    9 HIS
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain B residue  568 GLU
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  691 HIS
Chi-restraints excluded: chain B residue  820 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 106 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 99 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 162 optimal weight:    0.0980
   chunk 105 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0000
   chunk 24 optimal weight:    0.0010
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A 481 HIS
B   9 HIS
B 509 GLN
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.144035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.116974 restraints weight = 33834.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.120096 restraints weight = 19353.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.122131 restraints weight = 13305.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13759  Z= 0.106
  Angle     :  0.609   9.128  18618  Z= 0.313
  Chirality :  0.043   0.231   2006
  Planarity :  0.004   0.048   2359
  Dihedral  :  6.726 110.896   1798
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  9.43 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.55 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.19 (0.20), residues: 1601
  helix:  0.26 (0.22), residues: 610
  sheet: -1.48 (0.62), residues: 74
  loop : -2.83 (0.19), residues: 917

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 395 
 HIS   0.012   0.001   HIS B   9 
 PHE   0.033   0.001   PHE A 573 
 TYR   0.018   0.001   TYR B 622 
 ARG   0.004   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  426)
  hydrogen bonds       : angle       4.42451 ( 1239)
  covalent geometry    : bond        0.00230 (13759)
  covalent geometry    : angle       0.60923 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 1.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 CYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7881 (p)
REVERT: A  363 ASP cc_start: 0.7825 (t0) cc_final: 0.7533 (t0)
REVERT: A  507 TYR cc_start: 0.8160 (t80) cc_final: 0.7844 (t80)
REVERT: A  582 PHE cc_start: 0.7575 (m-80) cc_final: 0.7342 (m-80)
REVERT: A  593 TYR cc_start: 0.8633 (t80) cc_final: 0.8322 (t80)
REVERT: A  747 THR cc_start: 0.8319 (p) cc_final: 0.8026 (p)
REVERT: A  749 SER cc_start: 0.8790 (p) cc_final: 0.8293 (t)
REVERT: B   12 PHE cc_start: 0.5007 (OUTLIER) cc_final: 0.4575 (t80)
REVERT: B   80 CYS cc_start: 0.8963 (m) cc_final: 0.8603 (m)
REVERT: B  510 TRP cc_start: 0.6950 (t-100) cc_final: 0.6374 (t-100)
REVERT: B  568 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.9003 (pm20)
REVERT: B  744 TYR cc_start: 0.7110 (m-10) cc_final: 0.6560 (m-80)
REVERT: B  745 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6862 (tt)
  outliers start: 31
  outliers final: 16
  residues processed: 175
  average time/residue: 0.2019
  time to fit residues: 55.8827
Evaluate side-chains
  162 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  641 ILE
Chi-restraints excluded: chain A residue  662 GLU
Chi-restraints excluded: chain A residue  820 TYR
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain B residue    9 HIS
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  568 GLU
Chi-restraints excluded: chain B residue  575 LYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  820 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 92 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 110 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 149 optimal weight:   30.0000
   chunk 72 optimal weight:   10.0000
   chunk 141 optimal weight:   10.0000
   chunk 88 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 385 HIS
A 481 HIS
A 530 GLN
** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 730 ASN
B   9 HIS
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 HIS
B 509 GLN
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.136442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.112520 restraints weight = 37077.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.111991 restraints weight = 23078.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.113238 restraints weight = 17934.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.164  13759  Z= 0.319
  Angle     :  0.830   9.953  18618  Z= 0.434
  Chirality :  0.050   0.242   2006
  Planarity :  0.005   0.050   2359
  Dihedral  :  7.499 109.290   1798
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 12.43 %
    Favored  : 87.13 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.23 %
    Favored  : 76.46 %
  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: -2.71 (0.20), residues: 1601
  helix: -0.23 (0.21), residues: 608
  sheet: -2.08 (0.60), residues: 74
  loop : -3.06 (0.18), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  43 
 HIS   0.011   0.002   HIS B  89 
 PHE   0.036   0.003   PHE B  13 
 TYR   0.033   0.003   TYR A  45 
 ARG   0.006   0.001   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05073 (  426)
  hydrogen bonds       : angle       5.48085 ( 1239)
  covalent geometry    : bond        0.00723 (13759)
  covalent geometry    : angle       0.82972 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 137
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.7679 (tmm) cc_final: 0.7442 (ttm)
REVERT: A  363 ASP cc_start: 0.7835 (t0) cc_final: 0.7548 (t0)
REVERT: A  747 THR cc_start: 0.8816 (p) cc_final: 0.8578 (p)
REVERT: B   12 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5809 (t80)
REVERT: B   80 CYS cc_start: 0.9022 (m) cc_final: 0.8725 (m)
REVERT: B  154 LEU cc_start: 0.7688 (pt) cc_final: 0.7192 (tp)
REVERT: B  744 TYR cc_start: 0.7526 (m-10) cc_final: 0.6900 (m-80)
REVERT: B  848 PHE cc_start: 0.8101 (t80) cc_final: 0.7828 (t80)
  outliers start: 48
  outliers final: 41
  residues processed: 166
  average time/residue: 0.2023
  time to fit residues: 52.7558
Evaluate side-chains
  168 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 126
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 PHE
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  344 PHE
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  662 GLU
Chi-restraints excluded: chain A residue  689 TYR
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  820 TYR
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain B residue    9 HIS
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  537 LEU
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain B residue  575 LYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  691 HIS
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  796 GLU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  853 ILE
Chi-restraints excluded: chain B residue  855 LEU
Chi-restraints excluded: chain B residue  866 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 139 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 160 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 152 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A 481 HIS
B   9 HIS
B 355 HIS
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.143719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.116666 restraints weight = 36744.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.119763 restraints weight = 21138.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.121752 restraints weight = 14527.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13759  Z= 0.119
  Angle     :  0.651  13.982  18618  Z= 0.333
  Chirality :  0.044   0.214   2006
  Planarity :  0.004   0.051   2359
  Dihedral  :  6.900 103.955   1798
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  9.81 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.13 %
    Favored  : 76.05 %
  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: -2.34 (0.20), residues: 1601
  helix:  0.12 (0.21), residues: 619
  sheet: -1.67 (0.61), residues: 74
  loop : -2.93 (0.19), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 590 
 HIS   0.004   0.001   HIS A  89 
 PHE   0.018   0.001   PHE A 582 
 TYR   0.019   0.001   TYR B 414 
 ARG   0.003   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  426)
  hydrogen bonds       : angle       4.67103 ( 1239)
  covalent geometry    : bond        0.00260 (13759)
  covalent geometry    : angle       0.65070 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 137
  time to evaluate  : 1.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 CYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7770 (p)
REVERT: A  363 ASP cc_start: 0.7786 (t0) cc_final: 0.7495 (t0)
REVERT: A  640 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7390 (pp20)
REVERT: A  747 THR cc_start: 0.8419 (p) cc_final: 0.8163 (p)
REVERT: A  859 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7271 (pmm)
REVERT: B   42 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7232 (tm-30)
REVERT: B   80 CYS cc_start: 0.8953 (m) cc_final: 0.8627 (m)
REVERT: B   83 MET cc_start: 0.8384 (pmm) cc_final: 0.8138 (pmm)
REVERT: B  154 LEU cc_start: 0.7705 (pt) cc_final: 0.7176 (tp)
REVERT: B  509 GLN cc_start: 0.7777 (mp-120) cc_final: 0.7537 (mp10)
REVERT: B  568 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8994 (pm20)
REVERT: B  744 TYR cc_start: 0.7406 (m-10) cc_final: 0.6870 (m-80)
  outliers start: 41
  outliers final: 25
  residues processed: 162
  average time/residue: 0.2080
  time to fit residues: 53.0056
Evaluate side-chains
  158 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  640 GLU
Chi-restraints excluded: chain A residue  662 GLU
Chi-restraints excluded: chain A residue  820 TYR
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain B residue  568 GLU
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  691 HIS
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  796 GLU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  866 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 148 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 113 optimal weight:    8.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 567 ASN
** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.143089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.116270 restraints weight = 36454.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.119131 restraints weight = 21131.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.120987 restraints weight = 14778.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  13759  Z= 0.128
  Angle     :  0.650  10.869  18618  Z= 0.333
  Chirality :  0.044   0.292   2006
  Planarity :  0.004   0.052   2359
  Dihedral  :  6.795 103.760   1798
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.81 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 21.75 %
    Favored  : 75.84 %
  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: -2.24 (0.20), residues: 1601
  helix:  0.21 (0.21), residues: 614
  sheet: -1.61 (0.61), residues: 74
  loop : -2.86 (0.19), residues: 913

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 395 
 HIS   0.004   0.001   HIS A  89 
 PHE   0.036   0.001   PHE A 573 
 TYR   0.019   0.001   TYR B 460 
 ARG   0.005   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03546 (  426)
  hydrogen bonds       : angle       4.63098 ( 1239)
  covalent geometry    : bond        0.00292 (13759)
  covalent geometry    : angle       0.65041 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.7569 (tmm) cc_final: 0.7355 (ttm)
REVERT: A  115 CYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7886 (p)
REVERT: A  363 ASP cc_start: 0.7819 (t0) cc_final: 0.7554 (t0)
REVERT: A  507 TYR cc_start: 0.8019 (t80) cc_final: 0.7791 (t80)
REVERT: A  640 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7390 (pp20)
REVERT: A  747 THR cc_start: 0.8421 (p) cc_final: 0.8154 (p)
REVERT: A  859 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7323 (pmm)
REVERT: B   42 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7360 (tm-30)
REVERT: B   80 CYS cc_start: 0.8884 (m) cc_final: 0.8585 (m)
REVERT: B   83 MET cc_start: 0.8347 (pmm) cc_final: 0.8105 (pmm)
REVERT: B  509 GLN cc_start: 0.7780 (mp-120) cc_final: 0.7539 (mp10)
REVERT: B  568 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.9018 (pm20)
REVERT: B  689 TYR cc_start: 0.8046 (m-80) cc_final: 0.7804 (m-80)
REVERT: B  744 TYR cc_start: 0.7442 (m-10) cc_final: 0.6816 (m-80)
  outliers start: 35
  outliers final: 28
  residues processed: 153
  average time/residue: 0.2182
  time to fit residues: 53.1810
Evaluate side-chains
  161 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  640 GLU
Chi-restraints excluded: chain A residue  641 ILE
Chi-restraints excluded: chain A residue  662 GLU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  820 TYR
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain B residue  568 GLU
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  691 HIS
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  796 GLU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  866 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 146 optimal weight:   20.0000
   chunk 22 optimal weight:   10.0000
   chunk 154 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 142 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
** B 567 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 = 0.4141 r_free = 0.4141 target = 0.140919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.116161 restraints weight = 36903.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.117619 restraints weight = 20602.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.118558 restraints weight = 15168.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  13759  Z= 0.171
  Angle     :  0.679  10.078  18618  Z= 0.352
  Chirality :  0.045   0.320   2006
  Planarity :  0.004   0.051   2359
  Dihedral  :  6.884 103.167   1798
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 11.37 %
    Favored  : 88.26 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.02 %
    Favored  : 75.57 %
  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: -2.30 (0.20), residues: 1601
  helix:  0.16 (0.21), residues: 618
  sheet: -1.70 (0.61), residues: 74
  loop : -2.91 (0.19), residues: 909

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 395 
 HIS   0.004   0.001   HIS B  89 
 PHE   0.023   0.002   PHE A 582 
 TYR   0.020   0.002   TYR A  45 
 ARG   0.006   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03912 (  426)
  hydrogen bonds       : angle       4.83043 ( 1239)
  covalent geometry    : bond        0.00395 (13759)
  covalent geometry    : angle       0.67917 (18618)

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

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

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3202 Ramachandran restraints generated.
    1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 1.634 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.7588 (tmm) cc_final: 0.7365 (ttm)
REVERT: A  115 CYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7931 (p)
REVERT: A  363 ASP cc_start: 0.7859 (t0) cc_final: 0.7562 (t0)
REVERT: A  507 TYR cc_start: 0.8071 (t80) cc_final: 0.7798 (t80)
REVERT: A  573 PHE cc_start: 0.8309 (t80) cc_final: 0.8063 (t80)
REVERT: A  640 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7357 (pp20)
REVERT: A  747 THR cc_start: 0.8586 (p) cc_final: 0.8308 (p)
REVERT: A  859 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7486 (pmm)
REVERT: B   42 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7381 (tm-30)
REVERT: B   80 CYS cc_start: 0.8886 (m) cc_final: 0.8603 (m)
REVERT: B   83 MET cc_start: 0.8397 (pmm) cc_final: 0.8155 (pmm)
REVERT: B  154 LEU cc_start: 0.7683 (pt) cc_final: 0.7148 (tp)
REVERT: B  286 TRP cc_start: 0.7673 (t60) cc_final: 0.6828 (t60)
REVERT: B  295 PHE cc_start: 0.7438 (m-10) cc_final: 0.7114 (m-10)
REVERT: B  509 GLN cc_start: 0.7841 (mp-120) cc_final: 0.7629 (mp10)
REVERT: B  568 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.9025 (pm20)
REVERT: B  744 TYR cc_start: 0.7430 (m-10) cc_final: 0.6773 (m-80)
  outliers start: 35
  outliers final: 29
  residues processed: 150
  average time/residue: 0.2045
  time to fit residues: 48.7354
Evaluate side-chains
  157 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 CYS
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  640 GLU
Chi-restraints excluded: chain A residue  641 ILE
Chi-restraints excluded: chain A residue  662 GLU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  820 TYR
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue  256 PHE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  414 TYR
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  513 GLU
Chi-restraints excluded: chain B residue  537 LEU
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain B residue  568 GLU
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain B residue  691 HIS
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  779 ASP
Chi-restraints excluded: chain B residue  796 GLU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  866 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 154 optimal weight:    9.9990
   chunk 10 optimal weight:    0.1980
   chunk 37 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0670
   chunk 1 optimal weight:    0.9980
   chunk 152 optimal weight:    9.9990
   chunk 73 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 115 optimal weight:    0.0670
   chunk 6 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
** B 567 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 = 0.4215 r_free = 0.4215 target = 0.146315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.120058 restraints weight = 37063.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.123080 restraints weight = 21170.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.125074 restraints weight = 14592.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  13759  Z= 0.109
  Angle     :  0.627   9.963  18618  Z= 0.321
  Chirality :  0.043   0.277   2006
  Planarity :  0.004   0.052   2359
  Dihedral  :  6.482 104.561   1798
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.81 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 22.16 %
    Favored  : 75.77 %
  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: -2.09 (0.21), residues: 1601
  helix:  0.38 (0.22), residues: 608
  sheet: -1.59 (0.61), residues: 75
  loop : -2.78 (0.19), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 510 
 HIS   0.004   0.001   HIS A  89 
 PHE   0.053   0.001   PHE B 848 
 TYR   0.018   0.001   TYR B 414 
 ARG   0.005   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03210 (  426)
  hydrogen bonds       : angle       4.45797 ( 1239)
  covalent geometry    : bond        0.00232 (13759)
  covalent geometry    : angle       0.62738 (18618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3832.23 seconds
wall clock time: 68 minutes 25.29 seconds (4105.29 seconds total)