Starting phenix.real_space_refine
on Wed Apr 30 19:20:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k3t_36859/04_2025/8k3t_36859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k3t_36859/04_2025/8k3t_36859.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k3t_36859/04_2025/8k3t_36859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k3t_36859/04_2025/8k3t_36859.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k3t_36859/04_2025/8k3t_36859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k3t_36859/04_2025/8k3t_36859.cif"
  }
  resolution = 3.57
  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=   0.004 sd=   0.052
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      4      5.21       5
     S      58      5.16       5
     C    6178      2.51       5
     N    1482      2.21       5
     O    1682      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9410
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 4630
          Classifications: {'peptide': 627}
          Incomplete info: {'truncation_to_alanine': 122}
          Link IDs: {'PTRANS': 17, 'TRANS': 609}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 496
          Unresolved non-hydrogen angles: 603
          Unresolved non-hydrogen dihedrals: 418
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 283
    Chain: "B"
      Number of atoms: 4630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 4630
          Classifications: {'peptide': 627}
          Incomplete info: {'truncation_to_alanine': 122}
          Link IDs: {'PTRANS': 17, 'TRANS': 609}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 496
          Unresolved non-hydrogen angles: 603
          Unresolved non-hydrogen dihedrals: 418
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 283
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 75
          Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 75
          Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 6.23, per 1000 atoms: 0.66
  Number of scatterers: 9410
  At special positions: 0
  Unit cell: (113.42, 109.18, 100.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      58     16.00
     P       6     15.00
     Mg      4     11.99
     O    1682      8.00
     N    1482      7.00
     C    6178      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: 3.19
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2396

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 6 sheets defined
      67.5% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 410 through 415
    Processing helix  chain 'A' and resid 424 through 428
      removed outlier: 3.876A  pdb=" N   LEU A 428 " --> pdb=" O   PRO A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 440
      removed outlier: 3.538A  pdb=" N   TYR A 440 " --> pdb=" O   ARG A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 478
    Processing helix  chain 'A' and resid 488 through 491
    Processing helix  chain 'A' and resid 506 through 516
      removed outlier: 4.155A  pdb=" N   LEU A 512 " --> pdb=" O   ARG A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 587
      removed outlier: 3.617A  pdb=" N   ARG A 583 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 594
    Processing helix  chain 'A' and resid 610 through 618
      removed outlier: 3.817A  pdb=" N   GLU A 618 " --> pdb=" O   GLN A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 621
      No H-bonds generated for 'chain 'A' and resid 619 through 621'
    Processing helix  chain 'A' and resid 636 through 643
      removed outlier: 3.927A  pdb=" N   PHE A 639 " --> pdb=" O   GLY A 636 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   LYS A 641 " --> pdb=" O   ARG A 638 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU A 643 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 669
      removed outlier: 3.539A  pdb=" N   GLN A 650 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LYS A 662 " --> pdb=" O   ASN A 658 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   THR A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE A 668 " --> pdb=" O   THR A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 687
    Processing helix  chain 'A' and resid 688 through 697
      removed outlier: 3.748A  pdb=" N   GLY A 697 " --> pdb=" O   LYS A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 712
    Processing helix  chain 'A' and resid 715 through 726
      removed outlier: 4.470A  pdb=" N   LEU A 720 " --> pdb=" O   GLU A 716 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   CYS A 721 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 774
      removed outlier: 4.627A  pdb=" N   ARG A 759 " --> pdb=" O   LEU A 755 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TRP A 760 " --> pdb=" O   GLN A 756 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ASN A 762 " --> pdb=" O   ARG A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 781
      removed outlier: 3.602A  pdb=" N   TRP A 779 " --> pdb=" O   TYR A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 807
    Processing helix  chain 'A' and resid 807 through 828
    Processing helix  chain 'A' and resid 830 through 856
      removed outlier: 3.829A  pdb=" N   LEU A 834 " --> pdb=" O   ALA A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 860
      No H-bonds generated for 'chain 'A' and resid 858 through 860'
    Processing helix  chain 'A' and resid 861 through 893
      removed outlier: 3.776A  pdb=" N   TYR A 865 " --> pdb=" O   THR A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 933
    Processing helix  chain 'A' and resid 942 through 955
      Proline residue:  A 950  - end of helix
    Processing helix  chain 'A' and resid 955 through 963
    Processing helix  chain 'A' and resid 1027 through 1060
      removed outlier: 4.176A  pdb=" N   ILE A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1074
    Processing helix  chain 'A' and resid 1091 through 1130
      removed outlier: 4.073A  pdb=" N   SER A1095 " --> pdb=" O   THR A1091 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A1102 " --> pdb=" O   PHE A1098 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 415
    Processing helix  chain 'B' and resid 424 through 428
      removed outlier: 3.875A  pdb=" N   LEU B 428 " --> pdb=" O   PRO B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 440
      removed outlier: 3.538A  pdb=" N   TYR B 440 " --> pdb=" O   ARG B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 478
    Processing helix  chain 'B' and resid 488 through 491
    Processing helix  chain 'B' and resid 506 through 516
      removed outlier: 4.154A  pdb=" N   LEU B 512 " --> pdb=" O   ARG B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 587
      removed outlier: 3.615A  pdb=" N   ARG B 583 " --> pdb=" O   ILE B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 594
    Processing helix  chain 'B' and resid 610 through 618
      removed outlier: 3.818A  pdb=" N   GLU B 618 " --> pdb=" O   GLN B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 621
      No H-bonds generated for 'chain 'B' and resid 619 through 621'
    Processing helix  chain 'B' and resid 636 through 643
      removed outlier: 3.927A  pdb=" N   PHE B 639 " --> pdb=" O   GLY B 636 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   LYS B 641 " --> pdb=" O   ARG B 638 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU B 643 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 644 through 669
      removed outlier: 3.540A  pdb=" N   GLN B 650 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LYS B 662 " --> pdb=" O   ASN B 658 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   THR B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE B 668 " --> pdb=" O   THR B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 687
    Processing helix  chain 'B' and resid 688 through 697
      removed outlier: 3.749A  pdb=" N   GLY B 697 " --> pdb=" O   LYS B 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 712
    Processing helix  chain 'B' and resid 715 through 726
      removed outlier: 4.470A  pdb=" N   LEU B 720 " --> pdb=" O   GLU B 716 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   CYS B 721 " --> pdb=" O   ASP B 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 749 through 774
      removed outlier: 4.626A  pdb=" N   ARG B 759 " --> pdb=" O   LEU B 755 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   TRP B 760 " --> pdb=" O   GLN B 756 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ASN B 762 " --> pdb=" O   ARG B 758 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 781
      removed outlier: 3.603A  pdb=" N   TRP B 779 " --> pdb=" O   TYR B 776 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 784 through 807
    Processing helix  chain 'B' and resid 807 through 828
    Processing helix  chain 'B' and resid 830 through 856
      removed outlier: 3.829A  pdb=" N   LEU B 834 " --> pdb=" O   ALA B 830 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 858 through 860
      No H-bonds generated for 'chain 'B' and resid 858 through 860'
    Processing helix  chain 'B' and resid 861 through 893
      removed outlier: 3.776A  pdb=" N   TYR B 865 " --> pdb=" O   THR B 861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 911 through 933
    Processing helix  chain 'B' and resid 942 through 955
      Proline residue:  B 950  - end of helix
    Processing helix  chain 'B' and resid 955 through 963
    Processing helix  chain 'B' and resid 1027 through 1060
      removed outlier: 4.176A  pdb=" N   ILE B1045 " --> pdb=" O   SER B1041 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1063 through 1074
    Processing helix  chain 'B' and resid 1091 through 1130
      removed outlier: 4.071A  pdb=" N   SER B1095 " --> pdb=" O   THR B1091 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU B1102 " --> pdb=" O   PHE B1098 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 417 through 421
      removed outlier: 3.683A  pdb=" N   HIS A 540 " --> pdb=" O   LEU A 567 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   ILE A 493 " --> pdb=" O   GLN A 566 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   LEU A 568 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL A 495 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   CYS A 570 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ILE A 497 " --> pdb=" O   CYS A 570 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   LYS A 572 " --> pdb=" O   ILE A 497 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   SER A 499 " --> pdb=" O   LYS A 572 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU A 448 " --> pdb=" O   VAL A 494 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   CYS A 496 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   LEU A 450 " --> pdb=" O   CYS A 496 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ILE A 498 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   VAL A 452 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   MET A 449 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   LEU A 601 " --> pdb=" O   MET A 449 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   VAL A 451 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   PHE A 678 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY A 629 " --> pdb=" O   PHE A 678 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLY A 625 " --> pdb=" O   ARG A 682 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   LYS A 735 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ALA A 627 " --> pdb=" O   LYS A 735 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   CYS A 737 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   GLY A 629 " --> pdb=" O   CYS A 737 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   SER A 739 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 10.166A  pdb=" N   ILE A 631 " --> pdb=" O   SER A 739 " (cutoff:3.500A)
      removed outlier: 8.566A  pdb=" N   TYR A 741 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 9.945A  pdb=" N   THR A 633 " --> pdb=" O   TYR A 741 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   SER A 743 " --> pdb=" O   THR A 633 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528
    Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549
      removed outlier: 4.770A  pdb=" N   ILE A 546 " --> pdb=" O   GLU A 557 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   GLU A 557 " --> pdb=" O   ILE A 546 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASN A 548 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 421
      removed outlier: 3.682A  pdb=" N   HIS B 540 " --> pdb=" O   LEU B 567 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ILE B 493 " --> pdb=" O   GLN B 566 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   LEU B 568 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL B 495 " --> pdb=" O   LEU B 568 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   CYS B 570 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   ILE B 497 " --> pdb=" O   CYS B 570 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   LYS B 572 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   SER B 499 " --> pdb=" O   LYS B 572 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU B 448 " --> pdb=" O   VAL B 494 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   CYS B 496 " --> pdb=" O   LEU B 448 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   LEU B 450 " --> pdb=" O   CYS B 496 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ILE B 498 " --> pdb=" O   LEU B 450 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   VAL B 452 " --> pdb=" O   ILE B 498 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   MET B 449 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   LEU B 601 " --> pdb=" O   MET B 449 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL B 451 " --> pdb=" O   LEU B 601 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   PHE B 678 " --> pdb=" O   GLY B 629 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   GLY B 629 " --> pdb=" O   PHE B 678 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   GLY B 625 " --> pdb=" O   ARG B 682 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   LYS B 735 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ALA B 627 " --> pdb=" O   LYS B 735 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   CYS B 737 " --> pdb=" O   ALA B 627 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   GLY B 629 " --> pdb=" O   CYS B 737 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   SER B 739 " --> pdb=" O   GLY B 629 " (cutoff:3.500A)
      removed outlier: 10.167A  pdb=" N   ILE B 631 " --> pdb=" O   SER B 739 " (cutoff:3.500A)
      removed outlier: 8.566A  pdb=" N   TYR B 741 " --> pdb=" O   ILE B 631 " (cutoff:3.500A)
      removed outlier: 9.946A  pdb=" N   THR B 633 " --> pdb=" O   TYR B 741 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   SER B 743 " --> pdb=" O   THR B 633 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 527 through 528
    Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 549
      removed outlier: 4.769A  pdb=" N   ILE B 546 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   GLU B 557 " --> pdb=" O   ILE B 546 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASN B 548 " --> pdb=" O   SER B 555 " (cutoff:3.500A)

    625 hydrogen bonds defined for protein.
    1803 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.34

  Time building geometry restraints manager: 3.47 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: 1629
        1.32 -     1.45: 2673
        1.45 -     1.57: 5244
        1.57 -     1.69: 10
        1.69 -     1.81: 86
  Bond restraints: 9642
  Sorted by residual:
  bond pdb=" O1A UDP B1502 "
       pdb=" PA  UDP B1502 "
    ideal  model  delta    sigma   weight residual
    1.482  1.527 -0.045 1.00e-02 1.00e+04 1.99e+01
  bond pdb=" O1A UDP A1502 "
       pdb=" PA  UDP A1502 "
    ideal  model  delta    sigma   weight residual
    1.482  1.526 -0.044 1.00e-02 1.00e+04 1.92e+01
  bond pdb=" N   ILE A 493 "
       pdb=" CA  ILE A 493 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.037 1.15e-02 7.56e+03 1.01e+01
  bond pdb=" N   VAL B 533 "
       pdb=" CA  VAL B 533 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.035 1.15e-02 7.56e+03 9.53e+00
  bond pdb=" N   ILE B 493 "
       pdb=" CA  ILE B 493 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.15e-02 7.56e+03 9.37e+00
  ... (remaining 9637 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 12580
        2.05 -     4.09: 515
        4.09 -     6.14: 57
        6.14 -     8.18: 16
        8.18 -    10.23: 4
  Bond angle restraints: 13172
  Sorted by residual:
  angle pdb=" CA  PHE B 831 "
        pdb=" C   PHE B 831 "
        pdb=" N   ASN B 832 "
      ideal   model   delta    sigma   weight residual
     118.27  108.41    9.86 1.59e+00 3.96e-01 3.84e+01
  angle pdb=" CA  PHE A 831 "
        pdb=" C   PHE A 831 "
        pdb=" N   ASN A 832 "
      ideal   model   delta    sigma   weight residual
     118.27  108.42    9.85 1.59e+00 3.96e-01 3.84e+01
  angle pdb=" O5' UDP A1502 "
        pdb=" PA  UDP A1502 "
        pdb=" O1A UDP A1502 "
      ideal   model   delta    sigma   weight residual
     106.70  111.20   -4.50 1.00e+00 1.00e+00 2.03e+01
  angle pdb=" O5' UDP B1502 "
        pdb=" PA  UDP B1502 "
        pdb=" O1A UDP B1502 "
      ideal   model   delta    sigma   weight residual
     106.70  111.18   -4.48 1.00e+00 1.00e+00 2.01e+01
  angle pdb=" O2A UDP B1502 "
        pdb=" PA  UDP B1502 "
        pdb=" O3A UDP B1502 "
      ideal   model   delta    sigma   weight residual
     105.97  110.25   -4.28 1.00e+00 1.00e+00 1.83e+01
  ... (remaining 13167 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.20: 5282
       23.20 -    46.40: 230
       46.40 -    69.59: 42
       69.59 -    92.79: 24
       92.79 -   115.99: 2
  Dihedral angle restraints: 5580
    sinusoidal: 1878
      harmonic: 3702
  Sorted by residual:
  dihedral pdb=" C27 POV B1503 "
           pdb=" C28 POV B1503 "
           pdb=" C29 POV B1503 "
           pdb="C210 POV B1503 "
      ideal   model   delta sinusoidal    sigma   weight residual
     127.48 -116.53 -115.99     1      3.00e+01 1.11e-03 1.53e+01
  dihedral pdb=" C27 POV A1503 "
           pdb=" C28 POV A1503 "
           pdb=" C29 POV A1503 "
           pdb="C210 POV A1503 "
      ideal   model   delta sinusoidal    sigma   weight residual
     127.48 -116.59 -115.93     1      3.00e+01 1.11e-03 1.53e+01
  dihedral pdb=" CA  PHE A 911 "
           pdb=" C   PHE A 911 "
           pdb=" N   ARG A 912 "
           pdb=" CA  ARG A 912 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.62   18.38     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 5577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 939
       0.041 -    0.082: 444
       0.082 -    0.124: 128
       0.124 -    0.165: 29
       0.165 -    0.206: 10
  Chirality restraints: 1550
  Sorted by residual:
  chirality pdb=" CA  ILE B 719 "
            pdb=" N   ILE B 719 "
            pdb=" C   ILE B 719 "
            pdb=" CB  ILE B 719 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ILE A 719 "
            pdb=" N   ILE A 719 "
            pdb=" C   ILE A 719 "
            pdb=" CB  ILE A 719 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  VAL A 421 "
            pdb=" N   VAL A 421 "
            pdb=" C   VAL A 421 "
            pdb=" CB  VAL A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 1547 not shown)

  Planarity restraints: 1612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV A1503 "   -0.025 2.00e-02 2.50e+03   4.53e-02 2.06e+01
        pdb=" C29 POV A1503 "    0.059 2.00e-02 2.50e+03
        pdb="C210 POV A1503 "   -0.059 2.00e-02 2.50e+03
        pdb="C211 POV A1503 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV B1503 "    0.025 2.00e-02 2.50e+03   4.51e-02 2.04e+01
        pdb=" C29 POV B1503 "   -0.059 2.00e-02 2.50e+03
        pdb="C210 POV B1503 "    0.059 2.00e-02 2.50e+03
        pdb="C211 POV B1503 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 606 "    0.031 5.00e-02 4.00e+02   4.70e-02 3.54e+00
        pdb=" N   PRO A 607 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 607 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 607 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1609 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1967
        2.76 -     3.30: 10068
        3.30 -     3.83: 15870
        3.83 -     4.36: 17632
        4.36 -     4.90: 29939
  Nonbonded interactions: 75476
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 511 "
            pdb=" OG  SER A 515 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   ALA B 511 "
            pdb=" OG  SER B 515 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE2 GLU A1060 "
            pdb=" OG1 THR A1091 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OE2 GLU B1060 "
            pdb=" OG1 THR B1091 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O1A UDP B1502 "
            pdb="MG    MG B1504 "
     model   vdw
     2.287 2.170
  ... (remaining 75471 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             38.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.530
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   68.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
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      :  0.009   0.081   9642  Z= 0.478
  Angle     :  0.929  10.229  13172  Z= 0.555
  Chirality :  0.052   0.206   1550
  Planarity :  0.005   0.047   1612
  Dihedral  : 15.004 115.988   3184
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  1.34 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1234
  helix:  1.11 (0.20), residues: 672
  sheet: -0.96 (0.44), residues: 154
  loop : -0.47 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 806 
 HIS   0.006   0.002   HIS B 783 
 PHE   0.021   0.002   PHE A1052 
 TYR   0.028   0.002   TYR B 878 
 ARG   0.004   0.001   ARG B 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14551 (  625)
  hydrogen bonds       : angle       7.05484 ( 1803)
  covalent geometry    : bond        0.00935 ( 9642)
  covalent geometry    : angle       0.92936 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  411 ASN cc_start: 0.3025 (OUTLIER) cc_final: 0.2570 (p0)
REVERT: A  437 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8097 (mm110)
REVERT: A  560 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8429 (tp40)
REVERT: A  568 LEU cc_start: 0.7665 (tt) cc_final: 0.7193 (mp)
REVERT: A  823 ILE cc_start: 0.9063 (tt) cc_final: 0.8791 (tt)
REVERT: A  886 MET cc_start: 0.8323 (mtt) cc_final: 0.7679 (tmm)
REVERT: B  411 ASN cc_start: 0.3117 (OUTLIER) cc_final: 0.2657 (p0)
REVERT: B  437 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8137 (mm110)
REVERT: B  560 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8454 (tp40)
REVERT: B  568 LEU cc_start: 0.7621 (tt) cc_final: 0.7191 (mp)
REVERT: B  823 ILE cc_start: 0.9066 (tt) cc_final: 0.8786 (tt)
REVERT: B  886 MET cc_start: 0.8316 (mtt) cc_final: 0.7693 (tmm)
  outliers start: 10
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2168
  time to fit residues: 50.6196
Evaluate side-chains
  111 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain B residue  411 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0770
   chunk 97 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 72 optimal weight:   20.0000
   chunk 112 optimal weight:    7.9990
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A 411 ASN
B 411 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.128857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.096095 restraints weight = 19743.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.099623 restraints weight = 8560.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.101781 restraints weight = 5280.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9642  Z= 0.133
  Angle     :  0.557   7.060  13172  Z= 0.300
  Chirality :  0.041   0.157   1550
  Planarity :  0.003   0.037   1612
  Dihedral  : 12.669 118.097   1474
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  6.49 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1234
  helix:  1.83 (0.19), residues: 742
  sheet: -0.48 (0.45), residues: 152
  loop : -0.59 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1103 
 HIS   0.004   0.001   HIS A 828 
 PHE   0.016   0.001   PHE B 864 
 TYR   0.016   0.002   TYR A 713 
 ARG   0.003   0.000   ARG B 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05072 (  625)
  hydrogen bonds       : angle       4.67942 ( 1803)
  covalent geometry    : bond        0.00276 ( 9642)
  covalent geometry    : angle       0.55683 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.084 
Fit side-chains
REVERT: A  560 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8475 (tp40)
REVERT: A  823 ILE cc_start: 0.9178 (tt) cc_final: 0.8924 (tt)
REVERT: A  876 MET cc_start: 0.9009 (tpp) cc_final: 0.8776 (tpp)
REVERT: A  879 MET cc_start: 0.8488 (ttp) cc_final: 0.8223 (ttp)
REVERT: A  938 MET cc_start: 0.8741 (tpp) cc_final: 0.8491 (tpp)
REVERT: B  543 MET cc_start: 0.6631 (pmm) cc_final: 0.6312 (ptp)
REVERT: B  560 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8502 (tp40)
REVERT: B  823 ILE cc_start: 0.9177 (tt) cc_final: 0.8931 (tt)
REVERT: B  876 MET cc_start: 0.9009 (tpp) cc_final: 0.8778 (tpp)
REVERT: B  879 MET cc_start: 0.8478 (ttp) cc_final: 0.8216 (ttp)
REVERT: B  938 MET cc_start: 0.8744 (tpp) cc_final: 0.8471 (tpp)
  outliers start: 8
  outliers final: 5
  residues processed: 143
  average time/residue: 0.1613
  time to fit residues: 36.5221
Evaluate side-chains
  110 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1066 ASP
Chi-restraints excluded: chain A residue 1118 ILE
Chi-restraints excluded: chain B residue  804 ILE
Chi-restraints excluded: chain B residue 1066 ASP
Chi-restraints excluded: chain B residue 1118 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 109 optimal weight:    9.9990
   chunk 2 optimal weight:   30.0000
   chunk 99 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 44 optimal weight:    0.4980
   chunk 68 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 582 HIS
A 774 HIS
B 582 HIS
B 774 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.125014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.091662 restraints weight = 20180.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.094950 restraints weight = 8833.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.097029 restraints weight = 5458.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9642  Z= 0.207
  Angle     :  0.581   5.984  13172  Z= 0.310
  Chirality :  0.042   0.168   1550
  Planarity :  0.004   0.035   1612
  Dihedral  : 13.190 135.921   1470
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.52 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.25), residues: 1234
  helix:  2.00 (0.19), residues: 740
  sheet: -0.40 (0.45), residues: 152
  loop : -0.68 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 806 
 HIS   0.004   0.001   HIS B 828 
 PHE   0.025   0.002   PHE A1052 
 TYR   0.012   0.002   TYR B 713 
 ARG   0.006   0.001   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04826 (  625)
  hydrogen bonds       : angle       4.45941 ( 1803)
  covalent geometry    : bond        0.00482 ( 9642)
  covalent geometry    : angle       0.58073 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A  459 HIS cc_start: 0.7363 (p-80) cc_final: 0.6583 (p-80)
REVERT: A  543 MET cc_start: 0.6785 (pmm) cc_final: 0.6403 (ptp)
REVERT: A  560 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8483 (tp40)
REVERT: A  938 MET cc_start: 0.8865 (tpp) cc_final: 0.8316 (tpp)
REVERT: A 1070 MET cc_start: 0.8356 (tmm) cc_final: 0.8131 (tmm)
REVERT: B  543 MET cc_start: 0.6746 (pmm) cc_final: 0.6419 (ptp)
REVERT: B  560 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8490 (tp40)
REVERT: B  938 MET cc_start: 0.8864 (tpp) cc_final: 0.8295 (tpp)
  outliers start: 16
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1458
  time to fit residues: 27.7674
Evaluate side-chains
  116 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  850 PHE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1118 ILE
Chi-restraints excluded: chain B residue  633 THR
Chi-restraints excluded: chain B residue  810 SER
Chi-restraints excluded: chain B residue  850 PHE
Chi-restraints excluded: chain B residue 1029 ASP
Chi-restraints excluded: chain B residue 1118 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 65 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 98 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 78 optimal weight:   20.0000
   chunk 63 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 86 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 756 GLN
B 756 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.122835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.089438 restraints weight = 20963.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.092426 restraints weight = 9806.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.094290 restraints weight = 6262.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9642  Z= 0.221
  Angle     :  0.571   6.026  13172  Z= 0.308
  Chirality :  0.043   0.200   1550
  Planarity :  0.004   0.036   1612
  Dihedral  : 13.592 142.996   1470
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.77 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.25), residues: 1234
  helix:  1.92 (0.19), residues: 742
  sheet: -0.49 (0.45), residues: 152
  loop : -0.92 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 806 
 HIS   0.004   0.001   HIS A 828 
 PHE   0.024   0.002   PHE A1052 
 TYR   0.015   0.002   TYR A 878 
 ARG   0.006   0.001   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04705 (  625)
  hydrogen bonds       : angle       4.37521 ( 1803)
  covalent geometry    : bond        0.00513 ( 9642)
  covalent geometry    : angle       0.57116 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 1.151 
Fit side-chains
REVERT: A  437 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7487 (tp-100)
REVERT: A  543 MET cc_start: 0.6738 (pmm) cc_final: 0.6417 (ptp)
REVERT: A  560 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8560 (tp40)
REVERT: A  876 MET cc_start: 0.8983 (tpp) cc_final: 0.8597 (tpp)
REVERT: B  437 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7535 (tp-100)
REVERT: B  543 MET cc_start: 0.6560 (pmm) cc_final: 0.6313 (ptp)
REVERT: B  560 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8581 (tp40)
REVERT: B  876 MET cc_start: 0.8983 (tpp) cc_final: 0.8598 (tpp)
  outliers start: 18
  outliers final: 16
  residues processed: 118
  average time/residue: 0.1533
  time to fit residues: 28.7691
Evaluate side-chains
  118 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  850 PHE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1118 ILE
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain B residue  633 THR
Chi-restraints excluded: chain B residue  717 ASP
Chi-restraints excluded: chain B residue  810 SER
Chi-restraints excluded: chain B residue  850 PHE
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue 1029 ASP
Chi-restraints excluded: chain B residue 1118 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 3 optimal weight:   30.0000
   chunk 34 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0040
   chunk 39 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    1.0994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.125813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.092813 restraints weight = 20456.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.095960 restraints weight = 9489.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.097913 restraints weight = 6001.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9642  Z= 0.116
  Angle     :  0.485   6.222  13172  Z= 0.259
  Chirality :  0.040   0.202   1550
  Planarity :  0.003   0.034   1612
  Dihedral  : 12.946 139.201   1470
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.78 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.25), residues: 1234
  helix:  2.18 (0.19), residues: 750
  sheet: -0.27 (0.45), residues: 152
  loop : -0.85 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 806 
 HIS   0.004   0.001   HIS B 828 
 PHE   0.014   0.001   PHE A 864 
 TYR   0.011   0.001   TYR B 713 
 ARG   0.003   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  625)
  hydrogen bonds       : angle       4.14387 ( 1803)
  covalent geometry    : bond        0.00245 ( 9642)
  covalent geometry    : angle       0.48527 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A  437 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7351 (tp-100)
REVERT: A  476 MET cc_start: 0.8368 (mpp) cc_final: 0.7277 (mpp)
REVERT: A  543 MET cc_start: 0.6793 (pmm) cc_final: 0.6492 (ptp)
REVERT: A  560 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8546 (tp40)
REVERT: A  876 MET cc_start: 0.8937 (tpp) cc_final: 0.8468 (tpp)
REVERT: A  886 MET cc_start: 0.8303 (ttp) cc_final: 0.7567 (tmm)
REVERT: B  416 MET cc_start: 0.6305 (tmm) cc_final: 0.5285 (ttt)
REVERT: B  437 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7525 (tp-100)
REVERT: B  543 MET cc_start: 0.6652 (pmm) cc_final: 0.6429 (ptp)
REVERT: B  560 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8563 (tp40)
REVERT: B  876 MET cc_start: 0.8937 (tpp) cc_final: 0.8465 (tpp)
  outliers start: 20
  outliers final: 14
  residues processed: 126
  average time/residue: 0.1803
  time to fit residues: 36.1084
Evaluate side-chains
  123 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  850 PHE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1066 ASP
Chi-restraints excluded: chain A residue 1118 ILE
Chi-restraints excluded: chain B residue  810 SER
Chi-restraints excluded: chain B residue  850 PHE
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue  946 ILE
Chi-restraints excluded: chain B residue 1029 ASP
Chi-restraints excluded: chain B residue 1066 ASP
Chi-restraints excluded: chain B residue 1118 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.124617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.091232 restraints weight = 20812.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.094436 restraints weight = 9638.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.096354 restraints weight = 6074.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9642  Z= 0.143
  Angle     :  0.504   6.642  13172  Z= 0.271
  Chirality :  0.040   0.194   1550
  Planarity :  0.003   0.033   1612
  Dihedral  : 12.798 134.596   1470
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.23 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.25), residues: 1234
  helix:  2.24 (0.19), residues: 746
  sheet: -0.33 (0.44), residues: 152
  loop : -0.83 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 806 
 HIS   0.004   0.001   HIS A 828 
 PHE   0.021   0.001   PHE A 772 
 TYR   0.010   0.001   TYR A 613 
 ARG   0.004   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  625)
  hydrogen bonds       : angle       4.11852 ( 1803)
  covalent geometry    : bond        0.00323 ( 9642)
  covalent geometry    : angle       0.50384 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 1.071 
Fit side-chains
REVERT: A  437 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7329 (tp-100)
REVERT: A  476 MET cc_start: 0.8506 (mpp) cc_final: 0.8195 (mpp)
REVERT: A  543 MET cc_start: 0.6726 (pmm) cc_final: 0.6454 (ptp)
REVERT: A  560 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8552 (tp40)
REVERT: A  606 MET cc_start: 0.5894 (mtm) cc_final: 0.5236 (mtt)
REVERT: A  800 PHE cc_start: 0.8210 (t80) cc_final: 0.7860 (t80)
REVERT: A  876 MET cc_start: 0.8906 (tpp) cc_final: 0.8675 (tpp)
REVERT: A 1066 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8309 (t70)
REVERT: B  416 MET cc_start: 0.6319 (tmm) cc_final: 0.4906 (ttt)
REVERT: B  437 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7323 (tp-100)
REVERT: B  476 MET cc_start: 0.8434 (mpp) cc_final: 0.7238 (mpp)
REVERT: B  560 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8568 (tp40)
REVERT: B  606 MET cc_start: 0.5933 (mtm) cc_final: 0.5262 (mtt)
REVERT: B  810 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8653 (m)
REVERT: B  876 MET cc_start: 0.8903 (tpp) cc_final: 0.8672 (tpp)
  outliers start: 25
  outliers final: 16
  residues processed: 123
  average time/residue: 0.1701
  time to fit residues: 31.7482
Evaluate side-chains
  128 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  850 PHE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  946 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1066 ASP
Chi-restraints excluded: chain A residue 1118 ILE
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  810 SER
Chi-restraints excluded: chain B residue  850 PHE
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue  946 ILE
Chi-restraints excluded: chain B residue 1029 ASP
Chi-restraints excluded: chain B residue 1066 ASP
Chi-restraints excluded: chain B residue 1118 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0010
   chunk 123 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 78 optimal weight:   20.0000
   chunk 12 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 120 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   chunk 72 optimal weight:    6.9990
   overall best weight:    0.6186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.129361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.096085 restraints weight = 20150.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.099810 restraints weight = 8639.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.102072 restraints weight = 5199.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9642  Z= 0.104
  Angle     :  0.484   7.951  13172  Z= 0.255
  Chirality :  0.039   0.200   1550
  Planarity :  0.003   0.032   1612
  Dihedral  : 12.290 131.458   1470
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.12 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.25), residues: 1234
  helix:  2.36 (0.19), residues: 746
  sheet: -0.26 (0.44), residues: 152
  loop : -0.74 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 806 
 HIS   0.004   0.001   HIS A 828 
 PHE   0.019   0.001   PHE B 772 
 TYR   0.009   0.001   TYR B 613 
 ARG   0.003   0.000   ARG B 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  625)
  hydrogen bonds       : angle       3.99584 ( 1803)
  covalent geometry    : bond        0.00217 ( 9642)
  covalent geometry    : angle       0.48400 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A  437 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7260 (tp-100)
REVERT: A  543 MET cc_start: 0.6795 (pmm) cc_final: 0.6548 (ptp)
REVERT: A  560 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8550 (tp40)
REVERT: A  800 PHE cc_start: 0.8067 (t80) cc_final: 0.7768 (t80)
REVERT: A  810 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8518 (m)
REVERT: A  876 MET cc_start: 0.8937 (tpp) cc_final: 0.8732 (tpp)
REVERT: A  886 MET cc_start: 0.8002 (tmm) cc_final: 0.7448 (tmm)
REVERT: A  925 TYR cc_start: 0.8118 (m-10) cc_final: 0.7901 (m-80)
REVERT: A  938 MET cc_start: 0.8285 (tpp) cc_final: 0.7681 (tpp)
REVERT: A 1052 PHE cc_start: 0.8846 (t80) cc_final: 0.8594 (t80)
REVERT: A 1066 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (t70)
REVERT: B  416 MET cc_start: 0.6153 (tmm) cc_final: 0.4665 (ttt)
REVERT: B  437 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7324 (tp-100)
REVERT: B  560 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8560 (tp40)
REVERT: B  606 MET cc_start: 0.5699 (mtm) cc_final: 0.5068 (mtt)
REVERT: B  810 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8510 (m)
REVERT: B  886 MET cc_start: 0.8249 (ttp) cc_final: 0.7584 (tmm)
REVERT: B  925 TYR cc_start: 0.8098 (m-10) cc_final: 0.7875 (m-80)
REVERT: B  938 MET cc_start: 0.8285 (tpp) cc_final: 0.7667 (tpp)
  outliers start: 16
  outliers final: 9
  residues processed: 129
  average time/residue: 0.1956
  time to fit residues: 37.6595
Evaluate side-chains
  122 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  850 PHE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1066 ASP
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  810 SER
Chi-restraints excluded: chain B residue  850 PHE
Chi-restraints excluded: chain B residue 1029 ASP
Chi-restraints excluded: chain B residue 1066 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 65 optimal weight:   30.0000
   chunk 92 optimal weight:    0.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 472 ASN
B 472 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.126460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.093278 restraints weight = 20493.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.096897 restraints weight = 8741.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.099110 restraints weight = 5252.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9642  Z= 0.149
  Angle     :  0.529   7.991  13172  Z= 0.278
  Chirality :  0.040   0.190   1550
  Planarity :  0.003   0.032   1612
  Dihedral  : 11.745 123.627   1470
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.79 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.25), residues: 1234
  helix:  2.30 (0.19), residues: 746
  sheet: -0.41 (0.44), residues: 152
  loop : -0.74 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 806 
 HIS   0.003   0.001   HIS B 828 
 PHE   0.021   0.001   PHE B1052 
 TYR   0.011   0.001   TYR A 613 
 ARG   0.004   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  625)
  hydrogen bonds       : angle       4.05526 ( 1803)
  covalent geometry    : bond        0.00337 ( 9642)
  covalent geometry    : angle       0.52927 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.167 
Fit side-chains
REVERT: A  437 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7297 (tp-100)
REVERT: A  543 MET cc_start: 0.6752 (pmm) cc_final: 0.6507 (ptp)
REVERT: A  560 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8551 (tp40)
REVERT: A  606 MET cc_start: 0.5825 (mtm) cc_final: 0.5173 (mtt)
REVERT: A  800 PHE cc_start: 0.8144 (t80) cc_final: 0.7809 (t80)
REVERT: A  810 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8553 (m)
REVERT: A  886 MET cc_start: 0.7980 (tmm) cc_final: 0.7419 (tmm)
REVERT: B  437 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7355 (tp-100)
REVERT: B  560 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8564 (tp40)
REVERT: B  606 MET cc_start: 0.5836 (mtm) cc_final: 0.5198 (mtt)
REVERT: B  876 MET cc_start: 0.8976 (tpp) cc_final: 0.8706 (tpp)
REVERT: B  886 MET cc_start: 0.8280 (ttp) cc_final: 0.7570 (tmm)
  outliers start: 18
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1827
  time to fit residues: 33.3525
Evaluate side-chains
  120 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  850 PHE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  946 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  850 PHE
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue 1029 ASP
Chi-restraints excluded: chain B residue 1066 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   overall best weight:    2.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.123979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.090586 restraints weight = 20868.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.093689 restraints weight = 9601.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.095664 restraints weight = 6081.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9642  Z= 0.179
  Angle     :  0.561   6.670  13172  Z= 0.292
  Chirality :  0.041   0.181   1550
  Planarity :  0.003   0.032   1612
  Dihedral  : 10.783 112.814   1470
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.02 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.25), residues: 1234
  helix:  2.22 (0.19), residues: 746
  sheet: -0.47 (0.44), residues: 152
  loop : -0.81 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 806 
 HIS   0.005   0.001   HIS B 937 
 PHE   0.022   0.002   PHE A1052 
 TYR   0.020   0.001   TYR A 925 
 ARG   0.005   0.001   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04285 (  625)
  hydrogen bonds       : angle       4.16566 ( 1803)
  covalent geometry    : bond        0.00412 ( 9642)
  covalent geometry    : angle       0.56096 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 1.078 
Fit side-chains
REVERT: A  437 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7287 (tp-100)
REVERT: A  606 MET cc_start: 0.5747 (mtm) cc_final: 0.5085 (mtt)
REVERT: A  810 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8681 (m)
REVERT: A  876 MET cc_start: 0.9025 (tpp) cc_final: 0.8814 (tpp)
REVERT: A  886 MET cc_start: 0.7958 (tmm) cc_final: 0.7389 (tmm)
REVERT: B  437 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7392 (tp-100)
REVERT: B  560 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8556 (tp40)
REVERT: B  606 MET cc_start: 0.5786 (mtm) cc_final: 0.5121 (mtt)
REVERT: B  810 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8670 (m)
REVERT: B  876 MET cc_start: 0.8958 (tpp) cc_final: 0.8685 (tpp)
REVERT: B  886 MET cc_start: 0.8241 (ttp) cc_final: 0.7587 (tmm)
  outliers start: 21
  outliers final: 16
  residues processed: 114
  average time/residue: 0.1672
  time to fit residues: 29.4460
Evaluate side-chains
  121 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 HIS
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  850 PHE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  946 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  810 SER
Chi-restraints excluded: chain B residue  850 PHE
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue  946 ILE
Chi-restraints excluded: chain B residue 1029 ASP
Chi-restraints excluded: chain B residue 1066 ASP
Chi-restraints excluded: chain B residue 1114 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 14 optimal weight:    0.2980
   chunk 83 optimal weight:    9.9990
   chunk 111 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 79 optimal weight:    8.9990
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.127269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.094147 restraints weight = 20357.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.097763 restraints weight = 8690.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.099985 restraints weight = 5238.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9642  Z= 0.121
  Angle     :  0.525   7.290  13172  Z= 0.268
  Chirality :  0.040   0.182   1550
  Planarity :  0.003   0.032   1612
  Dihedral  : 10.128  98.302   1470
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.13 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.25), residues: 1234
  helix:  2.38 (0.19), residues: 744
  sheet: -0.42 (0.43), residues: 152
  loop : -0.71 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 806 
 HIS   0.005   0.001   HIS B 828 
 PHE   0.017   0.001   PHE B 772 
 TYR   0.018   0.001   TYR A 925 
 ARG   0.009   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03964 (  625)
  hydrogen bonds       : angle       4.04116 ( 1803)
  covalent geometry    : bond        0.00268 ( 9642)
  covalent geometry    : angle       0.52452 (13172)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.138 
Fit side-chains
REVERT: A  437 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7282 (tp-100)
REVERT: A  800 PHE cc_start: 0.8066 (t80) cc_final: 0.7768 (t80)
REVERT: A  810 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8549 (m)
REVERT: A  876 MET cc_start: 0.8981 (tpp) cc_final: 0.8737 (tpp)
REVERT: A  886 MET cc_start: 0.7968 (tmm) cc_final: 0.7406 (tmm)
REVERT: A 1052 PHE cc_start: 0.8949 (t80) cc_final: 0.8614 (t80)
REVERT: B  416 MET cc_start: 0.6702 (tmm) cc_final: 0.5010 (ttt)
REVERT: B  437 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7398 (tp-100)
REVERT: B  560 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8528 (tp40)
REVERT: B  606 MET cc_start: 0.5569 (mtm) cc_final: 0.4934 (mtt)
REVERT: B  876 MET cc_start: 0.8995 (tpp) cc_final: 0.8729 (tpp)
REVERT: B  886 MET cc_start: 0.8328 (ttp) cc_final: 0.7663 (tmm)
  outliers start: 18
  outliers final: 16
  residues processed: 116
  average time/residue: 0.1604
  time to fit residues: 28.8296
Evaluate side-chains
  125 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 HIS
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  850 PHE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  804 ILE
Chi-restraints excluded: chain B residue  850 PHE
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue 1029 ASP
Chi-restraints excluded: chain B residue 1066 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    2.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.125141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.091837 restraints weight = 20912.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.094993 restraints weight = 9594.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.097008 restraints weight = 6024.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9642  Z= 0.160
  Angle     :  0.546   6.765  13172  Z= 0.282
  Chirality :  0.040   0.183   1550
  Planarity :  0.003   0.032   1612
  Dihedral  : 10.092  89.224   1470
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.02 %
    Favored  : 78.30 %
  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:  1.76 (0.24), residues: 1234
  helix:  2.35 (0.19), residues: 744
  sheet: -0.46 (0.43), residues: 152
  loop : -0.75 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 806 
 HIS   0.004   0.001   HIS B 828 
 PHE   0.020   0.001   PHE A1052 
 TYR   0.019   0.001   TYR B 925 
 ARG   0.008   0.001   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04103 (  625)
  hydrogen bonds       : angle       4.09328 ( 1803)
  covalent geometry    : bond        0.00368 ( 9642)
  covalent geometry    : angle       0.54585 (13172)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3329.58 seconds
wall clock time: 60 minutes 22.10 seconds (3622.10 seconds total)