Starting phenix.real_space_refine
on Tue Jul 29 21:24:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k3v_36862/07_2025/8k3v_36862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k3v_36862/07_2025/8k3v_36862.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2025/8k3v_36862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2025/8k3v_36862.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2025/8k3v_36862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2025/8k3v_36862.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.081
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      2      5.21       5
     S      72      5.16       5
     C    7366      2.51       5
     N    1802      2.21       5
     O    2000      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11248
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 700, 5536
          Classifications: {'peptide': 700}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 20, 'TRANS': 679}
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 209
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 108
    Chain: "A"
      Number of atoms: 136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 136
          Unusual residues: {' MG': 1, 'POV': 2, 'UD1': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 39
          Unusual residues: {'UD1': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 13.06, per 1000 atoms: 1.16
  Number of scatterers: 11248
  At special positions: 0
  Unit cell: (132.5, 92.22, 111.3, 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      72     16.00
     P       6     15.00
     Mg      2     11.99
     O    2000      8.00
     N    1802      7.00
     C    7366      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.79
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2668

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 4 sheets defined
      64.7% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 392 through 401
    Processing helix  chain 'A' and resid 410 through 413
      removed outlier: 3.610A  pdb=" N   PHE A 413 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 410 through 413'
    Processing helix  chain 'A' and resid 424 through 428
      removed outlier: 3.862A  pdb=" N   LEU A 428 " --> pdb=" O   PRO A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 439
    Processing helix  chain 'A' and resid 458 through 478
      removed outlier: 3.516A  pdb=" N   LEU A 462 " --> pdb=" O   ASP A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 491
    Processing helix  chain 'A' and resid 506 through 517
      removed outlier: 3.550A  pdb=" N   LEU A 512 " --> pdb=" O   ARG A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 588
    Processing helix  chain 'A' and resid 588 through 594
      removed outlier: 3.554A  pdb=" N   LEU A 592 " --> pdb=" O   GLY A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 617
    Processing helix  chain 'A' and resid 618 through 621
      removed outlier: 4.033A  pdb=" N   ASN A 621 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 618 through 621'
    Processing helix  chain 'A' and resid 636 through 643
      removed outlier: 5.908A  pdb=" N   LYS A 641 " --> pdb=" O   ARG A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 669
      removed outlier: 3.633A  pdb=" N   SER A 649 " --> pdb=" O   PRO A 645 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLN A 650 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   LYS A 662 " --> pdb=" O   ASN A 658 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   THR A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
      removed outlier: 3.797A  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 696
    Processing helix  chain 'A' and resid 706 through 712
    Processing helix  chain 'A' and resid 713 through 716
      removed outlier: 3.831A  pdb=" N   GLU A 716 " --> pdb=" O   TYR A 713 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 713 through 716'
    Processing helix  chain 'A' and resid 717 through 726
      removed outlier: 3.749A  pdb=" N   CYS A 721 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 774
      removed outlier: 4.074A  pdb=" N   ARG A 759 " --> pdb=" O   LEU A 755 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TRP A 760 " --> pdb=" O   GLN A 756 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASN A 762 " --> pdb=" O   ARG A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 781
      removed outlier: 3.564A  pdb=" N   SER A 781 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 807
      removed outlier: 3.529A  pdb=" N   PHE A 807 " --> pdb=" O   LEU A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 828
      removed outlier: 3.736A  pdb=" N   PHE A 813 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 856
      removed outlier: 3.553A  pdb=" N   LEU A 834 " --> pdb=" O   ALA A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 894
      removed outlier: 3.956A  pdb=" N   TYR A 865 " --> pdb=" O   THR A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 932
      removed outlier: 4.529A  pdb=" N   ILE A 914 " --> pdb=" O   ALA A 910 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 915 " --> pdb=" O   PHE A 911 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 936 through 941
      removed outlier: 3.549A  pdb=" N   SER A 941 " --> pdb=" O   HIS A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 948
    Processing helix  chain 'A' and resid 949 through 955
    Processing helix  chain 'A' and resid 955 through 963
    Processing helix  chain 'A' and resid 997 through 1012
      removed outlier: 3.586A  pdb=" N   ILE A1001 " --> pdb=" O   SER A 997 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR A1005 " --> pdb=" O   ILE A1001 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LYS A1007 " --> pdb=" O   ALA A1003 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   TYR A1008 " --> pdb=" O   ASN A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1027 through 1060
    Processing helix  chain 'A' and resid 1063 through 1074
    Processing helix  chain 'A' and resid 1091 through 1127
      removed outlier: 4.200A  pdb=" N   SER A1095 " --> pdb=" O   THR A1091 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A1102 " --> pdb=" O   PHE A1098 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 401
    Processing helix  chain 'B' and resid 410 through 413
      removed outlier: 3.610A  pdb=" N   PHE B 413 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 410 through 413'
    Processing helix  chain 'B' and resid 424 through 428
      removed outlier: 3.862A  pdb=" N   LEU B 428 " --> pdb=" O   PRO B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 439
    Processing helix  chain 'B' and resid 458 through 478
      removed outlier: 3.516A  pdb=" N   LEU B 462 " --> pdb=" O   ASP B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 491
    Processing helix  chain 'B' and resid 506 through 517
      removed outlier: 3.551A  pdb=" N   LEU B 512 " --> pdb=" O   ARG B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 588
    Processing helix  chain 'B' and resid 588 through 594
      removed outlier: 3.554A  pdb=" N   LEU B 592 " --> pdb=" O   GLY B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 617
    Processing helix  chain 'B' and resid 618 through 621
      removed outlier: 4.033A  pdb=" N   ASN B 621 " --> pdb=" O   GLU B 618 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 618 through 621'
    Processing helix  chain 'B' and resid 636 through 643
      removed outlier: 5.909A  pdb=" N   LYS B 641 " --> pdb=" O   ARG B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 644 through 669
      removed outlier: 3.632A  pdb=" N   SER B 649 " --> pdb=" O   PRO B 645 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLN B 650 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LYS B 662 " --> pdb=" O   ASN B 658 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   THR B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
      removed outlier: 3.797A  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 696
    Processing helix  chain 'B' and resid 706 through 712
    Processing helix  chain 'B' and resid 713 through 716
      removed outlier: 3.831A  pdb=" N   GLU B 716 " --> pdb=" O   TYR B 713 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 713 through 716'
    Processing helix  chain 'B' and resid 717 through 726
      removed outlier: 3.749A  pdb=" N   CYS B 721 " --> pdb=" O   ASP B 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 749 through 774
      removed outlier: 4.074A  pdb=" N   ARG B 759 " --> pdb=" O   LEU B 755 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TRP B 760 " --> pdb=" O   GLN B 756 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN B 762 " --> pdb=" O   ARG B 758 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 781
      removed outlier: 3.565A  pdb=" N   SER B 781 " --> pdb=" O   VAL B 778 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 784 through 807
      removed outlier: 3.529A  pdb=" N   PHE B 807 " --> pdb=" O   LEU B 803 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 807 through 828
      removed outlier: 3.736A  pdb=" N   PHE B 813 " --> pdb=" O   LEU B 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 856
      removed outlier: 3.553A  pdb=" N   LEU B 834 " --> pdb=" O   ALA B 830 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 861 through 894
      removed outlier: 3.956A  pdb=" N   TYR B 865 " --> pdb=" O   THR B 861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 909 through 932
      removed outlier: 4.529A  pdb=" N   ILE B 914 " --> pdb=" O   ALA B 910 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL B 915 " --> pdb=" O   PHE B 911 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 936 through 941
      removed outlier: 3.549A  pdb=" N   SER B 941 " --> pdb=" O   HIS B 937 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 948
    Processing helix  chain 'B' and resid 949 through 955
    Processing helix  chain 'B' and resid 955 through 963
    Processing helix  chain 'B' and resid 997 through 1012
      removed outlier: 3.586A  pdb=" N   ILE B1001 " --> pdb=" O   SER B 997 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR B1005 " --> pdb=" O   ILE B1001 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LYS B1007 " --> pdb=" O   ALA B1003 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   TYR B1008 " --> pdb=" O   ASN B1004 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1027 through 1060
    Processing helix  chain 'B' and resid 1063 through 1074
    Processing helix  chain 'B' and resid 1091 through 1127
      removed outlier: 4.200A  pdb=" N   SER B1095 " --> pdb=" O   THR B1091 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU B1102 " --> pdb=" O   PHE B1098 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 386 through 390
      removed outlier: 7.694A  pdb=" N   PHE A 415 " --> pdb=" O   THR A 541 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   THR A 541 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   HIS A 540 " --> pdb=" O   LEU A 567 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   GLN A 566 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LEU A 448 " --> pdb=" O   VAL A 494 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   CYS A 496 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU A 450 " --> pdb=" O   CYS A 496 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ILE A 498 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL A 452 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   MET A 449 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   LEU A 601 " --> pdb=" O   MET A 449 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   VAL A 451 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   GLY A 625 " --> pdb=" O   ARG A 682 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   LYS A 735 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ALA A 627 " --> pdb=" O   LYS A 735 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   CYS A 737 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLY A 629 " --> pdb=" O   CYS A 737 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   SER A 739 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   ILE A 631 " --> pdb=" O   SER A 739 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   TYR A 741 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 9.951A  pdb=" N   THR A 633 " --> pdb=" O   TYR A 741 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   SER A 743 " --> pdb=" O   THR A 633 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 549
      removed outlier: 5.670A  pdb=" N   ILE A 546 " --> pdb=" O   GLU A 557 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLU A 557 " --> pdb=" O   ILE A 546 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASN A 548 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 386 through 390
      removed outlier: 7.693A  pdb=" N   PHE B 415 " --> pdb=" O   THR B 541 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   THR B 541 " --> pdb=" O   PHE B 415 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   HIS B 540 " --> pdb=" O   LEU B 567 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   GLN B 566 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LEU B 448 " --> pdb=" O   VAL B 494 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   CYS B 496 " --> pdb=" O   LEU B 448 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU B 450 " --> pdb=" O   CYS B 496 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ILE B 498 " --> pdb=" O   LEU B 450 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL B 452 " --> pdb=" O   ILE B 498 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   MET B 449 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   LEU B 601 " --> pdb=" O   MET B 449 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   VAL B 451 " --> pdb=" O   LEU B 601 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   GLY B 625 " --> pdb=" O   ARG B 682 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   LYS B 735 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ALA B 627 " --> pdb=" O   LYS B 735 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   CYS B 737 " --> pdb=" O   ALA B 627 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLY B 629 " --> pdb=" O   CYS B 737 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   SER B 739 " --> pdb=" O   GLY B 629 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   ILE B 631 " --> pdb=" O   SER B 739 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   TYR B 741 " --> pdb=" O   ILE B 631 " (cutoff:3.500A)
      removed outlier: 9.951A  pdb=" N   THR B 633 " --> pdb=" O   TYR B 741 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   SER B 743 " --> pdb=" O   THR B 633 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 545 through 549
      removed outlier: 5.671A  pdb=" N   ILE B 546 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLU B 557 " --> pdb=" O   ILE B 546 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASN B 548 " --> pdb=" O   SER B 555 " (cutoff:3.500A)

    664 hydrogen bonds defined for protein.
    1902 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: 3.98

  Time building geometry restraints manager: 3.37 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1706
        1.31 -     1.43: 3298
        1.43 -     1.56: 6390
        1.56 -     1.69: 12
        1.69 -     1.81: 112
  Bond restraints: 11518
  Sorted by residual:
  bond pdb=" C4  UD1 A1503 "
       pdb=" N3  UD1 A1503 "
    ideal  model  delta    sigma   weight residual
    1.386  1.277  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C4  UD1 B1502 "
       pdb=" N3  UD1 B1502 "
    ideal  model  delta    sigma   weight residual
    1.386  1.278  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" C2B UD1 A1503 "
       pdb=" C3B UD1 A1503 "
    ideal  model  delta    sigma   weight residual
    1.533  1.461  0.072 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" C2B UD1 B1502 "
       pdb=" C3B UD1 B1502 "
    ideal  model  delta    sigma   weight residual
    1.533  1.462  0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C4  UD1 B1502 "
       pdb=" C5  UD1 B1502 "
    ideal  model  delta    sigma   weight residual
    1.441  1.377  0.064 2.00e-02 2.50e+03 1.01e+01
  ... (remaining 11513 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.19: 15495
        4.19 -     8.37: 83
        8.37 -    12.56: 24
       12.56 -    16.74: 6
       16.74 -    20.93: 2
  Bond angle restraints: 15610
  Sorted by residual:
  angle pdb=" C1B UD1 A1503 "
        pdb=" C2B UD1 A1503 "
        pdb=" O2' UD1 A1503 "
      ideal   model   delta    sigma   weight residual
     109.46  130.39  -20.93 3.00e+00 1.11e-01 4.87e+01
  angle pdb=" C1B UD1 B1502 "
        pdb=" C2B UD1 B1502 "
        pdb=" O2' UD1 B1502 "
      ideal   model   delta    sigma   weight residual
     109.46  130.38  -20.92 3.00e+00 1.11e-01 4.86e+01
  angle pdb=" C2B UD1 B1502 "
        pdb=" C1B UD1 B1502 "
        pdb=" O4B UD1 B1502 "
      ideal   model   delta    sigma   weight residual
     106.74   91.14   15.60 3.00e+00 1.11e-01 2.71e+01
  angle pdb=" C2B UD1 A1503 "
        pdb=" C1B UD1 A1503 "
        pdb=" O4B UD1 A1503 "
      ideal   model   delta    sigma   weight residual
     106.74   91.15   15.59 3.00e+00 1.11e-01 2.70e+01
  angle pdb=" N   ARG B 912 "
        pdb=" CA  ARG B 912 "
        pdb=" C   ARG B 912 "
      ideal   model   delta    sigma   weight residual
     112.54  106.72    5.82 1.22e+00 6.72e-01 2.28e+01
  ... (remaining 15605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.01: 6543
       33.01 -    66.02: 243
       66.02 -    99.04: 32
       99.04 -   132.05: 6
      132.05 -   165.06: 2
  Dihedral angle restraints: 6826
    sinusoidal: 2702
      harmonic: 4124
  Sorted by residual:
  dihedral pdb=" C27 POV A1502 "
           pdb=" C28 POV A1502 "
           pdb=" C29 POV A1502 "
           pdb="C210 POV A1502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     127.48  -67.46 -165.06     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C27 POV A1504 "
           pdb=" C28 POV A1504 "
           pdb=" C29 POV A1504 "
           pdb="C210 POV A1504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     127.48  -67.55 -164.97     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" CA  ALA A 715 "
           pdb=" C   ALA A 715 "
           pdb=" N   GLU A 716 "
           pdb=" CA  GLU A 716 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 6823 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1526
       0.090 -    0.181: 214
       0.181 -    0.271: 20
       0.271 -    0.362: 6
       0.362 -    0.452: 4
  Chirality restraints: 1770
  Sorted by residual:
  chirality pdb=" C2B UD1 B1502 "
            pdb=" C1B UD1 B1502 "
            pdb=" C3B UD1 B1502 "
            pdb=" O2' UD1 B1502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.17   -0.45 2.00e-01 2.50e+01 5.11e+00
  chirality pdb=" C2B UD1 A1503 "
            pdb=" C1B UD1 A1503 "
            pdb=" C3B UD1 A1503 "
            pdb=" O2' UD1 A1503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.17   -0.45 2.00e-01 2.50e+01 5.11e+00
  chirality pdb=" C5' UD1 B1502 "
            pdb=" C4' UD1 B1502 "
            pdb=" C6' UD1 B1502 "
            pdb=" O5' UD1 B1502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.10   -0.42 2.00e-01 2.50e+01 4.40e+00
  ... (remaining 1767 not shown)

  Planarity restraints: 1900
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2' UD1 A1503 "    0.170 2.00e-02 2.50e+03   1.37e-01 2.33e+02
        pdb=" C7' UD1 A1503 "   -0.055 2.00e-02 2.50e+03
        pdb=" C8' UD1 A1503 "    0.133 2.00e-02 2.50e+03
        pdb=" N2' UD1 A1503 "   -0.205 2.00e-02 2.50e+03
        pdb=" O7' UD1 A1503 "   -0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2' UD1 B1502 "    0.169 2.00e-02 2.50e+03   1.37e-01 2.33e+02
        pdb=" C7' UD1 B1502 "   -0.054 2.00e-02 2.50e+03
        pdb=" C8' UD1 B1502 "    0.133 2.00e-02 2.50e+03
        pdb=" N2' UD1 B1502 "   -0.205 2.00e-02 2.50e+03
        pdb=" O7' UD1 B1502 "   -0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV A1502 "   -0.041 2.00e-02 2.50e+03   7.55e-02 5.70e+01
        pdb=" C29 POV A1502 "    0.099 2.00e-02 2.50e+03
        pdb="C210 POV A1502 "   -0.099 2.00e-02 2.50e+03
        pdb="C211 POV A1502 "    0.040 2.00e-02 2.50e+03
  ... (remaining 1897 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1947
        2.76 -     3.30: 11091
        3.30 -     3.83: 18126
        3.83 -     4.37: 21569
        4.37 -     4.90: 38362
  Nonbonded interactions: 91095
  Sorted by model distance:
  nonbonded pdb=" O   HIS B 706 "
            pdb=" OG  SER B 710 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   HIS A 706 "
            pdb=" OG  SER A 710 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O3' UD1 B1502 "
            pdb=" O7' UD1 B1502 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O3' UD1 A1503 "
            pdb=" O7' UD1 A1503 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   THR B 453 "
            pdb=" O3B UD1 B1502 "
     model   vdw
     2.307 3.040
  ... (remaining 91090 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 381 through 1127 or resid 1501))
  selection = (chain 'B' and (resid 381 through 1127 or resid 1501))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     36.090
  Find NCS groups from input model:        0.560
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
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      :  0.008   0.109  11518  Z= 0.469
  Angle     :  1.065  20.927  15610  Z= 0.623
  Chirality :  0.066   0.452   1770
  Planarity :  0.006   0.137   1900
  Dihedral  : 17.586 165.061   4158
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  :  2.37 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.15 %
  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: -0.31 (0.22), residues: 1376
  helix:  0.99 (0.19), residues: 760
  sheet: -1.44 (0.47), residues: 112
  loop : -1.77 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 779 
 HIS   0.004   0.001   HIS B 783 
 PHE   0.020   0.002   PHE B 885 
 TYR   0.040   0.002   TYR B 696 
 ARG   0.005   0.001   ARG B 718 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15935 (  664)
  hydrogen bonds       : angle       7.17806 ( 1902)
  covalent geometry    : bond        0.00790 (11518)
  covalent geometry    : angle       1.06502 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 172
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A  455 TYR cc_start: 0.8101 (t80) cc_final: 0.7559 (t80)
REVERT: A  471 ASP cc_start: 0.7287 (m-30) cc_final: 0.6795 (m-30)
REVERT: A  610 ASP cc_start: 0.7777 (t70) cc_final: 0.7238 (t0)
REVERT: A  672 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8145 (t)
REVERT: A  989 THR cc_start: 0.5520 (OUTLIER) cc_final: 0.5282 (p)
REVERT: A  991 LYS cc_start: 0.3042 (OUTLIER) cc_final: 0.2651 (mmtt)
REVERT: A  992 MET cc_start: 0.0382 (OUTLIER) cc_final: 0.0090 (pmm)
REVERT: A  998 SER cc_start: 0.4331 (OUTLIER) cc_final: 0.3757 (t)
REVERT: B  416 MET cc_start: 0.7878 (tmm) cc_final: 0.7641 (tmm)
REVERT: B  455 TYR cc_start: 0.8127 (t80) cc_final: 0.7661 (t80)
REVERT: B  464 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7174 (mtp-110)
REVERT: B  471 ASP cc_start: 0.7176 (m-30) cc_final: 0.6794 (m-30)
REVERT: B  610 ASP cc_start: 0.7753 (t70) cc_final: 0.7237 (t0)
REVERT: B  700 MET cc_start: 0.5425 (tmm) cc_final: 0.5097 (tmm)
REVERT: B  998 SER cc_start: 0.3779 (OUTLIER) cc_final: 0.3309 (t)
  outliers start: 58
  outliers final: 13
  residues processed: 206
  average time/residue: 0.2627
  time to fit residues: 75.3785
Evaluate side-chains
  140 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  880 ILE
Chi-restraints excluded: chain A residue  985 THR
Chi-restraints excluded: chain A residue  986 GLU
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue  998 SER
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  656 MET
Chi-restraints excluded: chain B residue  780 SER
Chi-restraints excluded: chain B residue  880 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue  986 GLU
Chi-restraints excluded: chain B residue  998 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.9980
   chunk 106 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 66 optimal weight:    0.1980
   chunk 81 optimal weight:    0.9990
   chunk 127 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 540 HIS
A 692 GLN
A1004 ASN
B 540 HIS
B 706 HIS
B1004 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.160014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.126198 restraints weight = 12866.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.05
r_work: 0.3329 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11518  Z= 0.124
  Angle     :  0.506   6.120  15610  Z= 0.274
  Chirality :  0.040   0.136   1770
  Planarity :  0.004   0.045   1900
  Dihedral  : 10.955 104.491   1732
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  7.36 %
    Favored  : 90.69 %
  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:  0.94 (0.23), residues: 1376
  helix:  1.85 (0.19), residues: 786
  sheet: -0.53 (0.44), residues: 142
  loop : -1.20 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 779 
 HIS   0.003   0.001   HIS A 459 
 PHE   0.017   0.001   PHE A1052 
 TYR   0.011   0.001   TYR B 925 
 ARG   0.003   0.000   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04441 (  664)
  hydrogen bonds       : angle       4.47013 ( 1902)
  covalent geometry    : bond        0.00274 (11518)
  covalent geometry    : angle       0.50551 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 1.220 
Fit side-chains
REVERT: A  455 TYR cc_start: 0.8138 (t80) cc_final: 0.7563 (t80)
REVERT: A  464 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7534 (mtp180)
REVERT: A  471 ASP cc_start: 0.7878 (m-30) cc_final: 0.7526 (m-30)
REVERT: A  610 ASP cc_start: 0.7781 (t70) cc_final: 0.7188 (t0)
REVERT: A  639 PHE cc_start: 0.8256 (m-80) cc_final: 0.8052 (m-80)
REVERT: A  859 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8307 (mppt)
REVERT: A  982 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7214 (mp)
REVERT: A  989 THR cc_start: 0.6389 (OUTLIER) cc_final: 0.6131 (p)
REVERT: A  991 LYS cc_start: 0.3695 (OUTLIER) cc_final: 0.3149 (mttm)
REVERT: B  455 TYR cc_start: 0.8187 (t80) cc_final: 0.7628 (t80)
REVERT: B  471 ASP cc_start: 0.7933 (m-30) cc_final: 0.7563 (m-30)
REVERT: B  529 ASN cc_start: 0.7075 (m-40) cc_final: 0.6855 (m-40)
REVERT: B  610 ASP cc_start: 0.7803 (t70) cc_final: 0.7256 (t0)
REVERT: B  700 MET cc_start: 0.5736 (tmm) cc_final: 0.5429 (tmm)
REVERT: B  859 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8212 (mppt)
REVERT: B  982 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7035 (mp)
  outliers start: 23
  outliers final: 11
  residues processed: 150
  average time/residue: 0.3146
  time to fit residues: 66.3280
Evaluate side-chains
  130 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  559 ASN
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 126 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 66 optimal weight:    0.1980
   chunk 57 optimal weight:    0.3980
   chunk 96 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 137 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 472 ASN
A 963 ASN
A1004 ASN
B 963 ASN
B1004 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.154880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.120592 restraints weight = 13162.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.11
r_work: 0.3237 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11518  Z= 0.199
  Angle     :  0.554   7.755  15610  Z= 0.298
  Chirality :  0.043   0.151   1770
  Planarity :  0.004   0.045   1900
  Dihedral  :  9.755  85.704   1708
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.90 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.23), residues: 1376
  helix:  1.88 (0.19), residues: 786
  sheet: -0.53 (0.43), residues: 142
  loop : -1.44 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 779 
 HIS   0.007   0.002   HIS B 459 
 PHE   0.020   0.002   PHE B1052 
 TYR   0.014   0.002   TYR A 925 
 ARG   0.004   0.001   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05275 (  664)
  hydrogen bonds       : angle       4.46262 ( 1902)
  covalent geometry    : bond        0.00477 (11518)
  covalent geometry    : angle       0.55416 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 2.547 
Fit side-chains
REVERT: A  455 TYR cc_start: 0.8341 (t80) cc_final: 0.7976 (t80)
REVERT: A  471 ASP cc_start: 0.7845 (m-30) cc_final: 0.7412 (m-30)
REVERT: A  620 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7721 (mtm180)
REVERT: A  800 PHE cc_start: 0.7819 (t80) cc_final: 0.7556 (t80)
REVERT: A  982 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7202 (mp)
REVERT: A  991 LYS cc_start: 0.4171 (OUTLIER) cc_final: 0.3093 (mttm)
REVERT: A 1105 VAL cc_start: 0.8094 (t) cc_final: 0.7849 (p)
REVERT: B  466 LEU cc_start: 0.8259 (mm) cc_final: 0.8020 (mp)
REVERT: B  471 ASP cc_start: 0.7846 (m-30) cc_final: 0.7397 (m-30)
REVERT: B  529 ASN cc_start: 0.7418 (m-40) cc_final: 0.7132 (m-40)
REVERT: B  620 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7760 (mtm180)
REVERT: B  641 LYS cc_start: 0.8524 (mttm) cc_final: 0.7860 (mtmt)
REVERT: B  700 MET cc_start: 0.5867 (tmm) cc_final: 0.5291 (tmm)
REVERT: B  859 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8345 (mppt)
REVERT: B  982 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7005 (mp)
REVERT: B 1105 VAL cc_start: 0.8058 (t) cc_final: 0.7818 (p)
  outliers start: 21
  outliers final: 13
  residues processed: 148
  average time/residue: 0.2939
  time to fit residues: 65.6132
Evaluate side-chains
  133 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  397 ASP
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  559 ASN
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 123 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 127 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A1004 ASN
B1004 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.155795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.121941 restraints weight = 12980.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.06
r_work: 0.3272 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11518  Z= 0.135
  Angle     :  0.474   6.403  15610  Z= 0.258
  Chirality :  0.040   0.137   1770
  Planarity :  0.003   0.042   1900
  Dihedral  :  9.321  77.119   1706
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.17 %
    Favored  : 87.06 %
  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:  1.22 (0.23), residues: 1376
  helix:  2.16 (0.18), residues: 786
  sheet: -0.38 (0.43), residues: 148
  loop : -1.31 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 779 
 HIS   0.004   0.001   HIS A 828 
 PHE   0.016   0.001   PHE A1052 
 TYR   0.012   0.001   TYR A 925 
 ARG   0.002   0.000   ARG A 464 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04287 (  664)
  hydrogen bonds       : angle       4.14316 ( 1902)
  covalent geometry    : bond        0.00313 (11518)
  covalent geometry    : angle       0.47425 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 1.103 
Fit side-chains
REVERT: A  455 TYR cc_start: 0.8433 (t80) cc_final: 0.8190 (t80)
REVERT: A  471 ASP cc_start: 0.7825 (m-30) cc_final: 0.7366 (m-30)
REVERT: A  699 ILE cc_start: 0.4366 (OUTLIER) cc_final: 0.4122 (tp)
REVERT: A  758 ARG cc_start: 0.8797 (tmm160) cc_final: 0.8529 (ttt-90)
REVERT: A  800 PHE cc_start: 0.7849 (t80) cc_final: 0.7590 (t80)
REVERT: A  982 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7209 (mp)
REVERT: A  991 LYS cc_start: 0.4047 (OUTLIER) cc_final: 0.3281 (ptpt)
REVERT: A 1105 VAL cc_start: 0.8082 (t) cc_final: 0.7841 (p)
REVERT: B  455 TYR cc_start: 0.8432 (t80) cc_final: 0.8142 (t80)
REVERT: B  471 ASP cc_start: 0.7811 (m-30) cc_final: 0.7395 (m-30)
REVERT: B  574 GLN cc_start: 0.8052 (pt0) cc_final: 0.7811 (pt0)
REVERT: B  578 LYS cc_start: 0.7871 (tttt) cc_final: 0.7628 (ttpp)
REVERT: B  700 MET cc_start: 0.5889 (tmm) cc_final: 0.5283 (tmm)
REVERT: B  982 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.6931 (mp)
REVERT: B 1105 VAL cc_start: 0.8093 (t) cc_final: 0.7853 (p)
  outliers start: 21
  outliers final: 10
  residues processed: 136
  average time/residue: 0.2349
  time to fit residues: 46.0126
Evaluate side-chains
  130 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  559 ASN
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 138 optimal weight:    2.9990
   chunk 139 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 135 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0000
   chunk 27 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A1004 ASN
B1004 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.156292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.122448 restraints weight = 12942.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.03
r_work: 0.3277 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11518  Z= 0.124
  Angle     :  0.454   6.062  15610  Z= 0.246
  Chirality :  0.039   0.133   1770
  Planarity :  0.003   0.040   1900
  Dihedral  :  8.958  74.690   1700
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.84 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.23), residues: 1376
  helix:  2.41 (0.18), residues: 784
  sheet: -0.40 (0.47), residues: 128
  loop : -1.27 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 779 
 HIS   0.003   0.001   HIS A 828 
 PHE   0.016   0.001   PHE B1052 
 TYR   0.011   0.001   TYR B 925 
 ARG   0.002   0.000   ARG B 759 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04059 (  664)
  hydrogen bonds       : angle       4.02300 ( 1902)
  covalent geometry    : bond        0.00286 (11518)
  covalent geometry    : angle       0.45388 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 1.215 
Fit side-chains
REVERT: A  386 VAL cc_start: 0.8044 (m) cc_final: 0.7734 (t)
REVERT: A  455 TYR cc_start: 0.8406 (t80) cc_final: 0.8142 (t80)
REVERT: A  471 ASP cc_start: 0.7852 (m-30) cc_final: 0.7382 (m-30)
REVERT: A  758 ARG cc_start: 0.8767 (tmm160) cc_final: 0.8509 (ttt-90)
REVERT: A  800 PHE cc_start: 0.7848 (t80) cc_final: 0.7596 (t80)
REVERT: A  938 MET cc_start: 0.6194 (tpt) cc_final: 0.5706 (tpt)
REVERT: A  982 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7252 (mp)
REVERT: A  989 THR cc_start: 0.6506 (OUTLIER) cc_final: 0.6238 (p)
REVERT: A  991 LYS cc_start: 0.3928 (OUTLIER) cc_final: 0.3121 (ptpt)
REVERT: A 1105 VAL cc_start: 0.8095 (t) cc_final: 0.7850 (p)
REVERT: B  386 VAL cc_start: 0.8084 (m) cc_final: 0.7778 (t)
REVERT: B  455 TYR cc_start: 0.8437 (t80) cc_final: 0.8155 (t80)
REVERT: B  471 ASP cc_start: 0.7816 (m-30) cc_final: 0.7364 (m-30)
REVERT: B  578 LYS cc_start: 0.7877 (tttt) cc_final: 0.7638 (ttpp)
REVERT: B  699 ILE cc_start: 0.3749 (OUTLIER) cc_final: 0.3547 (tp)
REVERT: B  700 MET cc_start: 0.5739 (tmm) cc_final: 0.5197 (tmm)
REVERT: B  800 PHE cc_start: 0.7837 (t80) cc_final: 0.7586 (t80)
REVERT: B  982 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6984 (mp)
REVERT: B 1105 VAL cc_start: 0.8063 (t) cc_final: 0.7828 (p)
  outliers start: 21
  outliers final: 11
  residues processed: 135
  average time/residue: 0.2409
  time to fit residues: 46.7388
Evaluate side-chains
  130 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  559 ASN
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 135 optimal weight:    0.4980
   chunk 59 optimal weight:    4.9990
   chunk 111 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 109 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.158060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.124245 restraints weight = 13061.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.07
r_work: 0.3274 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11518  Z= 0.121
  Angle     :  0.459   8.400  15610  Z= 0.245
  Chirality :  0.039   0.132   1770
  Planarity :  0.003   0.038   1900
  Dihedral  :  8.855  72.844   1700
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.18 %
    Favored  : 86.13 %
  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:  1.55 (0.23), residues: 1376
  helix:  2.53 (0.18), residues: 784
  sheet: -0.34 (0.46), residues: 128
  loop : -1.29 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 779 
 HIS   0.004   0.001   HIS A 828 
 PHE   0.018   0.001   PHE A1124 
 TYR   0.011   0.001   TYR B 925 
 ARG   0.004   0.000   ARG B 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  664)
  hydrogen bonds       : angle       3.96894 ( 1902)
  covalent geometry    : bond        0.00279 (11518)
  covalent geometry    : angle       0.45865 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.183 
Fit side-chains
REVERT: A  386 VAL cc_start: 0.8154 (m) cc_final: 0.7822 (t)
REVERT: A  471 ASP cc_start: 0.7844 (m-30) cc_final: 0.7373 (m-30)
REVERT: A  700 MET cc_start: 0.5308 (tmm) cc_final: 0.5064 (tmm)
REVERT: A  758 ARG cc_start: 0.8740 (tmm160) cc_final: 0.8493 (ttt-90)
REVERT: A  800 PHE cc_start: 0.7827 (t80) cc_final: 0.7573 (t80)
REVERT: A  938 MET cc_start: 0.6145 (tpt) cc_final: 0.5673 (tpt)
REVERT: A  982 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7224 (mp)
REVERT: A  989 THR cc_start: 0.6437 (OUTLIER) cc_final: 0.6158 (p)
REVERT: A  991 LYS cc_start: 0.3819 (OUTLIER) cc_final: 0.3113 (ptpt)
REVERT: A 1105 VAL cc_start: 0.8030 (t) cc_final: 0.7790 (p)
REVERT: B  386 VAL cc_start: 0.8196 (m) cc_final: 0.7885 (t)
REVERT: B  471 ASP cc_start: 0.7832 (m-30) cc_final: 0.7364 (m-30)
REVERT: B  578 LYS cc_start: 0.7853 (tttt) cc_final: 0.7591 (ttpp)
REVERT: B  699 ILE cc_start: 0.3744 (OUTLIER) cc_final: 0.3526 (tp)
REVERT: B  700 MET cc_start: 0.5833 (tmm) cc_final: 0.5222 (tmm)
REVERT: B  800 PHE cc_start: 0.7827 (t80) cc_final: 0.7576 (t80)
REVERT: B  982 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6956 (mp)
REVERT: B 1105 VAL cc_start: 0.8043 (t) cc_final: 0.7808 (p)
  outliers start: 20
  outliers final: 11
  residues processed: 127
  average time/residue: 0.2523
  time to fit residues: 45.5258
Evaluate side-chains
  124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  559 ASN
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 119 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0770
   overall best weight:    0.6340

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

Flipped N/Q/H residues before XYZ refinement:
A 459 HIS
B 459 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.158436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.124615 restraints weight = 13076.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.07
r_work: 0.3282 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11518  Z= 0.116
  Angle     :  0.457   7.737  15610  Z= 0.243
  Chirality :  0.039   0.130   1770
  Planarity :  0.003   0.037   1900
  Dihedral  :  8.772  71.804   1700
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.52 %
    Favored  : 85.87 %
  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 (0.23), residues: 1376
  helix:  2.60 (0.18), residues: 784
  sheet: -0.14 (0.46), residues: 128
  loop : -1.27 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 779 
 HIS   0.004   0.001   HIS B 828 
 PHE   0.016   0.001   PHE B1052 
 TYR   0.017   0.001   TYR B 827 
 ARG   0.004   0.000   ARG B 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  664)
  hydrogen bonds       : angle       3.94205 ( 1902)
  covalent geometry    : bond        0.00266 (11518)
  covalent geometry    : angle       0.45662 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 1.234 
Fit side-chains
REVERT: A  386 VAL cc_start: 0.8239 (m) cc_final: 0.7906 (t)
REVERT: A  471 ASP cc_start: 0.7839 (m-30) cc_final: 0.7372 (m-30)
REVERT: A  700 MET cc_start: 0.5369 (tmm) cc_final: 0.5065 (tmm)
REVERT: A  758 ARG cc_start: 0.8726 (tmm160) cc_final: 0.8483 (ttt-90)
REVERT: A  800 PHE cc_start: 0.7829 (t80) cc_final: 0.7579 (t80)
REVERT: A  982 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7240 (mp)
REVERT: A  989 THR cc_start: 0.6426 (OUTLIER) cc_final: 0.6157 (p)
REVERT: A  991 LYS cc_start: 0.3762 (OUTLIER) cc_final: 0.3039 (ptpt)
REVERT: A 1105 VAL cc_start: 0.8025 (t) cc_final: 0.7782 (p)
REVERT: B  386 VAL cc_start: 0.8282 (m) cc_final: 0.7974 (t)
REVERT: B  471 ASP cc_start: 0.7823 (m-30) cc_final: 0.7358 (m-30)
REVERT: B  578 LYS cc_start: 0.7917 (tttt) cc_final: 0.7644 (ttpp)
REVERT: B  699 ILE cc_start: 0.3636 (OUTLIER) cc_final: 0.3429 (tp)
REVERT: B  700 MET cc_start: 0.5839 (tmm) cc_final: 0.5213 (tmm)
REVERT: B  800 PHE cc_start: 0.7823 (t80) cc_final: 0.7572 (t80)
REVERT: B  982 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.6924 (mp)
REVERT: B 1105 VAL cc_start: 0.8042 (t) cc_final: 0.7800 (p)
  outliers start: 19
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2474
  time to fit residues: 45.0765
Evaluate side-chains
  124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  559 ASN
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  886 MET
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 123 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 101 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 125 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 127 optimal weight:    7.9990
   overall best weight:    1.1382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.153757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.119398 restraints weight = 13134.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.07
r_work: 0.3244 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11518  Z= 0.174
  Angle     :  0.519   9.307  15610  Z= 0.273
  Chirality :  0.041   0.149   1770
  Planarity :  0.003   0.033   1900
  Dihedral  :  9.042  73.549   1700
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.61 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.22), residues: 1376
  helix:  2.38 (0.18), residues: 784
  sheet: -0.24 (0.46), residues: 128
  loop : -1.44 (0.25), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1047 
 HIS   0.006   0.001   HIS B 828 
 PHE   0.020   0.002   PHE B1052 
 TYR   0.023   0.001   TYR A 827 
 ARG   0.004   0.001   ARG B 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  664)
  hydrogen bonds       : angle       4.17407 ( 1902)
  covalent geometry    : bond        0.00421 (11518)
  covalent geometry    : angle       0.51852 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 1.160 
Fit side-chains
REVERT: A  386 VAL cc_start: 0.8249 (m) cc_final: 0.7977 (t)
REVERT: A  471 ASP cc_start: 0.7841 (m-30) cc_final: 0.7367 (m-30)
REVERT: A  700 MET cc_start: 0.5682 (tmm) cc_final: 0.5313 (tmm)
REVERT: A  982 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7272 (mp)
REVERT: A  989 THR cc_start: 0.6433 (OUTLIER) cc_final: 0.6151 (p)
REVERT: A  991 LYS cc_start: 0.3789 (OUTLIER) cc_final: 0.2887 (ptpt)
REVERT: A 1105 VAL cc_start: 0.8054 (t) cc_final: 0.7819 (p)
REVERT: B  386 VAL cc_start: 0.8279 (m) cc_final: 0.8024 (t)
REVERT: B  391 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7027 (pt)
REVERT: B  471 ASP cc_start: 0.7830 (m-30) cc_final: 0.7360 (m-30)
REVERT: B  578 LYS cc_start: 0.7875 (tttt) cc_final: 0.7587 (ttpp)
REVERT: B  699 ILE cc_start: 0.3757 (OUTLIER) cc_final: 0.3509 (tp)
REVERT: B  700 MET cc_start: 0.5844 (tmm) cc_final: 0.5163 (tmm)
REVERT: B  982 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6991 (mp)
REVERT: B 1105 VAL cc_start: 0.8074 (t) cc_final: 0.7842 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 122
  average time/residue: 0.2676
  time to fit residues: 46.4570
Evaluate side-chains
  124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  559 ASN
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 138 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 119 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.155903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.121912 restraints weight = 13064.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.06
r_work: 0.3273 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  11518  Z= 0.121
  Angle     :  0.467   9.454  15610  Z= 0.246
  Chirality :  0.039   0.142   1770
  Planarity :  0.003   0.033   1900
  Dihedral  :  8.796  70.667   1700
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.03 %
    Favored  : 85.36 %
  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 (0.23), residues: 1376
  helix:  2.60 (0.18), residues: 784
  sheet: -0.09 (0.46), residues: 128
  loop : -1.39 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1047 
 HIS   0.004   0.001   HIS B 828 
 PHE   0.016   0.001   PHE A1052 
 TYR   0.020   0.001   TYR A 827 
 ARG   0.004   0.000   ARG B 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03999 (  664)
  hydrogen bonds       : angle       4.00102 ( 1902)
  covalent geometry    : bond        0.00280 (11518)
  covalent geometry    : angle       0.46748 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.303 
Fit side-chains
REVERT: A  386 VAL cc_start: 0.8254 (m) cc_final: 0.8009 (t)
REVERT: A  471 ASP cc_start: 0.7840 (m-30) cc_final: 0.7374 (m-30)
REVERT: A  700 MET cc_start: 0.5654 (tmm) cc_final: 0.5295 (tmm)
REVERT: A  800 PHE cc_start: 0.7835 (t80) cc_final: 0.7602 (t80)
REVERT: A  982 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7260 (mp)
REVERT: A  989 THR cc_start: 0.6399 (OUTLIER) cc_final: 0.6132 (p)
REVERT: A  991 LYS cc_start: 0.3766 (OUTLIER) cc_final: 0.2870 (ptpt)
REVERT: A 1105 VAL cc_start: 0.8027 (t) cc_final: 0.7781 (p)
REVERT: B  386 VAL cc_start: 0.8291 (m) cc_final: 0.8064 (t)
REVERT: B  391 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6965 (pt)
REVERT: B  471 ASP cc_start: 0.7828 (m-30) cc_final: 0.7362 (m-30)
REVERT: B  699 ILE cc_start: 0.3748 (OUTLIER) cc_final: 0.3488 (tp)
REVERT: B  700 MET cc_start: 0.5873 (tmm) cc_final: 0.5182 (tmm)
REVERT: B  800 PHE cc_start: 0.7826 (t80) cc_final: 0.7590 (t80)
REVERT: B  982 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.6973 (mp)
REVERT: B 1105 VAL cc_start: 0.8046 (t) cc_final: 0.7800 (p)
  outliers start: 19
  outliers final: 13
  residues processed: 124
  average time/residue: 0.2451
  time to fit residues: 43.5126
Evaluate side-chains
  123 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  559 ASN
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  886 MET
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 139 optimal weight:    3.9990
   chunk 134 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.152616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.118599 restraints weight = 13037.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.04
r_work: 0.3230 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11518  Z= 0.199
  Angle     :  0.546  10.661  15610  Z= 0.286
  Chirality :  0.042   0.144   1770
  Planarity :  0.003   0.032   1900
  Dihedral  :  9.134  74.649   1700
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.11 %
    Favored  : 85.19 %
  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:  1.32 (0.22), residues: 1376
  helix:  2.32 (0.18), residues: 784
  sheet: -0.04 (0.44), residues: 148
  loop : -1.55 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1047 
 HIS   0.006   0.001   HIS B 828 
 PHE   0.020   0.002   PHE B1052 
 TYR   0.020   0.002   TYR A 827 
 ARG   0.004   0.001   ARG B 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04946 (  664)
  hydrogen bonds       : angle       4.25408 ( 1902)
  covalent geometry    : bond        0.00485 (11518)
  covalent geometry    : angle       0.54574 (15610)

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

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

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2752 Ramachandran restraints generated.
    1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.609 
Fit side-chains
REVERT: A  386 VAL cc_start: 0.8348 (m) cc_final: 0.8141 (t)
REVERT: A  471 ASP cc_start: 0.7842 (m-30) cc_final: 0.7385 (m-30)
REVERT: A  527 GLU cc_start: 0.7804 (pt0) cc_final: 0.7602 (pt0)
REVERT: A  982 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7308 (mp)
REVERT: A  991 LYS cc_start: 0.3260 (OUTLIER) cc_final: 0.2544 (ptpt)
REVERT: A 1105 VAL cc_start: 0.8083 (t) cc_final: 0.7841 (p)
REVERT: B  391 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7048 (pt)
REVERT: B  471 ASP cc_start: 0.7827 (m-30) cc_final: 0.7348 (m-30)
REVERT: B  699 ILE cc_start: 0.3929 (OUTLIER) cc_final: 0.3621 (tp)
REVERT: B  700 MET cc_start: 0.5968 (tmm) cc_final: 0.5225 (tmm)
REVERT: B  982 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7018 (mp)
REVERT: B 1105 VAL cc_start: 0.8107 (t) cc_final: 0.7873 (p)
  outliers start: 20
  outliers final: 13
  residues processed: 121
  average time/residue: 0.3290
  time to fit residues: 58.3914
Evaluate side-chains
  121 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  559 ASN
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  991 LYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  539 GLU
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  886 MET
Chi-restraints excluded: chain B residue  982 ILE
Chi-restraints excluded: chain B residue  985 THR
Chi-restraints excluded: chain B residue 1042 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 126 optimal weight:    0.6980
   chunk 130 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.155524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.121655 restraints weight = 12935.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.03
r_work: 0.3268 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11518  Z= 0.126
  Angle     :  0.478   9.677  15610  Z= 0.251
  Chirality :  0.040   0.150   1770
  Planarity :  0.003   0.032   1900
  Dihedral  :  8.814  71.480   1699
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.62 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.23), residues: 1376
  helix:  2.57 (0.18), residues: 784
  sheet: -0.01 (0.46), residues: 128
  loop : -1.46 (0.25), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1047 
 HIS   0.004   0.001   HIS A 828 
 PHE   0.016   0.001   PHE B1052 
 TYR   0.020   0.001   TYR A 827 
 ARG   0.004   0.000   ARG A 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  664)
  hydrogen bonds       : angle       4.03485 ( 1902)
  covalent geometry    : bond        0.00294 (11518)
  covalent geometry    : angle       0.47757 (15610)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6445.70 seconds
wall clock time: 114 minutes 24.20 seconds (6864.20 seconds total)