Starting phenix.real_space_refine
on Wed Mar  4 01:53:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y63_33632/03_2026/7y63_33632.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y63_33632/03_2026/7y63_33632.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y63_33632/03_2026/7y63_33632.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y63_33632/03_2026/7y63_33632.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y63_33632/03_2026/7y63_33632.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y63_33632/03_2026/7y63_33632.map"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.061
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      66      5.16       5
     C    6430      2.51       5
     N    1604      2.21       5
     O    1822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9924
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 619, 4863
          Classifications: {'peptide': 619}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 598}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 4, 'TYR:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 59
    Chain: "B"
      Number of atoms: 4863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 619, 4863
          Classifications: {'peptide': 619}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 598}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 4, 'TYR:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 59
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.58, per 1000 atoms: 0.26
  Number of scatterers: 9924
  At special positions: 0
  Unit cell: (108.692, 80.1467, 133.944, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      66     16.00
     O    1822      8.00
     N    1604      7.00
     C    6430      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 197 " - pdb=" SG  CYS A 256 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 484 " - pdb=" SG  CYS A 570 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 490 " - pdb=" SG  CYS A 787 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 117 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 197 " - pdb=" SG  CYS B 256 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 484 " - pdb=" SG  CYS B 570 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 490 " - pdb=" SG  CYS B 787 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 902 " - " ASN A  27 "
      " NAG A 903 " - " ASN A 141 "
      " NAG A 904 " - " ASN A 123 "
      " NAG B 902 " - " ASN B  27 "
      " NAG B 903 " - " ASN B 141 "
      " NAG B 904 " - " ASN B 123 "
      " NAG C   1 " - " ASN A  54 "
      " NAG D   1 " - " ASN A 165 "
      " NAG E   1 " - " ASN B  54 "
      " NAG F   1 " - " ASN B 165 "
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 455.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 796 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 800 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 568 "
      pdb="  ZN B 901 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 800 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 568 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 796 "


  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      45.7% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 253 through 257
    Processing helix  chain 'A' and resid 290 through 320
      removed outlier: 3.538A  pdb=" N   VAL A 294 " --> pdb=" O   SER A 290 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   PHE A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TRP A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   TRP A 320 " --> pdb=" O   CYS A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 479
      removed outlier: 3.579A  pdb=" N   LEU A 462 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      Proline residue:  A 463  - end of helix
      removed outlier: 3.916A  pdb=" N   GLN A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU A 467 " --> pdb=" O   PRO A 463 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR A 473 " --> pdb=" O   ILE A 469 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL A 475 " --> pdb=" O   TYR A 471 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 505
      removed outlier: 3.617A  pdb=" N   LEU A 504 " --> pdb=" O   PHE A 500 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER A 505 " --> pdb=" O   ASN A 501 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 500 through 505'
    Processing helix  chain 'A' and resid 506 through 533
      removed outlier: 3.972A  pdb=" N   ILE A 510 " --> pdb=" O   ASN A 506 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LEU A 514 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 515 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU A 517 " --> pdb=" O   GLY A 513 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 529 " --> pdb=" O   ILE A 525 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA A 530 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 531 " --> pdb=" O   HIS A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 541
    Processing helix  chain 'A' and resid 549 through 561
      removed outlier: 3.538A  pdb=" N   MET A 558 " --> pdb=" O   GLY A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 599
      removed outlier: 4.578A  pdb=" N   THR A 580 " --> pdb=" O   PHE A 576 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   PHE A 582 " --> pdb=" O   PHE A 578 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   MET A 585 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE A 586 " --> pdb=" O   PHE A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 626
    Processing helix  chain 'A' and resid 630 through 652
      removed outlier: 3.851A  pdb=" N   THR A 650 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN A 651 " --> pdb=" O   LEU A 647 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU A 652 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 710
      removed outlier: 3.966A  pdb=" N   LEU A 692 " --> pdb=" O   ARG A 688 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL A 693 " --> pdb=" O   MET A 689 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   MET A 694 " --> pdb=" O   VAL A 690 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ASN A 699 " --> pdb=" O   GLY A 695 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TYR A 705 " --> pdb=" O   SER A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 739
      removed outlier: 3.906A  pdb=" N   LEU A 728 " --> pdb=" O   CYS A 724 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA A 731 " --> pdb=" O   LEU A 727 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET A 736 " --> pdb=" O   PHE A 732 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS A 737 " --> pdb=" O   TYR A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 769
      removed outlier: 3.556A  pdb=" N   CYS A 751 " --> pdb=" O   ILE A 747 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   CYS A 754 " --> pdb=" O   LEU A 750 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   THR A 755 " --> pdb=" O   CYS A 751 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLY A 760 " --> pdb=" O   SER A 756 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A 763 " --> pdb=" O   TRP A 759 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE A 767 " --> pdb=" O   LEU A 763 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY A 769 " --> pdb=" O   PHE A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 794 through 818
      removed outlier: 3.918A  pdb=" N   SER A 804 " --> pdb=" O   HIS A 800 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL A 813 " --> pdb=" O   GLY A 809 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A 814 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   THR A 816 " --> pdb=" O   LEU A 812 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ASP A 818 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 257
    Processing helix  chain 'B' and resid 290 through 320
      removed outlier: 3.538A  pdb=" N   VAL B 294 " --> pdb=" O   SER B 290 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   PHE B 299 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLY B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   PHE B 307 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TRP B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   TRP B 320 " --> pdb=" O   CYS B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 479
      removed outlier: 3.580A  pdb=" N   LEU B 462 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
      Proline residue:  B 463  - end of helix
      removed outlier: 3.917A  pdb=" N   GLN B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU B 467 " --> pdb=" O   PRO B 463 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR B 473 " --> pdb=" O   ILE B 469 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   VAL B 474 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL B 475 " --> pdb=" O   TYR B 471 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN B 476 " --> pdb=" O   GLN B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 505
      removed outlier: 3.617A  pdb=" N   LEU B 504 " --> pdb=" O   PHE B 500 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER B 505 " --> pdb=" O   ASN B 501 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 500 through 505'
    Processing helix  chain 'B' and resid 506 through 533
      removed outlier: 3.972A  pdb=" N   ILE B 510 " --> pdb=" O   ASN B 506 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LEU B 514 " --> pdb=" O   ILE B 510 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU B 515 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU B 517 " --> pdb=" O   GLY B 513 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG B 529 " --> pdb=" O   ILE B 525 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA B 530 " --> pdb=" O   ASN B 526 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B 531 " --> pdb=" O   HIS B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 541
    Processing helix  chain 'B' and resid 549 through 561
      removed outlier: 3.539A  pdb=" N   MET B 558 " --> pdb=" O   GLY B 554 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 599
      removed outlier: 4.578A  pdb=" N   THR B 580 " --> pdb=" O   PHE B 576 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   PHE B 582 " --> pdb=" O   PHE B 578 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   MET B 585 " --> pdb=" O   SER B 581 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE B 586 " --> pdb=" O   PHE B 582 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 626
    Processing helix  chain 'B' and resid 630 through 652
      removed outlier: 3.850A  pdb=" N   THR B 650 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN B 651 " --> pdb=" O   LEU B 647 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU B 652 " --> pdb=" O   LEU B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 710
      removed outlier: 3.966A  pdb=" N   LEU B 692 " --> pdb=" O   ARG B 688 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL B 693 " --> pdb=" O   MET B 689 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   MET B 694 " --> pdb=" O   VAL B 690 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASN B 699 " --> pdb=" O   GLY B 695 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TYR B 705 " --> pdb=" O   SER B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 739
      removed outlier: 3.907A  pdb=" N   LEU B 728 " --> pdb=" O   CYS B 724 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA B 731 " --> pdb=" O   LEU B 727 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET B 736 " --> pdb=" O   PHE B 732 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS B 737 " --> pdb=" O   TYR B 733 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 745 through 769
      removed outlier: 3.555A  pdb=" N   CYS B 751 " --> pdb=" O   ILE B 747 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   CYS B 754 " --> pdb=" O   LEU B 750 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   THR B 755 " --> pdb=" O   CYS B 751 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLY B 760 " --> pdb=" O   SER B 756 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B 763 " --> pdb=" O   TRP B 759 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE B 767 " --> pdb=" O   LEU B 763 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY B 769 " --> pdb=" O   PHE B 765 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 794 through 818
      removed outlier: 3.918A  pdb=" N   SER B 804 " --> pdb=" O   HIS B 800 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL B 813 " --> pdb=" O   GLY B 809 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU B 814 " --> pdb=" O   SER B 810 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   THR B 816 " --> pdb=" O   LEU B 812 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ASP B 818 " --> pdb=" O   LEU B 814 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43
      removed outlier: 3.849A  pdb=" N   ASP A  41 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115
    Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100
      removed outlier: 6.910A  pdb=" N   LYS A 106 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166
      removed outlier: 3.602A  pdb=" N   PHE A 164 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   SER A 285 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 177
      removed outlier: 4.473A  pdb=" N   CYS A 197 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31
    Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 43
      removed outlier: 3.849A  pdb=" N   ASP B  41 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 115
    Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 100
      removed outlier: 6.910A  pdb=" N   LYS B 106 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 163 through 166
      removed outlier: 3.601A  pdb=" N   PHE B 164 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER B 285 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177
      removed outlier: 4.472A  pdb=" N   CYS B 197 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)

    478 hydrogen bonds defined for protein.
    1386 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: 1.43

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3094
        1.34 -     1.46: 2472
        1.46 -     1.58: 4476
        1.58 -     1.70: 0
        1.70 -     1.83: 98
  Bond restraints: 10140
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" CA  ARG B  85 "
       pdb=" CB  ARG B  85 "
    ideal  model  delta    sigma   weight residual
    1.528  1.500  0.027 1.39e-02 5.18e+03 3.91e+00
  bond pdb=" CA  ARG A  85 "
       pdb=" CB  ARG A  85 "
    ideal  model  delta    sigma   weight residual
    1.528  1.500  0.027 1.39e-02 5.18e+03 3.91e+00
  bond pdb=" CA  ARG B 235 "
       pdb=" C   ARG B 235 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.80e-02 3.09e+03 2.60e+00
  ... (remaining 10135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 13203
        1.53 -     3.06: 487
        3.06 -     4.60: 77
        4.60 -     6.13: 15
        6.13 -     7.66: 6
  Bond angle restraints: 13788
  Sorted by residual:
  angle pdb=" C   ALA A 715 "
        pdb=" CA  ALA A 715 "
        pdb=" CB  ALA A 715 "
      ideal   model   delta    sigma   weight residual
     110.88  116.78   -5.90 1.57e+00 4.06e-01 1.41e+01
  angle pdb=" N   PHE A 195 "
        pdb=" CA  PHE A 195 "
        pdb=" C   PHE A 195 "
      ideal   model   delta    sigma   weight residual
     109.81  117.47   -7.66 2.21e+00 2.05e-01 1.20e+01
  angle pdb=" N   PHE B 195 "
        pdb=" CA  PHE B 195 "
        pdb=" C   PHE B 195 "
      ideal   model   delta    sigma   weight residual
     109.81  117.46   -7.65 2.21e+00 2.05e-01 1.20e+01
  angle pdb=" N   SER A 716 "
        pdb=" CA  SER A 716 "
        pdb=" C   SER A 716 "
      ideal   model   delta    sigma   weight residual
     111.75  115.84   -4.09 1.28e+00 6.10e-01 1.02e+01
  angle pdb=" C   ALA B 194 "
        pdb=" N   PHE B 195 "
        pdb=" CA  PHE B 195 "
      ideal   model   delta    sigma   weight residual
     121.80  114.40    7.40 2.44e+00 1.68e-01 9.19e+00
  ... (remaining 13783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.21: 5690
       23.21 -    46.42: 346
       46.42 -    69.63: 69
       69.63 -    92.83: 25
       92.83 -   116.04: 30
  Dihedral angle restraints: 6160
    sinusoidal: 2526
      harmonic: 3634
  Sorted by residual:
  dihedral pdb=" CA  PHE A 195 "
           pdb=" C   PHE A 195 "
           pdb=" N   PRO A 196 "
           pdb=" CA  PRO A 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.86   52.14     0      5.00e+00 4.00e-02 1.09e+02
  dihedral pdb=" CA  PHE B 195 "
           pdb=" C   PHE B 195 "
           pdb=" N   PRO B 196 "
           pdb=" CA  PRO B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  127.89   52.11     0      5.00e+00 4.00e-02 1.09e+02
  dihedral pdb=" CB  CYS B 197 "
           pdb=" SG  CYS B 197 "
           pdb=" SG  CYS B 256 "
           pdb=" CB  CYS B 256 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.68  -79.68     1      1.00e+01 1.00e-02 7.88e+01
  ... (remaining 6157 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1574
       0.104 -    0.207: 61
       0.207 -    0.311: 5
       0.311 -    0.415: 2
       0.415 -    0.519: 2
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A  54 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-01 2.50e+01 6.72e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B  54 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-01 2.50e+01 6.70e+00
  chirality pdb=" C1  NAG A 903 "
            pdb=" ND2 ASN A 141 "
            pdb=" C2  NAG A 903 "
            pdb=" O5  NAG A 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.09e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1728
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 195 "   -0.065 5.00e-02 4.00e+02   9.79e-02 1.53e+01
        pdb=" N   PRO A 196 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO A 196 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 196 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 195 "   -0.065 5.00e-02 4.00e+02   9.79e-02 1.53e+01
        pdb=" N   PRO B 196 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO B 196 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 196 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  78 "    0.044 5.00e-02 4.00e+02   6.65e-02 7.07e+00
        pdb=" N   PRO A  79 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A  79 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A  79 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1725 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1457
        2.75 -     3.29: 9676
        3.29 -     3.83: 15673
        3.83 -     4.36: 19202
        4.36 -     4.90: 32813
  Nonbonded interactions: 78821
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  59 "
            pdb=" O   LYS A 122 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" NH2 ARG B  59 "
            pdb=" O   LYS B 122 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" O   THR A 224 "
            pdb=" NH1 ARG A 781 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   THR B 224 "
            pdb=" NH1 ARG B 781 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" CD2 LEU A  81 "
            pdb=" CG2 VAL B  90 "
     model   vdw
     2.228 3.880
  ... (remaining 78816 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.550
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.630
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
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      :  0.006   0.083  10168  Z= 0.249
  Angle     :  0.739   9.947  13846  Z= 0.391
  Chirality :  0.053   0.519   1644
  Planarity :  0.005   0.098   1718
  Dihedral  : 18.687 116.042   3784
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.23), residues: 1218
  helix: -1.22 (0.23), residues: 468
  sheet: -1.13 (0.30), residues: 296
  loop : -1.79 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 785 
 TYR   0.018   0.002   TYR A 173 
 PHE   0.016   0.002   PHE A 576 
 TRP   0.008   0.001   TRP B 700 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (10140)
  covalent geometry    : angle       0.70238 (13788)
  SS BOND              : bond        0.00295 (    8)
  SS BOND              : angle       1.50042 (   16)
  hydrogen bonds       : bond        0.26634 (  478)
  hydrogen bonds       : angle       9.30574 ( 1386)
  metal coordination   : bond        0.00190 (    6)
  link_BETA1-4         : bond        0.00878 (    4)
  link_BETA1-4         : angle       2.29671 (   12)
  link_NAG-ASN         : bond        0.00798 (   10)
  link_NAG-ASN         : angle       4.72251 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  694 MET cc_start: 0.5732 (mpp) cc_final: 0.5361 (mpp)
REVERT: A  728 LEU cc_start: 0.9087 (mt) cc_final: 0.8840 (mt)
REVERT: A  749 LEU cc_start: 0.8529 (tp) cc_final: 0.8255 (pp)
REVERT: B  694 MET cc_start: 0.5776 (mpp) cc_final: 0.5413 (mpp)
REVERT: B  728 LEU cc_start: 0.9073 (mt) cc_final: 0.8828 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0877
  time to fit residues: 19.4545
Evaluate side-chains
  132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 699 ASN
A 774 GLN
B 110 GLN
B 286 GLN
B 699 ASN
B 774 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.162729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.109254 restraints weight = 13622.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.74
r_work: 0.3337 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10168  Z= 0.214
  Angle     :  0.762  11.602  13846  Z= 0.373
  Chirality :  0.050   0.297   1644
  Planarity :  0.006   0.090   1718
  Dihedral  : 14.578  87.763   1620
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.81 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.24), residues: 1218
  helix: -0.42 (0.22), residues: 508
  sheet: -0.94 (0.30), residues: 296
  loop : -1.63 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 781 
 TYR   0.026   0.002   TYR B 584 
 PHE   0.015   0.002   PHE A 582 
 TRP   0.011   0.001   TRP A 320 
 HIS   0.003   0.001   HIS B 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (10140)
  covalent geometry    : angle       0.72854 (13788)
  SS BOND              : bond        0.00281 (    8)
  SS BOND              : angle       1.22171 (   16)
  hydrogen bonds       : bond        0.05986 (  478)
  hydrogen bonds       : angle       5.93142 ( 1386)
  metal coordination   : bond        0.00172 (    6)
  link_BETA1-4         : bond        0.00672 (    4)
  link_BETA1-4         : angle       2.36146 (   12)
  link_NAG-ASN         : bond        0.00721 (   10)
  link_NAG-ASN         : angle       4.59347 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 138
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.8857 (pm20) cc_final: 0.8449 (pm20)
REVERT: A  161 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: A  297 MET cc_start: 0.7580 (ptt) cc_final: 0.6889 (ptt)
REVERT: A  694 MET cc_start: 0.5959 (mpp) cc_final: 0.5657 (mpp)
REVERT: A  728 LEU cc_start: 0.9025 (mt) cc_final: 0.8799 (mt)
REVERT: B  104 GLN cc_start: 0.8851 (pm20) cc_final: 0.8486 (pm20)
REVERT: B  161 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: B  297 MET cc_start: 0.7504 (ptt) cc_final: 0.6786 (ptt)
REVERT: B  694 MET cc_start: 0.5949 (mpp) cc_final: 0.5640 (mpp)
REVERT: B  728 LEU cc_start: 0.9008 (mt) cc_final: 0.8790 (mt)
  outliers start: 9
  outliers final: 5
  residues processed: 145
  average time/residue: 0.0825
  time to fit residues: 17.8190
Evaluate side-chains
  133 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  583 MET
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 106 optimal weight:   30.0000
   chunk 44 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.4183 r_free = 0.4183 target = 0.163684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.110080 restraints weight = 13544.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.75
r_work: 0.3351 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10168  Z= 0.171
  Angle     :  0.685  11.370  13846  Z= 0.330
  Chirality :  0.047   0.262   1644
  Planarity :  0.005   0.085   1718
  Dihedral  : 10.496  65.515   1620
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.84 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.24), residues: 1218
  helix:  0.07 (0.23), residues: 514
  sheet: -0.78 (0.30), residues: 296
  loop : -1.74 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.014   0.001   TYR A 485 
 PHE   0.013   0.001   PHE A 130 
 TRP   0.011   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10140)
  covalent geometry    : angle       0.65002 (13788)
  SS BOND              : bond        0.00150 (    8)
  SS BOND              : angle       1.08804 (   16)
  hydrogen bonds       : bond        0.05121 (  478)
  hydrogen bonds       : angle       5.39649 ( 1386)
  metal coordination   : bond        0.00171 (    6)
  link_BETA1-4         : bond        0.00356 (    4)
  link_BETA1-4         : angle       2.72599 (   12)
  link_NAG-ASN         : bond        0.00731 (   10)
  link_NAG-ASN         : angle       4.31398 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A   61 ARG cc_start: 0.6866 (mpt180) cc_final: 0.6514 (mtm-85)
REVERT: A   94 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7762 (pp30)
REVERT: A  193 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8466 (ttpp)
REVERT: A  297 MET cc_start: 0.7533 (ptt) cc_final: 0.6862 (ptt)
REVERT: A  714 PHE cc_start: 0.8333 (t80) cc_final: 0.8131 (t80)
REVERT: A  728 LEU cc_start: 0.8988 (mt) cc_final: 0.8784 (mt)
REVERT: A  779 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8344 (mt-10)
REVERT: B   61 ARG cc_start: 0.6892 (mpt180) cc_final: 0.6540 (mtm-85)
REVERT: B   94 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7745 (pp30)
REVERT: B  104 GLN cc_start: 0.8845 (pm20) cc_final: 0.8477 (pm20)
REVERT: B  193 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8491 (ttpp)
REVERT: B  297 MET cc_start: 0.7457 (ptt) cc_final: 0.6760 (ptt)
REVERT: B  728 LEU cc_start: 0.9036 (mt) cc_final: 0.8811 (mt)
REVERT: B  779 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8368 (mt-10)
  outliers start: 11
  outliers final: 4
  residues processed: 140
  average time/residue: 0.0867
  time to fit residues: 17.7054
Evaluate side-chains
  123 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  583 MET
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  583 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:   30.0000
   chunk 52 optimal weight:    7.9990
   chunk 84 optimal weight:    0.4980
   chunk 45 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 13 optimal weight:    0.1980
   chunk 80 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.4200 r_free = 0.4200 target = 0.164904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.110922 restraints weight = 13789.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.78
r_work: 0.3369 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10168  Z= 0.140
  Angle     :  0.632  10.002  13846  Z= 0.306
  Chirality :  0.045   0.246   1644
  Planarity :  0.004   0.080   1718
  Dihedral  :  7.811  52.973   1620
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.49 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.24), residues: 1218
  helix:  0.43 (0.23), residues: 514
  sheet: -0.70 (0.29), residues: 296
  loop : -1.72 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 235 
 TYR   0.024   0.001   TYR A 584 
 PHE   0.013   0.001   PHE A 130 
 TRP   0.010   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10140)
  covalent geometry    : angle       0.59733 (13788)
  SS BOND              : bond        0.00108 (    8)
  SS BOND              : angle       0.92152 (   16)
  hydrogen bonds       : bond        0.04358 (  478)
  hydrogen bonds       : angle       5.06276 ( 1386)
  metal coordination   : bond        0.00086 (    6)
  link_BETA1-4         : bond        0.00143 (    4)
  link_BETA1-4         : angle       2.75721 (   12)
  link_NAG-ASN         : bond        0.00708 (   10)
  link_NAG-ASN         : angle       4.09000 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A   61 ARG cc_start: 0.6882 (mpt180) cc_final: 0.6575 (mtm-85)
REVERT: A   94 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7678 (pp30)
REVERT: A  297 MET cc_start: 0.7447 (ptt) cc_final: 0.6815 (ptt)
REVERT: A  714 PHE cc_start: 0.8293 (t80) cc_final: 0.8062 (t80)
REVERT: A  779 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8189 (mt-10)
REVERT: B   61 ARG cc_start: 0.6889 (mpt180) cc_final: 0.6573 (mtm-85)
REVERT: B   94 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7668 (pp30)
REVERT: B  104 GLN cc_start: 0.8833 (pm20) cc_final: 0.8472 (pm20)
REVERT: B  297 MET cc_start: 0.7313 (ptt) cc_final: 0.6653 (ptt)
REVERT: B  779 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8185 (mt-10)
  outliers start: 15
  outliers final: 4
  residues processed: 140
  average time/residue: 0.0761
  time to fit residues: 16.1254
Evaluate side-chains
  119 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  712 ASN
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  583 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 121 optimal weight:    0.7980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.4205 r_free = 0.4205 target = 0.165070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.111165 restraints weight = 13683.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.77
r_work: 0.3363 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10168  Z= 0.140
  Angle     :  0.602   9.212  13846  Z= 0.297
  Chirality :  0.044   0.236   1644
  Planarity :  0.004   0.080   1718
  Dihedral  :  7.110  53.263   1620
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.29 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.24), residues: 1218
  helix:  0.55 (0.23), residues: 516
  sheet: -0.65 (0.29), residues: 296
  loop : -1.74 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.013   0.001   TYR A 551 
 PHE   0.015   0.001   PHE B 304 
 TRP   0.010   0.001   TRP A 320 
 HIS   0.006   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10140)
  covalent geometry    : angle       0.57206 (13788)
  SS BOND              : bond        0.00114 (    8)
  SS BOND              : angle       0.86612 (   16)
  hydrogen bonds       : bond        0.04176 (  478)
  hydrogen bonds       : angle       4.96084 ( 1386)
  metal coordination   : bond        0.00127 (    6)
  link_BETA1-4         : bond        0.00321 (    4)
  link_BETA1-4         : angle       2.39799 (   12)
  link_NAG-ASN         : bond        0.00641 (   10)
  link_NAG-ASN         : angle       3.78436 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A   61 ARG cc_start: 0.6895 (mpt180) cc_final: 0.6648 (mtm-85)
REVERT: A   94 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7680 (pp30)
REVERT: A  297 MET cc_start: 0.7395 (ptt) cc_final: 0.6817 (ptt)
REVERT: A  714 PHE cc_start: 0.8281 (t80) cc_final: 0.8021 (t80)
REVERT: A  728 LEU cc_start: 0.9128 (mt) cc_final: 0.8755 (pp)
REVERT: B   61 ARG cc_start: 0.6896 (mpt180) cc_final: 0.6636 (mtm-85)
REVERT: B   94 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7664 (pp30)
REVERT: B  297 MET cc_start: 0.7340 (ptt) cc_final: 0.6717 (ptt)
REVERT: B  728 LEU cc_start: 0.9101 (mt) cc_final: 0.8759 (pp)
  outliers start: 12
  outliers final: 4
  residues processed: 138
  average time/residue: 0.0810
  time to fit residues: 17.0213
Evaluate side-chains
  128 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  583 MET
Chi-restraints excluded: chain B residue  712 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0370
   chunk 9 optimal weight:    1.9990
   chunk 80 optimal weight:    0.3980
   chunk 89 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.6658

-------------------------------------------------------------------------------
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 = 0.4221 r_free = 0.4221 target = 0.166284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.112309 restraints weight = 13704.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.79
r_work: 0.3389 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10168  Z= 0.120
  Angle     :  0.566   8.558  13846  Z= 0.281
  Chirality :  0.043   0.231   1644
  Planarity :  0.004   0.077   1718
  Dihedral  :  6.505  52.779   1620
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.95 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.24), residues: 1218
  helix:  0.88 (0.23), residues: 504
  sheet: -0.60 (0.29), residues: 296
  loop : -1.63 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 781 
 TYR   0.026   0.001   TYR A 584 
 PHE   0.014   0.001   PHE B 714 
 TRP   0.009   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10140)
  covalent geometry    : angle       0.53817 (13788)
  SS BOND              : bond        0.00112 (    8)
  SS BOND              : angle       0.85589 (   16)
  hydrogen bonds       : bond        0.03846 (  478)
  hydrogen bonds       : angle       4.81647 ( 1386)
  metal coordination   : bond        0.00031 (    6)
  link_BETA1-4         : bond        0.00146 (    4)
  link_BETA1-4         : angle       2.20189 (   12)
  link_NAG-ASN         : bond        0.00654 (   10)
  link_NAG-ASN         : angle       3.52802 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.6893 (mpt180) cc_final: 0.6623 (mtm-85)
REVERT: A   94 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7645 (pp30)
REVERT: A  297 MET cc_start: 0.7292 (ptt) cc_final: 0.6748 (ptt)
REVERT: A  714 PHE cc_start: 0.8256 (t80) cc_final: 0.7953 (t80)
REVERT: B   61 ARG cc_start: 0.6868 (mpt180) cc_final: 0.6634 (mtm-85)
REVERT: B   94 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7630 (pp30)
REVERT: B  297 MET cc_start: 0.7213 (ptt) cc_final: 0.6653 (ptt)
REVERT: B  728 LEU cc_start: 0.9096 (mt) cc_final: 0.8838 (pp)
  outliers start: 17
  outliers final: 12
  residues processed: 141
  average time/residue: 0.0856
  time to fit residues: 18.0025
Evaluate side-chains
  136 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  712 ASN
Chi-restraints excluded: chain A residue  761 PHE
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  583 MET
Chi-restraints excluded: chain B residue  712 ASN
Chi-restraints excluded: chain B residue  761 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 107 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0970
   chunk 66 optimal weight:    0.6980
   chunk 114 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 36 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 109 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4216 r_free = 0.4216 target = 0.165846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.111945 restraints weight = 13655.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.77
r_work: 0.3377 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10168  Z= 0.135
  Angle     :  0.568   8.035  13846  Z= 0.283
  Chirality :  0.044   0.227   1644
  Planarity :  0.004   0.078   1718
  Dihedral  :  6.296  53.861   1620
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.05 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.24), residues: 1218
  helix:  1.00 (0.23), residues: 508
  sheet: -0.56 (0.29), residues: 296
  loop : -1.64 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.022   0.001   TYR A 584 
 PHE   0.016   0.001   PHE A 304 
 TRP   0.009   0.001   TRP A 320 
 HIS   0.004   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10140)
  covalent geometry    : angle       0.54301 (13788)
  SS BOND              : bond        0.00136 (    8)
  SS BOND              : angle       0.85169 (   16)
  hydrogen bonds       : bond        0.03815 (  478)
  hydrogen bonds       : angle       4.80190 ( 1386)
  metal coordination   : bond        0.00102 (    6)
  link_BETA1-4         : bond        0.00225 (    4)
  link_BETA1-4         : angle       1.99439 (   12)
  link_NAG-ASN         : bond        0.00639 (   10)
  link_NAG-ASN         : angle       3.39470 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.6958 (mpt180) cc_final: 0.6657 (mtm-85)
REVERT: A   94 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7651 (pp30)
REVERT: A  297 MET cc_start: 0.7325 (ptt) cc_final: 0.6740 (ptt)
REVERT: A  313 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7846 (tp)
REVERT: A  714 PHE cc_start: 0.8259 (t80) cc_final: 0.7948 (t80)
REVERT: B   61 ARG cc_start: 0.6939 (mpt180) cc_final: 0.6630 (mtm-85)
REVERT: B   94 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7630 (pp30)
REVERT: B  297 MET cc_start: 0.7260 (ptt) cc_final: 0.6655 (ptt)
REVERT: B  313 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7855 (tp)
REVERT: B  728 LEU cc_start: 0.9174 (mt) cc_final: 0.8868 (pp)
  outliers start: 22
  outliers final: 14
  residues processed: 136
  average time/residue: 0.0743
  time to fit residues: 15.5369
Evaluate side-chains
  136 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  712 ASN
Chi-restraints excluded: chain A residue  761 PHE
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  583 MET
Chi-restraints excluded: chain B residue  712 ASN
Chi-restraints excluded: chain B residue  761 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 108 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.163579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.109444 restraints weight = 13584.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.73
r_work: 0.3339 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10168  Z= 0.209
  Angle     :  0.611   7.540  13846  Z= 0.307
  Chirality :  0.045   0.225   1644
  Planarity :  0.004   0.081   1718
  Dihedral  :  6.472  56.132   1620
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.52 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.24), residues: 1218
  helix:  1.08 (0.23), residues: 500
  sheet: -0.55 (0.30), residues: 296
  loop : -1.52 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 276 
 TYR   0.019   0.002   TYR A 584 
 PHE   0.015   0.002   PHE B 714 
 TRP   0.010   0.001   TRP A 320 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 (10140)
  covalent geometry    : angle       0.58911 (13788)
  SS BOND              : bond        0.00144 (    8)
  SS BOND              : angle       1.11224 (   16)
  hydrogen bonds       : bond        0.04051 (  478)
  hydrogen bonds       : angle       4.88050 ( 1386)
  metal coordination   : bond        0.00217 (    6)
  link_BETA1-4         : bond        0.00260 (    4)
  link_BETA1-4         : angle       1.82633 (   12)
  link_NAG-ASN         : bond        0.00538 (   10)
  link_NAG-ASN         : angle       3.27945 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.7045 (mpt180) cc_final: 0.6727 (mtm-85)
REVERT: A   94 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7733 (pp30)
REVERT: A  313 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7832 (tp)
REVERT: A  714 PHE cc_start: 0.8320 (t80) cc_final: 0.8001 (t80)
REVERT: B   61 ARG cc_start: 0.7018 (mpt180) cc_final: 0.6694 (mtm-85)
REVERT: B   94 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7731 (pp30)
REVERT: B  313 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7839 (tp)
REVERT: B  728 LEU cc_start: 0.9131 (mt) cc_final: 0.8839 (pp)
REVERT: B  812 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8234 (mp)
  outliers start: 26
  outliers final: 17
  residues processed: 144
  average time/residue: 0.0783
  time to fit residues: 17.3192
Evaluate side-chains
  147 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  576 PHE
Chi-restraints excluded: chain A residue  712 ASN
Chi-restraints excluded: chain A residue  761 PHE
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  576 PHE
Chi-restraints excluded: chain B residue  583 MET
Chi-restraints excluded: chain B residue  712 ASN
Chi-restraints excluded: chain B residue  761 PHE
Chi-restraints excluded: chain B residue  812 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0770
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 121 optimal weight:    0.6980
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A  44 ASN
B 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.166184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.112212 restraints weight = 13555.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.76
r_work: 0.3382 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10168  Z= 0.126
  Angle     :  0.566   7.375  13846  Z= 0.285
  Chirality :  0.043   0.233   1644
  Planarity :  0.004   0.076   1718
  Dihedral  :  6.069  53.152   1620
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.56 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.25), residues: 1218
  helix:  1.22 (0.23), residues: 508
  sheet: -0.54 (0.29), residues: 296
  loop : -1.54 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 781 
 TYR   0.021   0.001   TYR A 584 
 PHE   0.018   0.001   PHE B 714 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.004   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10140)
  covalent geometry    : angle       0.54467 (13788)
  SS BOND              : bond        0.00097 (    8)
  SS BOND              : angle       0.75170 (   16)
  hydrogen bonds       : bond        0.03769 (  478)
  hydrogen bonds       : angle       4.75650 ( 1386)
  metal coordination   : bond        0.00101 (    6)
  link_BETA1-4         : bond        0.00193 (    4)
  link_BETA1-4         : angle       1.71197 (   12)
  link_NAG-ASN         : bond        0.00634 (   10)
  link_NAG-ASN         : angle       3.15815 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   61 ARG cc_start: 0.6967 (mpt180) cc_final: 0.6636 (mtm-85)
REVERT: A   94 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7678 (pp30)
REVERT: A  313 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7822 (tp)
REVERT: A  714 PHE cc_start: 0.8269 (t80) cc_final: 0.7954 (t80)
REVERT: A  812 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8259 (mp)
REVERT: B   61 ARG cc_start: 0.6970 (mpt180) cc_final: 0.6633 (mtm-85)
REVERT: B   94 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7680 (pp30)
REVERT: B  313 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7832 (tp)
REVERT: B  728 LEU cc_start: 0.9121 (mt) cc_final: 0.8826 (pp)
  outliers start: 17
  outliers final: 9
  residues processed: 142
  average time/residue: 0.0740
  time to fit residues: 16.2075
Evaluate side-chains
  135 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  576 PHE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  712 ASN
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  576 PHE
Chi-restraints excluded: chain B residue  712 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 111 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.164736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.110818 restraints weight = 13382.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.72
r_work: 0.3357 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10168  Z= 0.181
  Angle     :  0.610   8.899  13846  Z= 0.307
  Chirality :  0.044   0.221   1644
  Planarity :  0.004   0.080   1718
  Dihedral  :  6.215  55.187   1620
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.66 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.25), residues: 1218
  helix:  1.22 (0.23), residues: 508
  sheet: -0.49 (0.30), residues: 296
  loop : -1.54 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 276 
 TYR   0.019   0.002   TYR A 584 
 PHE   0.012   0.001   PHE A 130 
 TRP   0.009   0.001   TRP A 320 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (10140)
  covalent geometry    : angle       0.58591 (13788)
  SS BOND              : bond        0.00131 (    8)
  SS BOND              : angle       2.40588 (   16)
  hydrogen bonds       : bond        0.03895 (  478)
  hydrogen bonds       : angle       4.79131 ( 1386)
  metal coordination   : bond        0.00273 (    6)
  link_BETA1-4         : bond        0.00224 (    4)
  link_BETA1-4         : angle       1.64519 (   12)
  link_NAG-ASN         : bond        0.00547 (   10)
  link_NAG-ASN         : angle       3.13385 (   30)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   61 ARG cc_start: 0.7042 (mpt180) cc_final: 0.6711 (mtm-85)
REVERT: A   94 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7747 (pp30)
REVERT: A  313 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7818 (tp)
REVERT: A  714 PHE cc_start: 0.8332 (t80) cc_final: 0.7993 (t80)
REVERT: A  812 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8253 (mp)
REVERT: B   61 ARG cc_start: 0.7049 (mpt180) cc_final: 0.6711 (mtm-85)
REVERT: B   94 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7727 (pp30)
REVERT: B  313 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7825 (tp)
REVERT: B  728 LEU cc_start: 0.9143 (mt) cc_final: 0.8840 (pp)
  outliers start: 19
  outliers final: 10
  residues processed: 139
  average time/residue: 0.0775
  time to fit residues: 16.5809
Evaluate side-chains
  137 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  712 ASN
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  576 PHE
Chi-restraints excluded: chain B residue  712 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 107 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 46 optimal weight:    9.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.4174 r_free = 0.4174 target = 0.163853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.109088 restraints weight = 13701.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.82
r_work: 0.3371 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10168  Z= 0.139
  Angle     :  0.584   7.679  13846  Z= 0.293
  Chirality :  0.044   0.229   1644
  Planarity :  0.004   0.076   1718
  Dihedral  :  6.045  53.951   1620
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.66 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.25), residues: 1218
  helix:  1.31 (0.23), residues: 508
  sheet: -0.47 (0.29), residues: 296
  loop : -1.51 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 100 
 TYR   0.019   0.001   TYR A 584 
 PHE   0.026   0.001   PHE B 714 
 TRP   0.007   0.001   TRP A 320 
 HIS   0.003   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10140)
  covalent geometry    : angle       0.56308 (13788)
  SS BOND              : bond        0.00092 (    8)
  SS BOND              : angle       1.61044 (   16)
  hydrogen bonds       : bond        0.03765 (  478)
  hydrogen bonds       : angle       4.75149 ( 1386)
  metal coordination   : bond        0.00142 (    6)
  link_BETA1-4         : bond        0.00252 (    4)
  link_BETA1-4         : angle       1.54616 (   12)
  link_NAG-ASN         : bond        0.00591 (   10)
  link_NAG-ASN         : angle       3.06407 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2320.39 seconds
wall clock time: 40 minutes 24.94 seconds (2424.94 seconds total)