Starting phenix.real_space_refine
on Wed Mar  4 02:24:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y69_33638/03_2026/7y69_33638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y69_33638/03_2026/7y69_33638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y69_33638/03_2026/7y69_33638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y69_33638/03_2026/7y69_33638.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y69_33638/03_2026/7y69_33638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y69_33638/03_2026/7y69_33638.map"
  }
  resolution = 3.21
  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=   0.000 sd=   0.070
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      62      5.16       5
     C    6532      2.51       5
     N    1640      2.21       5
     O    1854      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 76 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: 10090
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 637, 4946
          Classifications: {'peptide': 637}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 615}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 171
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 148
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 4, 'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 100
    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: "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
  Restraints were copied for chains:
    B, E, F
  Time building chain proxies: 3.84, per 1000 atoms: 0.38
  Number of scatterers: 10090
  At special positions: 0
  Unit cell: (105.002, 79.0225, 134.23, 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      62     16.00
     O    1854      8.00
     N    1640      7.00
     C    6532      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: 0.84
  Conformation dependent library (CDL) restraints added in 548.4 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 568 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 800 "
      pdb="  ZN B 901 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 796 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 568 "


  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2424

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      46.6% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 236 through 238
      No H-bonds generated for 'chain 'A' and resid 236 through 238'
    Processing helix  chain 'A' and resid 253 through 257
    Processing helix  chain 'A' and resid 290 through 320
      removed outlier: 3.618A  pdb=" N   GLY A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A 303 " --> pdb=" O   PHE A 299 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   SER A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   TYR A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   CYS A 316 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 479
      removed outlier: 3.974A  pdb=" N   LEU A 462 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      Proline residue:  A 463  - end of helix
      removed outlier: 3.514A  pdb=" N   THR A 473 " --> pdb=" O   ILE A 469 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL A 475 " --> pdb=" O   TYR A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 505
    Processing helix  chain 'A' and resid 506 through 533
      removed outlier: 3.769A  pdb=" N   ILE A 510 " --> pdb=" O   ASN A 506 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN A 522 " --> pdb=" O   LEU A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 564
      removed outlier: 4.498A  pdb=" N   PHE A 550 " --> pdb=" O   HIS A 546 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   MET A 558 " --> pdb=" O   GLY A 554 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 562 " --> pdb=" O   MET A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 570
      removed outlier: 3.543A  pdb=" N   VAL A 569 " --> pdb=" O   CYS A 566 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   CYS A 570 " --> pdb=" O   TYR A 567 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 566 through 570'
    Processing helix  chain 'A' and resid 577 through 597
      removed outlier: 4.152A  pdb=" N   PHE A 582 " --> pdb=" O   PHE A 578 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   MET A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR A 584 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET A 585 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ILE A 586 " --> pdb=" O   PHE A 582 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   CYS A 590 " --> pdb=" O   ILE A 586 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   MET A 591 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 626
      removed outlier: 3.536A  pdb=" N   TYR A 607 " --> pdb=" O   ASN A 603 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   SER A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 652
      removed outlier: 3.616A  pdb=" N   THR A 650 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN A 651 " --> pdb=" O   LEU A 647 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A 652 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 710
      removed outlier: 3.545A  pdb=" N   VAL A 693 " --> pdb=" O   MET A 689 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL A 697 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE A 698 " --> pdb=" O   MET A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 739
      removed outlier: 3.864A  pdb=" N   ALA A 720 " --> pdb=" O   SER A 716 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE A 721 " --> pdb=" O   TYR A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 769
      removed outlier: 3.851A  pdb=" N   CYS A 751 " --> pdb=" O   ILE A 747 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE A 764 " --> pdb=" O   GLY A 760 " (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 778 through 782
    Processing helix  chain 'A' and resid 794 through 817
      removed outlier: 3.820A  pdb=" N   PHE A 801 " --> pdb=" O   ASP A 797 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   SER A 804 " --> pdb=" O   HIS A 800 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 238
      No H-bonds generated for 'chain 'B' and resid 236 through 238'
    Processing helix  chain 'B' and resid 253 through 257
    Processing helix  chain 'B' and resid 290 through 320
      removed outlier: 3.618A  pdb=" N   GLY B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE B 303 " --> pdb=" O   PHE B 299 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   SER B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   TYR B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   CYS B 316 " --> pdb=" O   VAL B 312 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 479
      removed outlier: 3.975A  pdb=" N   LEU B 462 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
      Proline residue:  B 463  - end of helix
      removed outlier: 3.514A  pdb=" N   THR B 473 " --> pdb=" O   ILE B 469 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL B 475 " --> pdb=" O   TYR B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 505
    Processing helix  chain 'B' and resid 506 through 533
      removed outlier: 3.769A  pdb=" N   ILE B 510 " --> pdb=" O   ASN B 506 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLN B 522 " --> pdb=" O   LEU B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 564
      removed outlier: 4.497A  pdb=" N   PHE B 550 " --> pdb=" O   HIS B 546 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   MET B 558 " --> pdb=" O   GLY B 554 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 562 " --> pdb=" O   MET B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 570
      removed outlier: 3.543A  pdb=" N   VAL B 569 " --> pdb=" O   CYS B 566 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   CYS B 570 " --> pdb=" O   TYR B 567 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 566 through 570'
    Processing helix  chain 'B' and resid 577 through 597
      removed outlier: 4.151A  pdb=" N   PHE B 582 " --> pdb=" O   PHE B 578 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   MET B 583 " --> pdb=" O   ASP B 579 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR B 584 " --> pdb=" O   THR B 580 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET B 585 " --> pdb=" O   SER B 581 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ILE B 586 " --> pdb=" O   PHE B 582 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   CYS B 590 " --> pdb=" O   ILE B 586 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   MET B 591 " --> pdb=" O   ALA B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 626
      removed outlier: 3.536A  pdb=" N   TYR B 607 " --> pdb=" O   ASN B 603 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   SER B 608 " --> pdb=" O   ALA B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 652
      removed outlier: 3.616A  pdb=" N   THR B 650 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLN B 651 " --> pdb=" O   LEU B 647 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU B 652 " --> pdb=" O   LEU B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 710
      removed outlier: 3.545A  pdb=" N   VAL B 693 " --> pdb=" O   MET B 689 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL B 697 " --> pdb=" O   VAL B 693 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE B 698 " --> pdb=" O   MET B 694 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 739
      removed outlier: 3.863A  pdb=" N   ALA B 720 " --> pdb=" O   SER B 716 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE B 721 " --> pdb=" O   TYR B 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 745 through 769
      removed outlier: 3.851A  pdb=" N   CYS B 751 " --> pdb=" O   ILE B 747 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE B 764 " --> pdb=" O   GLY B 760 " (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 778 through 782
    Processing helix  chain 'B' and resid 794 through 817
      removed outlier: 3.820A  pdb=" N   PHE B 801 " --> pdb=" O   ASP B 797 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   SER B 804 " --> pdb=" O   HIS B 800 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 32
      removed outlier: 6.762A  pdb=" N   ASN A  27 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE A  50 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   SER A  29 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   THR A  52 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   LYS A  31 " --> pdb=" O   THR A  52 " (cutoff:3.500A)
      removed outlier: 8.651A  pdb=" N   ASN A  54 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   LEU A  47 " --> pdb=" O   THR A 136 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   THR A 136 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 115
    Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100
      removed outlier: 6.628A  pdb=" N   LYS A 106 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 165
      removed outlier: 3.555A  pdb=" N   PHE A 164 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER A 281 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 176
    Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 32
      removed outlier: 6.762A  pdb=" N   ASN B  27 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ILE B  50 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   SER B  29 " --> pdb=" O   ILE B  50 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   THR B  52 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   LYS B  31 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 8.650A  pdb=" N   ASN B  54 " --> pdb=" O   LYS B  31 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   LEU B  47 " --> pdb=" O   THR B 136 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   THR B 136 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 115
    Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100
      removed outlier: 6.627A  pdb=" N   LYS B 106 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165
      removed outlier: 3.555A  pdb=" N   PHE B 164 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER B 281 " --> pdb=" O   THR B 190 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 176

    508 hydrogen bonds defined for protein.
    1458 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: 1.59

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3075
        1.34 -     1.46: 2074
        1.46 -     1.58: 5067
        1.58 -     1.70: 0
        1.70 -     1.82: 94
  Bond restraints: 10310
  Sorted by residual:
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.500 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.500 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.490 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.490 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" CA  ASN B 502 "
       pdb=" C   ASN B 502 "
    ideal  model  delta    sigma   weight residual
    1.523  1.475  0.048 1.34e-02 5.57e+03 1.29e+01
  ... (remaining 10305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 13452
        1.86 -     3.72: 501
        3.72 -     5.58: 61
        5.58 -     7.43: 11
        7.43 -     9.29: 9
  Bond angle restraints: 14034
  Sorted by residual:
  angle pdb=" N   PHE A 195 "
        pdb=" CA  PHE A 195 "
        pdb=" C   PHE A 195 "
      ideal   model   delta    sigma   weight residual
     109.81  116.74   -6.93 2.21e+00 2.05e-01 9.82e+00
  angle pdb=" N   PHE B 195 "
        pdb=" CA  PHE B 195 "
        pdb=" C   PHE B 195 "
      ideal   model   delta    sigma   weight residual
     109.81  116.74   -6.93 2.21e+00 2.05e-01 9.82e+00
  angle pdb=" N   CYS A 570 "
        pdb=" CA  CYS A 570 "
        pdb=" CB  CYS A 570 "
      ideal   model   delta    sigma   weight residual
     111.09  114.81   -3.72 1.24e+00 6.50e-01 9.02e+00
  angle pdb=" N   CYS B 570 "
        pdb=" CA  CYS B 570 "
        pdb=" CB  CYS B 570 "
      ideal   model   delta    sigma   weight residual
     111.09  114.77   -3.68 1.24e+00 6.50e-01 8.80e+00
  angle pdb=" C   VAL B  95 "
        pdb=" N   PRO B  96 "
        pdb=" CA  PRO B  96 "
      ideal   model   delta    sigma   weight residual
     127.00  134.10   -7.10 2.40e+00 1.74e-01 8.74e+00
  ... (remaining 14029 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.47: 5737
       23.47 -    46.94: 373
       46.94 -    70.41: 68
       70.41 -    93.88: 18
       93.88 -   117.35: 66
  Dihedral angle restraints: 6262
    sinusoidal: 2518
      harmonic: 3744
  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  129.13   50.87     0      5.00e+00 4.00e-02 1.03e+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  129.20   50.80     0      5.00e+00 4.00e-02 1.03e+02
  dihedral pdb=" CB  CYS A 197 "
           pdb=" SG  CYS A 197 "
           pdb=" SG  CYS A 256 "
           pdb=" CB  CYS A 256 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.03  -64.03     1      1.00e+01 1.00e-02 5.40e+01
  ... (remaining 6259 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1569
       0.096 -    0.192: 95
       0.192 -    0.288: 8
       0.288 -    0.383: 0
       0.383 -    0.479: 6
  Chirality restraints: 1678
  Sorted by residual:
  chirality pdb=" C1  NAG A 904 "
            pdb=" ND2 ASN A 123 "
            pdb=" C2  NAG A 904 "
            pdb=" O5  NAG A 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-01 2.50e+01 5.74e+00
  chirality pdb=" C1  NAG B 904 "
            pdb=" ND2 ASN B 123 "
            pdb=" C2  NAG B 904 "
            pdb=" O5  NAG B 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-01 2.50e+01 5.66e+00
  chirality pdb=" C1  NAG A 902 "
            pdb=" ND2 ASN A  27 "
            pdb=" C2  NAG A 902 "
            pdb=" O5  NAG A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.45e+00
  ... (remaining 1675 not shown)

  Planarity restraints: 1766
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 195 "   -0.067 5.00e-02 4.00e+02   1.01e-01 1.63e+01
        pdb=" N   PRO B 196 "    0.175 5.00e-02 4.00e+02
        pdb=" CA  PRO B 196 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 196 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 195 "   -0.067 5.00e-02 4.00e+02   1.01e-01 1.63e+01
        pdb=" N   PRO A 196 "    0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO A 196 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 196 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 747 "   -0.042 5.00e-02 4.00e+02   6.39e-02 6.52e+00
        pdb=" N   PRO B 748 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 748 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 748 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1763 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1140
        2.74 -     3.28: 10315
        3.28 -     3.82: 16485
        3.82 -     4.36: 19442
        4.36 -     4.90: 33598
  Nonbonded interactions: 80980
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  51 "
            pdb=" OH  TYR A 144 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OH  TYR B  51 "
            pdb=" OH  TYR B 144 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG1 THR A 121 "
            pdb=" OE2 GLU A 126 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG1 THR B 121 "
            pdb=" OE2 GLU B 126 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" NZ  LYS A 188 "
            pdb=" OG  SER A 285 "
     model   vdw
     2.213 3.120
  ... (remaining 80975 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:             1.480
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.490
  Find NCS groups from input model:        0.140
  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:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
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      :  0.011   0.684  10337  Z= 0.439
  Angle     :  0.880  16.844  14092  Z= 0.453
  Chirality :  0.058   0.479   1678
  Planarity :  0.006   0.101   1756
  Dihedral  : 21.161 117.351   3814
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.22 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: 1258
  helix: -0.64 (0.21), residues: 532
  sheet: -1.86 (0.28), residues: 296
  loop : -2.04 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 114 
 TYR   0.025   0.002   TYR A 173 
 PHE   0.037   0.003   PHE A 637 
 TRP   0.012   0.002   TRP A 773 
 HIS   0.006   0.002   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00831 (10310)
  covalent geometry    : angle       0.83027 (14034)
  SS BOND              : bond        0.00317 (    8)
  SS BOND              : angle       1.65013 (   16)
  hydrogen bonds       : bond        0.15619 (  508)
  hydrogen bonds       : angle       6.89491 ( 1458)
  metal coordination   : bond        0.32520 (    5)
  link_BETA1-4         : bond        0.02299 (    4)
  link_BETA1-4         : angle       7.51236 (   12)
  link_NAG-ASN         : bond        0.00725 (   10)
  link_NAG-ASN         : angle       4.18165 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  721 ILE cc_start: 0.8995 (mp) cc_final: 0.8775 (mp)
REVERT: B  297 MET cc_start: 0.7426 (mpp) cc_final: 0.7120 (mpp)
REVERT: B  721 ILE cc_start: 0.8997 (mp) cc_final: 0.8773 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0906
  time to fit residues: 15.8042
Evaluate side-chains
  93 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:   50.0000
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.2980
   chunk 123 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:   20.0000
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
A 145 GLN
B 104 GLN
B 145 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.127861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.087904 restraints weight = 18431.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.93
r_work: 0.3165 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10337  Z= 0.146
  Angle     :  0.789  13.033  14092  Z= 0.363
  Chirality :  0.051   0.350   1678
  Planarity :  0.005   0.081   1756
  Dihedral  : 18.092  96.857   1658
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.19 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -1.41 (0.23), residues: 1258
  helix:  0.21 (0.22), residues: 552
  sheet: -1.44 (0.28), residues: 296
  loop : -1.95 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 688 
 TYR   0.023   0.002   TYR B 595 
 PHE   0.052   0.002   PHE B 633 
 TRP   0.009   0.001   TRP A 773 
 HIS   0.009   0.002   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10310)
  covalent geometry    : angle       0.76029 (14034)
  SS BOND              : bond        0.00206 (    8)
  SS BOND              : angle       1.19423 (   16)
  hydrogen bonds       : bond        0.04966 (  508)
  hydrogen bonds       : angle       4.94144 ( 1458)
  metal coordination   : bond        0.00676 (    5)
  link_BETA1-4         : bond        0.01867 (    4)
  link_BETA1-4         : angle       5.90018 (   12)
  link_NAG-ASN         : bond        0.00865 (   10)
  link_NAG-ASN         : angle       2.75209 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  733 TYR cc_start: 0.7579 (t80) cc_final: 0.7351 (t80)
REVERT: A  751 CYS cc_start: 0.7585 (m) cc_final: 0.7282 (m)
REVERT: B  583 MET cc_start: 0.8633 (mmm) cc_final: 0.8372 (mmm)
REVERT: B  733 TYR cc_start: 0.7593 (t80) cc_final: 0.7376 (t80)
  outliers start: 10
  outliers final: 4
  residues processed: 113
  average time/residue: 0.0894
  time to fit residues: 14.7191
Evaluate side-chains
  103 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  812 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0270
   chunk 14 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0570
   chunk 45 optimal weight:   50.0000
   chunk 9 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.9358

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 699 ASN
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 699 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.128844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.088619 restraints weight = 18454.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.94
r_work: 0.3173 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10337  Z= 0.137
  Angle     :  0.725  12.698  14092  Z= 0.331
  Chirality :  0.046   0.277   1678
  Planarity :  0.005   0.088   1756
  Dihedral  : 12.109  86.274   1658
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.24 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -0.96 (0.23), residues: 1258
  helix:  0.47 (0.21), residues: 562
  sheet: -1.02 (0.29), residues: 296
  loop : -1.76 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.015   0.001   TYR A 173 
 PHE   0.051   0.002   PHE B 633 
 TRP   0.006   0.001   TRP B 773 
 HIS   0.016   0.002   HIS B 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10310)
  covalent geometry    : angle       0.69281 (14034)
  SS BOND              : bond        0.00167 (    8)
  SS BOND              : angle       0.99310 (   16)
  hydrogen bonds       : bond        0.04424 (  508)
  hydrogen bonds       : angle       4.55895 ( 1458)
  metal coordination   : bond        0.00143 (    5)
  link_BETA1-4         : bond        0.02070 (    4)
  link_BETA1-4         : angle       5.06340 (   12)
  link_NAG-ASN         : bond        0.00827 (   10)
  link_NAG-ASN         : angle       3.42151 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  128 GLN cc_start: 0.8053 (mt0) cc_final: 0.7796 (mt0)
REVERT: A  721 ILE cc_start: 0.8523 (mp) cc_final: 0.8047 (tp)
REVERT: A  726 LEU cc_start: 0.9108 (tp) cc_final: 0.8771 (mm)
REVERT: A  733 TYR cc_start: 0.7479 (t80) cc_final: 0.7166 (t80)
REVERT: B  128 GLN cc_start: 0.8019 (mt0) cc_final: 0.7737 (mt0)
REVERT: B  726 LEU cc_start: 0.9099 (tp) cc_final: 0.8763 (mm)
REVERT: B  733 TYR cc_start: 0.7481 (t80) cc_final: 0.7182 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 123
  average time/residue: 0.0913
  time to fit residues: 16.5996
Evaluate side-chains
  114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 93 optimal weight:   20.0000
   chunk 109 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.127426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.087106 restraints weight = 18397.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.93
r_work: 0.3144 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10337  Z= 0.180
  Angle     :  0.717  11.694  14092  Z= 0.335
  Chirality :  0.046   0.305   1678
  Planarity :  0.005   0.084   1756
  Dihedral  : 10.158  85.961   1658
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.52 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -0.75 (0.24), residues: 1258
  helix:  0.69 (0.21), residues: 560
  sheet: -0.89 (0.29), residues: 296
  loop : -1.75 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.019   0.002   TYR A 173 
 PHE   0.046   0.002   PHE A 633 
 TRP   0.005   0.001   TRP A 773 
 HIS   0.005   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (10310)
  covalent geometry    : angle       0.68444 (14034)
  SS BOND              : bond        0.00180 (    8)
  SS BOND              : angle       1.12902 (   16)
  hydrogen bonds       : bond        0.04323 (  508)
  hydrogen bonds       : angle       4.55154 ( 1458)
  metal coordination   : bond        0.00396 (    5)
  link_BETA1-4         : bond        0.01832 (    4)
  link_BETA1-4         : angle       5.07284 (   12)
  link_NAG-ASN         : bond        0.00671 (   10)
  link_NAG-ASN         : angle       3.36978 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7704 (pp30)
REVERT: A  128 GLN cc_start: 0.8060 (mt0) cc_final: 0.7696 (mt0)
REVERT: A  721 ILE cc_start: 0.8675 (mp) cc_final: 0.8257 (tp)
REVERT: A  726 LEU cc_start: 0.9124 (tp) cc_final: 0.8798 (mm)
REVERT: B   94 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7686 (pp30)
REVERT: B  128 GLN cc_start: 0.8059 (mt0) cc_final: 0.7684 (mt0)
REVERT: B  721 ILE cc_start: 0.8675 (mp) cc_final: 0.8251 (tp)
REVERT: B  726 LEU cc_start: 0.9114 (tp) cc_final: 0.8767 (mm)
  outliers start: 18
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0848
  time to fit residues: 15.1774
Evaluate side-chains
  124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  776 THR
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 115 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 76 optimal weight:    0.3980
   chunk 117 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.128698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.088154 restraints weight = 18347.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.94
r_work: 0.3162 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10337  Z= 0.146
  Angle     :  0.685  14.193  14092  Z= 0.319
  Chirality :  0.045   0.313   1678
  Planarity :  0.005   0.086   1756
  Dihedral  :  9.581  83.875   1658
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.19 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -0.50 (0.24), residues: 1258
  helix:  0.88 (0.22), residues: 562
  sheet: -0.73 (0.30), residues: 296
  loop : -1.65 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.017   0.001   TYR A 173 
 PHE   0.048   0.002   PHE B 633 
 TRP   0.004   0.001   TRP B 773 
 HIS   0.004   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10310)
  covalent geometry    : angle       0.64782 (14034)
  SS BOND              : bond        0.00152 (    8)
  SS BOND              : angle       1.03833 (   16)
  hydrogen bonds       : bond        0.04168 (  508)
  hydrogen bonds       : angle       4.40385 ( 1458)
  metal coordination   : bond        0.00288 (    5)
  link_BETA1-4         : bond        0.01716 (    4)
  link_BETA1-4         : angle       5.36458 (   12)
  link_NAG-ASN         : bond        0.00631 (   10)
  link_NAG-ASN         : angle       3.42534 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7656 (pp30)
REVERT: A  721 ILE cc_start: 0.8663 (mp) cc_final: 0.8266 (tp)
REVERT: A  726 LEU cc_start: 0.9088 (tp) cc_final: 0.8775 (mm)
REVERT: B   94 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7646 (pp30)
REVERT: B  466 GLN cc_start: 0.8713 (mm110) cc_final: 0.8081 (mm-40)
REVERT: B  595 TYR cc_start: 0.7588 (t80) cc_final: 0.7327 (t80)
REVERT: B  689 MET cc_start: 0.7156 (pmm) cc_final: 0.6807 (mpp)
REVERT: B  721 ILE cc_start: 0.8664 (mp) cc_final: 0.8261 (tp)
REVERT: B  726 LEU cc_start: 0.9107 (tp) cc_final: 0.8780 (mm)
  outliers start: 25
  outliers final: 17
  residues processed: 128
  average time/residue: 0.0878
  time to fit residues: 16.5873
Evaluate side-chains
  129 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  776 THR
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 45 optimal weight:   50.0000
   chunk 51 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 124 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 GLN
B  86 GLN
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.126153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.085453 restraints weight = 18526.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.92
r_work: 0.3111 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  10337  Z= 0.292
  Angle     :  0.759  12.792  14092  Z= 0.361
  Chirality :  0.048   0.314   1678
  Planarity :  0.005   0.091   1756
  Dihedral  :  9.730  84.081   1658
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.67 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -0.66 (0.24), residues: 1258
  helix:  0.76 (0.22), residues: 570
  sheet: -0.92 (0.30), residues: 300
  loop : -1.71 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 114 
 TYR   0.025   0.002   TYR B 173 
 PHE   0.032   0.002   PHE A 633 
 TRP   0.007   0.001   TRP B 759 
 HIS   0.005   0.002   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 (10310)
  covalent geometry    : angle       0.72581 (14034)
  SS BOND              : bond        0.00207 (    8)
  SS BOND              : angle       1.33709 (   16)
  hydrogen bonds       : bond        0.04516 (  508)
  hydrogen bonds       : angle       4.62884 ( 1458)
  metal coordination   : bond        0.00807 (    5)
  link_BETA1-4         : bond        0.01755 (    4)
  link_BETA1-4         : angle       5.21931 (   12)
  link_NAG-ASN         : bond        0.00591 (   10)
  link_NAG-ASN         : angle       3.46360 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7735 (pp30)
REVERT: A  466 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8047 (mm-40)
REVERT: A  726 LEU cc_start: 0.9103 (tp) cc_final: 0.8779 (mm)
REVERT: B   94 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7734 (pp30)
REVERT: B  297 MET cc_start: 0.7745 (mpp) cc_final: 0.7493 (mpp)
REVERT: B  466 GLN cc_start: 0.8723 (mm110) cc_final: 0.8077 (mm-40)
REVERT: B  726 LEU cc_start: 0.9091 (tp) cc_final: 0.8779 (mm)
  outliers start: 34
  outliers final: 20
  residues processed: 122
  average time/residue: 0.0909
  time to fit residues: 16.4370
Evaluate side-chains
  125 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  466 GLN
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  718 LEU
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  776 THR
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 48 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 110 optimal weight:   20.0000
   chunk 72 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 107 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 GLN
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.126777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.086261 restraints weight = 18323.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.91
r_work: 0.3129 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10337  Z= 0.221
  Angle     :  0.726  13.464  14092  Z= 0.345
  Chirality :  0.046   0.309   1678
  Planarity :  0.005   0.086   1756
  Dihedral  :  9.623  83.111   1658
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.48 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -0.63 (0.24), residues: 1258
  helix:  0.81 (0.22), residues: 570
  sheet: -0.92 (0.30), residues: 300
  loop : -1.71 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 114 
 TYR   0.020   0.002   TYR A 173 
 PHE   0.031   0.002   PHE A 633 
 TRP   0.006   0.001   TRP A 759 
 HIS   0.006   0.001   HIS B 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (10310)
  covalent geometry    : angle       0.69153 (14034)
  SS BOND              : bond        0.00175 (    8)
  SS BOND              : angle       1.20444 (   16)
  hydrogen bonds       : bond        0.04404 (  508)
  hydrogen bonds       : angle       4.55629 ( 1458)
  metal coordination   : bond        0.00525 (    5)
  link_BETA1-4         : bond        0.01697 (    4)
  link_BETA1-4         : angle       5.30786 (   12)
  link_NAG-ASN         : bond        0.00563 (   10)
  link_NAG-ASN         : angle       3.42501 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7723 (pp30)
REVERT: A  466 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8073 (mm-40)
REVERT: A  721 ILE cc_start: 0.8457 (mp) cc_final: 0.8085 (tp)
REVERT: A  726 LEU cc_start: 0.9118 (tp) cc_final: 0.8788 (mm)
REVERT: B   94 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7718 (pp30)
REVERT: B  466 GLN cc_start: 0.8722 (mm110) cc_final: 0.8105 (mm-40)
REVERT: B  721 ILE cc_start: 0.8464 (mp) cc_final: 0.8089 (tp)
REVERT: B  726 LEU cc_start: 0.9109 (tp) cc_final: 0.8793 (mm)
  outliers start: 23
  outliers final: 18
  residues processed: 118
  average time/residue: 0.0877
  time to fit residues: 15.3132
Evaluate side-chains
  127 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  466 GLN
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  776 THR
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 105 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 45 optimal weight:   50.0000
   chunk 114 optimal weight:   20.0000
   chunk 78 optimal weight:    0.8980
   chunk 118 optimal weight:    0.8980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 GLN
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.128078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.087625 restraints weight = 18246.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.94
r_work: 0.3153 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10337  Z= 0.148
  Angle     :  0.689  12.441  14092  Z= 0.323
  Chirality :  0.045   0.304   1678
  Planarity :  0.005   0.084   1756
  Dihedral  :  9.329  82.189   1658
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.95 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: 1258
  helix:  0.95 (0.22), residues: 572
  sheet: -0.72 (0.30), residues: 296
  loop : -1.69 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 105 
 TYR   0.018   0.002   TYR A 733 
 PHE   0.031   0.002   PHE A 633 
 TRP   0.004   0.001   TRP B 773 
 HIS   0.005   0.001   HIS B 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10310)
  covalent geometry    : angle       0.65278 (14034)
  SS BOND              : bond        0.00159 (    8)
  SS BOND              : angle       1.04455 (   16)
  hydrogen bonds       : bond        0.04142 (  508)
  hydrogen bonds       : angle       4.39830 ( 1458)
  metal coordination   : bond        0.00265 (    5)
  link_BETA1-4         : bond        0.01716 (    4)
  link_BETA1-4         : angle       5.42327 (   12)
  link_NAG-ASN         : bond        0.00559 (   10)
  link_NAG-ASN         : angle       3.39918 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7642 (pp30)
REVERT: A  466 GLN cc_start: 0.8705 (mm110) cc_final: 0.8006 (mm-40)
REVERT: A  721 ILE cc_start: 0.8435 (mp) cc_final: 0.8107 (tp)
REVERT: A  726 LEU cc_start: 0.9103 (tp) cc_final: 0.8777 (mm)
REVERT: B   94 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7638 (pp30)
REVERT: B  466 GLN cc_start: 0.8711 (mm110) cc_final: 0.8080 (mm-40)
REVERT: B  721 ILE cc_start: 0.8445 (mp) cc_final: 0.8113 (tp)
REVERT: B  726 LEU cc_start: 0.9095 (tp) cc_final: 0.8776 (mm)
  outliers start: 23
  outliers final: 18
  residues processed: 125
  average time/residue: 0.0901
  time to fit residues: 16.4779
Evaluate side-chains
  132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  776 THR
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 104 optimal weight:    0.5980
   chunk 13 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 105 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0050
   chunk 42 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 55 optimal weight:    0.1980
   chunk 106 optimal weight:    2.9990
   chunk 112 optimal weight:    8.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.130186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.089776 restraints weight = 18205.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.94
r_work: 0.3192 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10337  Z= 0.111
  Angle     :  0.658  12.344  14092  Z= 0.306
  Chirality :  0.044   0.293   1678
  Planarity :  0.004   0.081   1756
  Dihedral  :  8.775  80.724   1658
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.05 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -0.09 (0.24), residues: 1258
  helix:  1.29 (0.22), residues: 562
  sheet: -0.52 (0.30), residues: 296
  loop : -1.59 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 105 
 TYR   0.017   0.001   TYR B 733 
 PHE   0.025   0.002   PHE A 633 
 TRP   0.005   0.001   TRP B 634 
 HIS   0.004   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10310)
  covalent geometry    : angle       0.61852 (14034)
  SS BOND              : bond        0.00154 (    8)
  SS BOND              : angle       0.93317 (   16)
  hydrogen bonds       : bond        0.03757 (  508)
  hydrogen bonds       : angle       4.21278 ( 1458)
  metal coordination   : bond        0.00112 (    5)
  link_BETA1-4         : bond        0.01694 (    4)
  link_BETA1-4         : angle       5.58987 (   12)
  link_NAG-ASN         : bond        0.00585 (   10)
  link_NAG-ASN         : angle       3.42107 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7690 (pp30)
REVERT: A  466 GLN cc_start: 0.8667 (mm110) cc_final: 0.7955 (mm-40)
REVERT: A  595 TYR cc_start: 0.7557 (t80) cc_final: 0.7276 (t80)
REVERT: A  726 LEU cc_start: 0.9099 (tp) cc_final: 0.8770 (mm)
REVERT: B   94 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7688 (pp30)
REVERT: B  466 GLN cc_start: 0.8624 (mm110) cc_final: 0.8031 (mm-40)
REVERT: B  595 TYR cc_start: 0.7558 (t80) cc_final: 0.7282 (t80)
REVERT: B  726 LEU cc_start: 0.9090 (tp) cc_final: 0.8769 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 130
  average time/residue: 0.0774
  time to fit residues: 15.3838
Evaluate side-chains
  128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  576 PHE
Chi-restraints excluded: chain B residue  776 THR
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.128942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.088322 restraints weight = 17980.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.93
r_work: 0.3165 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10337  Z= 0.154
  Angle     :  0.685  11.757  14092  Z= 0.317
  Chirality :  0.045   0.293   1678
  Planarity :  0.005   0.086   1756
  Dihedral  :  8.689  79.988   1658
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.00 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -0.05 (0.24), residues: 1258
  helix:  1.30 (0.22), residues: 550
  sheet: -0.51 (0.30), residues: 300
  loop : -1.43 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 114 
 TYR   0.022   0.002   TYR B 733 
 PHE   0.026   0.002   PHE A 633 
 TRP   0.005   0.001   TRP B 759 
 HIS   0.004   0.001   HIS B 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10310)
  covalent geometry    : angle       0.64746 (14034)
  SS BOND              : bond        0.00150 (    8)
  SS BOND              : angle       0.97233 (   16)
  hydrogen bonds       : bond        0.03906 (  508)
  hydrogen bonds       : angle       4.27941 ( 1458)
  metal coordination   : bond        0.00293 (    5)
  link_BETA1-4         : bond        0.01642 (    4)
  link_BETA1-4         : angle       5.43585 (   12)
  link_NAG-ASN         : bond        0.00537 (   10)
  link_NAG-ASN         : angle       3.42242 (   30)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7711 (pp30)
REVERT: A  128 GLN cc_start: 0.8080 (mt0) cc_final: 0.7751 (mt0)
REVERT: A  466 GLN cc_start: 0.8638 (mm110) cc_final: 0.7982 (mm-40)
REVERT: A  595 TYR cc_start: 0.7625 (t80) cc_final: 0.7378 (t80)
REVERT: A  726 LEU cc_start: 0.9092 (tp) cc_final: 0.8752 (mm)
REVERT: B   94 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7701 (pp30)
REVERT: B  466 GLN cc_start: 0.8599 (mm110) cc_final: 0.8022 (mm-40)
REVERT: B  595 TYR cc_start: 0.7629 (t80) cc_final: 0.7385 (t80)
REVERT: B  726 LEU cc_start: 0.9085 (tp) cc_final: 0.8751 (mm)
  outliers start: 16
  outliers final: 13
  residues processed: 125
  average time/residue: 0.0771
  time to fit residues: 14.7251
Evaluate side-chains
  128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  776 THR
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 92 optimal weight:    8.9990
   chunk 115 optimal weight:    0.6980
   chunk 108 optimal weight:   40.0000
   chunk 96 optimal weight:    0.7980
   chunk 58 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.129220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.089170 restraints weight = 18151.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.77
r_work: 0.3186 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10337  Z= 0.152
  Angle     :  0.684  11.771  14092  Z= 0.318
  Chirality :  0.045   0.293   1678
  Planarity :  0.004   0.082   1756
  Dihedral  :  8.574  78.714   1658
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.81 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    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: -0.05 (0.24), residues: 1258
  helix:  1.28 (0.22), residues: 550
  sheet: -0.49 (0.30), residues: 300
  loop : -1.41 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 105 
 TYR   0.021   0.002   TYR A 733 
 PHE   0.026   0.002   PHE A 633 
 TRP   0.005   0.001   TRP B 700 
 HIS   0.003   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10310)
  covalent geometry    : angle       0.64648 (14034)
  SS BOND              : bond        0.00146 (    8)
  SS BOND              : angle       0.96275 (   16)
  hydrogen bonds       : bond        0.03961 (  508)
  hydrogen bonds       : angle       4.27913 ( 1458)
  metal coordination   : bond        0.00307 (    5)
  link_BETA1-4         : bond        0.01648 (    4)
  link_BETA1-4         : angle       5.46278 (   12)
  link_NAG-ASN         : bond        0.00531 (   10)
  link_NAG-ASN         : angle       3.45094 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2274.11 seconds
wall clock time: 39 minutes 42.35 seconds (2382.35 seconds total)