Starting phenix.real_space_refine
on Thu May  1 02:31:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y69_33638/05_2025/7y69_33638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y69_33638/05_2025/7y69_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y69_33638/05_2025/7y69_33638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y69_33638/05_2025/7y69_33638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y69_33638/05_2025/7y69_33638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y69_33638/05_2025/7y69_33638.cif"
  }
  resolution = 3.21
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3}
          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: 10.18, per 1000 atoms: 1.01
  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: 4.03
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  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: 1.03
  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: 3.27

  Time building geometry restraints manager: 3.75 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: 0.00
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:             1.840
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     33.410
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.970
-------------------------------------------------------------------------------
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 : 16.09
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.23), 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
 TRP   0.012   0.002   TRP A 773 
 HIS   0.006   0.002   HIS A 275 
 PHE   0.037   0.003   PHE A 637 
 TYR   0.025   0.002   TYR A 173 
 ARG   0.003   0.000   ARG A 114 

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

*********************** 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  : 1.304 
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: 0.2588
  time to fit residues: 44.7470
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  : 1.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 95 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 114 optimal weight:   30.0000
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.126397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.086586 restraints weight = 18307.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.89
r_work: 0.3137 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10337  Z= 0.195
  Angle     :  0.817  13.123  14092  Z= 0.378
  Chirality :  0.052   0.345   1678
  Planarity :  0.006   0.085   1756
  Dihedral  : 18.093  97.076   1658
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.95 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.23), residues: 1258
  helix:  0.09 (0.22), residues: 550
  sheet: -1.51 (0.28), residues: 300
  loop : -1.98 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 773 
 HIS   0.009   0.001   HIS B 568 
 PHE   0.051   0.002   PHE A 633 
 TYR   0.023   0.002   TYR B 595 
 ARG   0.011   0.001   ARG B 688 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00746 (   10)
  link_NAG-ASN         : angle       2.73641 (   30)
  link_BETA1-4         : bond        0.01936 (    4)
  link_BETA1-4         : angle       5.91558 (   12)
  hydrogen bonds       : bond        0.05102 (  508)
  hydrogen bonds       : angle       5.03929 ( 1458)
  metal coordination   : bond        0.00792 (    5)
  SS BOND              : bond        0.00274 (    8)
  SS BOND              : angle       1.31212 (   16)
  covalent geometry    : bond        0.00440 (10310)
  covalent geometry    : angle       0.78906 (14034)

*********************** 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
  117 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 1.214 
Fit side-chains
REVERT: A  583 MET cc_start: 0.8669 (mmm) cc_final: 0.8416 (mmm)
REVERT: A  733 TYR cc_start: 0.7650 (t80) cc_final: 0.7426 (t80)
REVERT: B  583 MET cc_start: 0.8660 (mmm) cc_final: 0.8384 (mmm)
REVERT: B  733 TYR cc_start: 0.7655 (t80) cc_final: 0.7441 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 110
  average time/residue: 0.2115
  time to fit residues: 34.0233
Evaluate side-chains
  101 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue  166 THR
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 97 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 70 optimal weight:    0.0030
   chunk 52 optimal weight:    2.9990
   chunk 113 optimal weight:   20.0000
   chunk 120 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    2.5796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.126102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.085975 restraints weight = 18586.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.90
r_work: 0.3125 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1420

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= 0.224
  Angle     :  0.797  12.298  14092  Z= 0.368
  Chirality :  0.048   0.305   1678
  Planarity :  0.005   0.093   1756
  Dihedral  : 13.252  88.510   1658
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 13.62 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.23), residues: 1258
  helix:  0.20 (0.21), residues: 564
  sheet: -1.34 (0.28), residues: 300
  loop : -1.89 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 773 
 HIS   0.007   0.001   HIS B 641 
 PHE   0.052   0.002   PHE A 633 
 TYR   0.020   0.002   TYR A 173 
 ARG   0.002   0.000   ARG A 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00720 (   10)
  link_NAG-ASN         : angle       3.30569 (   30)
  link_BETA1-4         : bond        0.02096 (    4)
  link_BETA1-4         : angle       5.33322 (   12)
  hydrogen bonds       : bond        0.04888 (  508)
  hydrogen bonds       : angle       4.86370 ( 1458)
  metal coordination   : bond        0.00551 (    5)
  SS BOND              : bond        0.00202 (    8)
  SS BOND              : angle       1.23687 (   16)
  covalent geometry    : bond        0.00513 (10310)
  covalent geometry    : angle       0.76757 (14034)

*********************** 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
  114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7701 (pp30)
REVERT: A  726 LEU cc_start: 0.9148 (tp) cc_final: 0.8791 (mm)
REVERT: A  733 TYR cc_start: 0.7584 (t80) cc_final: 0.7333 (t80)
REVERT: B   94 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7699 (pp30)
REVERT: B  726 LEU cc_start: 0.9144 (tp) cc_final: 0.8786 (mm)
REVERT: B  733 TYR cc_start: 0.7584 (t80) cc_final: 0.7340 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 108
  average time/residue: 0.2047
  time to fit residues: 32.3309
Evaluate side-chains
  112 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLN
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  812 LEU
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 49 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 122 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 699 ASN
B  86 GLN
B 699 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.124943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.085144 restraints weight = 18438.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.83
r_work: 0.3109 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  10337  Z= 0.293
  Angle     :  0.810  11.977  14092  Z= 0.383
  Chirality :  0.048   0.286   1678
  Planarity :  0.005   0.092   1756
  Dihedral  : 10.788  84.347   1658
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.67 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.23), residues: 1258
  helix:  0.26 (0.21), residues: 564
  sheet: -1.32 (0.29), residues: 300
  loop : -1.85 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 773 
 HIS   0.011   0.002   HIS B 641 
 PHE   0.051   0.002   PHE A 633 
 TYR   0.022   0.002   TYR A 173 
 ARG   0.004   0.001   ARG B 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00634 (   10)
  link_NAG-ASN         : angle       3.81849 (   30)
  link_BETA1-4         : bond        0.01936 (    4)
  link_BETA1-4         : angle       5.07195 (   12)
  hydrogen bonds       : bond        0.04878 (  508)
  hydrogen bonds       : angle       4.86890 ( 1458)
  metal coordination   : bond        0.00750 (    5)
  SS BOND              : bond        0.00229 (    8)
  SS BOND              : angle       1.31489 (   16)
  covalent geometry    : bond        0.00679 (10310)
  covalent geometry    : angle       0.77680 (14034)

*********************** 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
  135 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.253 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7669 (pp30)
REVERT: A  297 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7790 (mpp)
REVERT: A  689 MET cc_start: 0.7712 (mpp) cc_final: 0.7212 (pmm)
REVERT: A  721 ILE cc_start: 0.8696 (mp) cc_final: 0.8236 (tp)
REVERT: A  726 LEU cc_start: 0.9162 (tp) cc_final: 0.8826 (mm)
REVERT: A  733 TYR cc_start: 0.7626 (t80) cc_final: 0.7426 (t80)
REVERT: B   94 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7731 (pp30)
REVERT: B  689 MET cc_start: 0.7722 (mpp) cc_final: 0.7224 (pmm)
REVERT: B  721 ILE cc_start: 0.8700 (mp) cc_final: 0.8241 (tp)
REVERT: B  726 LEU cc_start: 0.9156 (tp) cc_final: 0.8803 (mm)
  outliers start: 28
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1993
  time to fit residues: 35.0399
Evaluate side-chains
  119 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
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  297 MET
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  812 LEU
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  297 MET
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  723 ILE
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 46 optimal weight:   50.0000
   chunk 121 optimal weight:    8.9990
   chunk 48 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   chunk 123 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0030
   chunk 69 optimal weight:    0.9990
   chunk 118 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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 = 0.128913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.088456 restraints weight = 18019.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.95
r_work: 0.3156 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10337  Z= 0.118
  Angle     :  0.676  12.092  14092  Z= 0.315
  Chirality :  0.044   0.297   1678
  Planarity :  0.005   0.080   1756
  Dihedral  :  9.749  83.442   1658
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.10 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.23), residues: 1258
  helix:  0.72 (0.21), residues: 566
  sheet: -1.07 (0.29), residues: 296
  loop : -1.76 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 700 
 HIS   0.006   0.001   HIS B 641 
 PHE   0.047   0.002   PHE A 633 
 TYR   0.016   0.001   TYR B 733 
 ARG   0.002   0.000   ARG A 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00606 (   10)
  link_NAG-ASN         : angle       3.52504 (   30)
  link_BETA1-4         : bond        0.01616 (    4)
  link_BETA1-4         : angle       5.39720 (   12)
  hydrogen bonds       : bond        0.04150 (  508)
  hydrogen bonds       : angle       4.45370 ( 1458)
  metal coordination   : bond        0.00120 (    5)
  SS BOND              : bond        0.00147 (    8)
  SS BOND              : angle       0.94743 (   16)
  covalent geometry    : bond        0.00246 (10310)
  covalent geometry    : angle       0.63792 (14034)

*********************** 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
  137 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 GLN cc_start: 0.8100 (mt0) cc_final: 0.7808 (mt0)
REVERT: A  689 MET cc_start: 0.7678 (mpp) cc_final: 0.7163 (pmm)
REVERT: A  721 ILE cc_start: 0.8671 (mp) cc_final: 0.8250 (tp)
REVERT: A  726 LEU cc_start: 0.9111 (tp) cc_final: 0.8800 (mm)
REVERT: A  733 TYR cc_start: 0.7499 (t80) cc_final: 0.7247 (t80)
REVERT: B  128 GLN cc_start: 0.8090 (mt0) cc_final: 0.7797 (mt0)
REVERT: B  689 MET cc_start: 0.7697 (mpp) cc_final: 0.7194 (pmm)
REVERT: B  721 ILE cc_start: 0.8719 (mp) cc_final: 0.8310 (tp)
REVERT: B  726 LEU cc_start: 0.9106 (tp) cc_final: 0.8791 (mm)
  outliers start: 21
  outliers final: 11
  residues processed: 126
  average time/residue: 0.2116
  time to fit residues: 39.9995
Evaluate side-chains
  123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 1.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 THR
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  817 LEU
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  297 MET
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  817 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 115 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 120 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   chunk 105 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3929 r_free = 0.3929 target = 0.128209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.087601 restraints weight = 18167.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.94
r_work: 0.3140 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10337  Z= 0.154
  Angle     :  0.680  13.789  14092  Z= 0.316
  Chirality :  0.045   0.302   1678
  Planarity :  0.005   0.088   1756
  Dihedral  :  9.372  83.791   1658
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.24), residues: 1258
  helix:  0.73 (0.21), residues: 566
  sheet: -0.87 (0.29), residues: 296
  loop : -1.64 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 700 
 HIS   0.004   0.001   HIS B 568 
 PHE   0.030   0.002   PHE B 633 
 TYR   0.017   0.001   TYR B 173 
 ARG   0.002   0.000   ARG B 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00574 (   10)
  link_NAG-ASN         : angle       3.51373 (   30)
  link_BETA1-4         : bond        0.01700 (    4)
  link_BETA1-4         : angle       5.35851 (   12)
  hydrogen bonds       : bond        0.04113 (  508)
  hydrogen bonds       : angle       4.41115 ( 1458)
  metal coordination   : bond        0.00331 (    5)
  SS BOND              : bond        0.00172 (    8)
  SS BOND              : angle       1.02173 (   16)
  covalent geometry    : bond        0.00345 (10310)
  covalent geometry    : angle       0.64208 (14034)

*********************** 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: 21
    poor density    : 119
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7616 (pp30)
REVERT: A  637 PHE cc_start: 0.8092 (m-10) cc_final: 0.7884 (m-10)
REVERT: A  721 ILE cc_start: 0.8663 (mp) cc_final: 0.8278 (tp)
REVERT: A  726 LEU cc_start: 0.9085 (tp) cc_final: 0.8773 (mm)
REVERT: B   94 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7655 (pp30)
REVERT: B  637 PHE cc_start: 0.8095 (m-10) cc_final: 0.7890 (m-10)
REVERT: B  721 ILE cc_start: 0.8670 (mp) cc_final: 0.8304 (tp)
REVERT: B  726 LEU cc_start: 0.9073 (tp) cc_final: 0.8764 (mm)
  outliers start: 21
  outliers final: 15
  residues processed: 129
  average time/residue: 0.2393
  time to fit residues: 45.2811
Evaluate side-chains
  129 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
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  570 CYS
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  756 SER
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 95 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 93 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3940 r_free = 0.3940 target = 0.129481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.088787 restraints weight = 18319.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.99
r_work: 0.3162 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10337  Z= 0.121
  Angle     :  0.673  14.077  14092  Z= 0.305
  Chirality :  0.044   0.291   1678
  Planarity :  0.004   0.079   1756
  Dihedral  :  8.963  82.611   1658
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.00 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.24), residues: 1258
  helix:  0.92 (0.21), residues: 568
  sheet: -0.68 (0.30), residues: 296
  loop : -1.62 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 700 
 HIS   0.003   0.001   HIS B 568 
 PHE   0.023   0.001   PHE A 633 
 TYR   0.015   0.001   TYR B 173 
 ARG   0.001   0.000   ARG A 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00563 (   10)
  link_NAG-ASN         : angle       3.46643 (   30)
  link_BETA1-4         : bond        0.01683 (    4)
  link_BETA1-4         : angle       5.44714 (   12)
  hydrogen bonds       : bond        0.03869 (  508)
  hydrogen bonds       : angle       4.27461 ( 1458)
  metal coordination   : bond        0.00164 (    5)
  SS BOND              : bond        0.00164 (    8)
  SS BOND              : angle       0.90242 (   16)
  covalent geometry    : bond        0.00261 (10310)
  covalent geometry    : angle       0.63423 (14034)

*********************** 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
  147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7671 (pp30)
REVERT: A  466 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8060 (mm-40)
REVERT: A  721 ILE cc_start: 0.8648 (mp) cc_final: 0.8292 (tp)
REVERT: A  726 LEU cc_start: 0.9054 (tp) cc_final: 0.8718 (mm)
REVERT: B   94 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7673 (pp30)
REVERT: B  466 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8259 (mm-40)
REVERT: B  595 TYR cc_start: 0.7573 (t80) cc_final: 0.7307 (t80)
REVERT: B  721 ILE cc_start: 0.8672 (mp) cc_final: 0.8313 (tp)
REVERT: B  726 LEU cc_start: 0.9033 (tp) cc_final: 0.8685 (mm)
  outliers start: 25
  outliers final: 18
  residues processed: 131
  average time/residue: 0.3103
  time to fit residues: 60.5072
Evaluate side-chains
  139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.848 
-------------------------------------------------------------------------------
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  549 LEU
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  723 ILE
Chi-restraints excluded: chain A residue  756 SER
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  309 LEU
Chi-restraints excluded: chain B residue  570 CYS
Chi-restraints excluded: chain B residue  576 PHE
Chi-restraints excluded: chain B residue  723 ILE
Chi-restraints excluded: chain B residue  776 THR
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 104 optimal weight:    0.0020
   chunk 56 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 5 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.6588

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.130543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.089936 restraints weight = 18327.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.98
r_work: 0.3197 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10337  Z= 0.112
  Angle     :  0.648  13.560  14092  Z= 0.294
  Chirality :  0.044   0.282   1678
  Planarity :  0.004   0.084   1756
  Dihedral  :  8.521  80.931   1658
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.86 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.24), residues: 1258
  helix:  1.30 (0.22), residues: 544
  sheet: -0.51 (0.30), residues: 296
  loop : -1.48 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 700 
 HIS   0.002   0.001   HIS B 568 
 PHE   0.033   0.001   PHE A 732 
 TYR   0.014   0.001   TYR A 173 
 ARG   0.001   0.000   ARG B 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00537 (   10)
  link_NAG-ASN         : angle       3.45315 (   30)
  link_BETA1-4         : bond        0.01614 (    4)
  link_BETA1-4         : angle       5.55387 (   12)
  hydrogen bonds       : bond        0.03637 (  508)
  hydrogen bonds       : angle       4.16948 ( 1458)
  metal coordination   : bond        0.00173 (    5)
  SS BOND              : bond        0.00155 (    8)
  SS BOND              : angle       0.80946 (   16)
  covalent geometry    : bond        0.00239 (10310)
  covalent geometry    : angle       0.60709 (14034)

*********************** 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
  142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7760 (pp30)
REVERT: A  466 GLN cc_start: 0.8642 (mm-40) cc_final: 0.7988 (mm-40)
REVERT: A  559 MET cc_start: 0.7948 (mmt) cc_final: 0.7735 (tpp)
REVERT: A  595 TYR cc_start: 0.7594 (t80) cc_final: 0.7330 (t80)
REVERT: A  721 ILE cc_start: 0.8622 (mp) cc_final: 0.8296 (tp)
REVERT: A  726 LEU cc_start: 0.9027 (tp) cc_final: 0.8672 (mm)
REVERT: B   94 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7759 (pp30)
REVERT: B  466 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8232 (mm-40)
REVERT: B  559 MET cc_start: 0.7958 (mmt) cc_final: 0.7735 (tpp)
REVERT: B  595 TYR cc_start: 0.7597 (t80) cc_final: 0.7355 (t80)
REVERT: B  694 MET cc_start: 0.5758 (mmt) cc_final: 0.5394 (mmt)
REVERT: B  721 ILE cc_start: 0.8661 (mp) cc_final: 0.8347 (tp)
REVERT: B  726 LEU cc_start: 0.9020 (tp) cc_final: 0.8668 (mm)
  outliers start: 21
  outliers final: 14
  residues processed: 128
  average time/residue: 0.2043
  time to fit residues: 39.1986
Evaluate side-chains
  129 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
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  756 SER
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  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 103 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 47 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.127454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.086646 restraints weight = 18356.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.92
r_work: 0.3134 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  10337  Z= 0.246
  Angle     :  0.717  13.307  14092  Z= 0.336
  Chirality :  0.046   0.292   1678
  Planarity :  0.005   0.087   1756
  Dihedral  :  8.784  80.801   1658
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.90 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.24), residues: 1258
  helix:  1.04 (0.22), residues: 556
  sheet: -0.66 (0.30), residues: 300
  loop : -1.49 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 759 
 HIS   0.004   0.001   HIS A 275 
 PHE   0.027   0.002   PHE A 732 
 TYR   0.024   0.002   TYR B 173 
 ARG   0.004   0.000   ARG B 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00491 (   10)
  link_NAG-ASN         : angle       3.47907 (   30)
  link_BETA1-4         : bond        0.01415 (    4)
  link_BETA1-4         : angle       5.23347 (   12)
  hydrogen bonds       : bond        0.04068 (  508)
  hydrogen bonds       : angle       4.35295 ( 1458)
  metal coordination   : bond        0.00680 (    5)
  SS BOND              : bond        0.00194 (    8)
  SS BOND              : angle       1.07714 (   16)
  covalent geometry    : bond        0.00578 (10310)
  covalent geometry    : angle       0.68279 (14034)

*********************** 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
  136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7688 (pp30)
REVERT: A  466 GLN cc_start: 0.8622 (mm-40) cc_final: 0.7919 (mm-40)
REVERT: A  726 LEU cc_start: 0.9104 (tp) cc_final: 0.8760 (mm)
REVERT: B   94 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7693 (pp30)
REVERT: B  466 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8078 (mm-40)
REVERT: B  726 LEU cc_start: 0.9094 (tp) cc_final: 0.8755 (mm)
  outliers start: 18
  outliers final: 14
  residues processed: 129
  average time/residue: 0.2054
  time to fit residues: 39.0768
Evaluate side-chains
  131 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
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  297 MET
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  756 SER
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   90 VAL
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 81 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.129556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.088759 restraints weight = 18055.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.96
r_work: 0.3175 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10337  Z= 0.128
  Angle     :  0.669  13.349  14092  Z= 0.310
  Chirality :  0.044   0.284   1678
  Planarity :  0.005   0.079   1756
  Dihedral  :  8.546  78.975   1658
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.81 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.24), residues: 1258
  helix:  1.15 (0.22), residues: 544
  sheet: -0.52 (0.30), residues: 296
  loop : -1.41 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 700 
 HIS   0.003   0.001   HIS B 568 
 PHE   0.054   0.002   PHE A 633 
 TYR   0.017   0.001   TYR B 595 
 ARG   0.001   0.000   ARG A 781 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00505 (   10)
  link_NAG-ASN         : angle       3.45990 (   30)
  link_BETA1-4         : bond        0.01582 (    4)
  link_BETA1-4         : angle       5.48198 (   12)
  hydrogen bonds       : bond        0.03964 (  508)
  hydrogen bonds       : angle       4.22068 ( 1458)
  metal coordination   : bond        0.00209 (    5)
  SS BOND              : bond        0.00135 (    8)
  SS BOND              : angle       0.87322 (   16)
  covalent geometry    : bond        0.00281 (10310)
  covalent geometry    : angle       0.63027 (14034)

********************** 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
  147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7629 (pp30)
REVERT: A  466 GLN cc_start: 0.8607 (mm-40) cc_final: 0.7947 (mm-40)
REVERT: A  721 ILE cc_start: 0.8345 (mp) cc_final: 0.8098 (tp)
REVERT: A  726 LEU cc_start: 0.9054 (tp) cc_final: 0.8700 (mm)
REVERT: B   94 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7626 (pp30)
REVERT: B  466 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8171 (mm-40)
REVERT: B  721 ILE cc_start: 0.8370 (mp) cc_final: 0.8121 (tp)
REVERT: B  726 LEU cc_start: 0.9018 (tp) cc_final: 0.8650 (mm)
  outliers start: 21
  outliers final: 16
  residues processed: 136
  average time/residue: 0.1951
  time to fit residues: 39.4246
Evaluate side-chains
  142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
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  297 MET
Chi-restraints excluded: chain A residue  570 CYS
Chi-restraints excluded: chain A residue  756 SER
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   90 VAL
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  576 PHE
Chi-restraints excluded: chain B residue  776 THR
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 45 optimal weight:   50.0000
   chunk 64 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 117 optimal weight:    9.9990
   chunk 51 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 30 optimal weight:   40.0000
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.128844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.088096 restraints weight = 18156.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.95
r_work: 0.3163 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10337  Z= 0.156
  Angle     :  0.677  13.194  14092  Z= 0.316
  Chirality :  0.045   0.286   1678
  Planarity :  0.005   0.086   1756
  Dihedral  :  8.468  78.081   1658
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 19.81 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.24), residues: 1258
  helix:  1.20 (0.22), residues: 544
  sheet: -0.54 (0.30), residues: 300
  loop : -1.35 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 759 
 HIS   0.003   0.001   HIS B 568 
 PHE   0.048   0.002   PHE A 633 
 TYR   0.018   0.001   TYR A 173 
 ARG   0.002   0.000   ARG B 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00483 (   10)
  link_NAG-ASN         : angle       3.46241 (   30)
  link_BETA1-4         : bond        0.01534 (    4)
  link_BETA1-4         : angle       5.39312 (   12)
  hydrogen bonds       : bond        0.03988 (  508)
  hydrogen bonds       : angle       4.22040 ( 1458)
  metal coordination   : bond        0.00332 (    5)
  SS BOND              : bond        0.00154 (    8)
  SS BOND              : angle       0.96052 (   16)
  covalent geometry    : bond        0.00357 (10310)
  covalent geometry    : angle       0.63958 (14034)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5157.12 seconds
wall clock time: 91 minutes 52.09 seconds (5512.09 seconds total)