Starting phenix.real_space_refine
on Wed Mar  4 13:04:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7aiq_11802/03_2026/7aiq_11802.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7aiq_11802/03_2026/7aiq_11802.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7aiq_11802/03_2026/7aiq_11802.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7aiq_11802/03_2026/7aiq_11802.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7aiq_11802/03_2026/7aiq_11802.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7aiq_11802/03_2026/7aiq_11802.map"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.039
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
     P       4      5.49       5
     S      96      5.16       5
     C    8769      2.51       5
     N    2223      2.21       5
     O    2422      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13514
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 878, 6695
          Classifications: {'peptide': 878}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 38, 'TRANS': 839}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 67
    Chain: "B"
      Number of atoms: 6659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 867, 6659
          Classifications: {'peptide': 867}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 37, 'TRANS': 829}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'ATP': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'ATP': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.20, per 1000 atoms: 0.24
  Number of scatterers: 13514
  At special positions: 0
  Unit cell: (107.1, 111.35, 151.3, 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)
     S      96     16.00
     P       4     15.00
     O    2422      8.00
     N    2223      7.00
     C    8769      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 163 " - pdb=" SG  CYS A 626 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 353 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 163 " - pdb=" SG  CYS B 626 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 308 " - pdb=" SG  CYS B 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 343 " - pdb=" SG  CYS B 353 " 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 C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A1101 " - " ASN A 361 "
      " NAG B1101 " - " ASN B 361 "
      " NAG C   1 " - " ASN A 312 "
      " NAG D   1 " - " ASN B 312 "
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 529.8 milliseconds
  

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3210

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 8 sheets defined
      61.9% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 133
      removed outlier: 6.010A  pdb=" N   LEU A 126 " --> pdb=" O   MET A 122 " (cutoff:3.500A)
      Proline residue:  A 127  - end of helix
    Processing helix  chain 'A' and resid 135 through 141
    Processing helix  chain 'A' and resid 141 through 177
      removed outlier: 6.496A  pdb=" N   VAL A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 9.341A  pdb=" N   LEU A 151 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLN A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   CYS A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   THR A 164 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 194
      removed outlier: 4.234A  pdb=" N   MET A 188 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ILE A 189 " --> pdb=" O   SER A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 227
      removed outlier: 3.518A  pdb=" N   LEU A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   TYR A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 269
    Processing helix  chain 'A' and resid 269 through 301
      removed outlier: 5.445A  pdb=" N   SER A 278 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   LEU A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   PHE A 280 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU A 281 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   PHE A 300 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 343
    Processing helix  chain 'A' and resid 354 through 360
      removed outlier: 3.878A  pdb=" N   MET A 358 " --> pdb=" O   ASP A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 379
    Processing helix  chain 'A' and resid 407 through 411
    Processing helix  chain 'A' and resid 419 through 428
      removed outlier: 3.743A  pdb=" N   LEU A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.605A  pdb=" N   LEU A 444 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 477
      Proline residue:  A 452  - end of helix
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 504 through 536
      removed outlier: 4.035A  pdb=" N   VAL A 508 " --> pdb=" O   PRO A 504 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A 509 " --> pdb=" O   TRP A 505 " (cutoff:3.500A)
      Proline residue:  A 527  - end of helix
    Processing helix  chain 'A' and resid 539 through 547
      removed outlier: 3.899A  pdb=" N   LEU A 542 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG A 543 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   VAL A 544 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A 545 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 570
    Processing helix  chain 'A' and resid 573 through 602
      Proline residue:  A 579  - end of helix
    Processing helix  chain 'A' and resid 615 through 634
      removed outlier: 3.824A  pdb=" N   SER A 619 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER A 634 " --> pdb=" O   MET A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 661
    Processing helix  chain 'A' and resid 664 through 682
      removed outlier: 4.127A  pdb=" N   GLU A 682 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 720
      removed outlier: 3.746A  pdb=" N   THR A 713 " --> pdb=" O   PRO A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 756
      removed outlier: 3.544A  pdb=" N   ALA A 742 " --> pdb=" O   SER A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 780
    Processing helix  chain 'A' and resid 805 through 820
      removed outlier: 3.623A  pdb=" N   LYS A 809 " --> pdb=" O   PRO A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 834
      removed outlier: 3.527A  pdb=" N   TYR A 834 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 867
      Proline residue:  A 862  - end of helix
    Processing helix  chain 'A' and resid 868 through 872
    Processing helix  chain 'A' and resid 887 through 903
      removed outlier: 4.000A  pdb=" N   MET A 891 " --> pdb=" O   ASN A 887 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   HIS A 901 " --> pdb=" O   VAL A 897 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 902 " --> pdb=" O   PHE A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 932
      removed outlier: 3.861A  pdb=" N   GLU A 924 " --> pdb=" O   ALA A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1033
      removed outlier: 3.604A  pdb=" N   ARG A1017 " --> pdb=" O   GLN A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1052 through 1064
      removed outlier: 3.632A  pdb=" N   THR A1064 " --> pdb=" O   LEU A1060 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 133
      removed outlier: 5.912A  pdb=" N   LEU B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
      Proline residue:  B 127  - end of helix
    Processing helix  chain 'B' and resid 135 through 141
    Processing helix  chain 'B' and resid 141 through 177
      removed outlier: 6.623A  pdb=" N   VAL B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 9.329A  pdb=" N   LEU B 151 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   GLN B 152 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   CYS B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR B 164 " --> pdb=" O   CYS B 160 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 194
    Processing helix  chain 'B' and resid 194 through 227
      removed outlier: 3.603A  pdb=" N   LEU B 203 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   CYS B 204 " --> pdb=" O   ALA B 200 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR B 227 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 269
    Processing helix  chain 'B' and resid 269 through 301
      removed outlier: 5.652A  pdb=" N   SER B 278 " --> pdb=" O   ASN B 274 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   LEU B 279 " --> pdb=" O   LYS B 275 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   PHE B 280 " --> pdb=" O   PHE B 276 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU B 281 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   PHE B 300 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 343
    Processing helix  chain 'B' and resid 354 through 360
      removed outlier: 3.937A  pdb=" N   MET B 358 " --> pdb=" O   ASP B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 379
      removed outlier: 3.985A  pdb=" N   LEU B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 411
    Processing helix  chain 'B' and resid 420 through 428
    Processing helix  chain 'B' and resid 429 through 432
    Processing helix  chain 'B' and resid 440 through 444
      removed outlier: 3.685A  pdb=" N   LEU B 444 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 477
      Proline residue:  B 452  - end of helix
    Processing helix  chain 'B' and resid 494 through 498
    Processing helix  chain 'B' and resid 504 through 536
      removed outlier: 3.922A  pdb=" N   VAL B 508 " --> pdb=" O   PRO B 504 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE B 509 " --> pdb=" O   TRP B 505 " (cutoff:3.500A)
      Proline residue:  B 527  - end of helix
    Processing helix  chain 'B' and resid 543 through 547
    Processing helix  chain 'B' and resid 557 through 570
    Processing helix  chain 'B' and resid 573 through 603
      Proline residue:  B 579  - end of helix
    Processing helix  chain 'B' and resid 615 through 634
      removed outlier: 3.630A  pdb=" N   SER B 619 " --> pdb=" O   HIS B 615 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER B 634 " --> pdb=" O   MET B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 661
    Processing helix  chain 'B' and resid 664 through 682
      removed outlier: 4.081A  pdb=" N   GLU B 682 " --> pdb=" O   LEU B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 720
      removed outlier: 3.784A  pdb=" N   THR B 713 " --> pdb=" O   PRO B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 756
      removed outlier: 3.730A  pdb=" N   ALA B 742 " --> pdb=" O   SER B 738 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU B 756 " --> pdb=" O   MET B 752 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 769 through 780
      removed outlier: 3.622A  pdb=" N   ALA B 775 " --> pdb=" O   ARG B 771 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 805 through 820
      removed outlier: 3.551A  pdb=" N   LYS B 809 " --> pdb=" O   PRO B 805 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASP B 813 " --> pdb=" O   LYS B 809 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 820 " --> pdb=" O   ARG B 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 834
      removed outlier: 3.642A  pdb=" N   TYR B 834 " --> pdb=" O   ILE B 831 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 854 through 867
      Proline residue:  B 862  - end of helix
    Processing helix  chain 'B' and resid 868 through 872
    Processing helix  chain 'B' and resid 888 through 903
      removed outlier: 3.832A  pdb=" N   HIS B 901 " --> pdb=" O   VAL B 897 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU B 902 " --> pdb=" O   PHE B 898 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 914 through 926
      removed outlier: 5.263A  pdb=" N   ALA B 920 " --> pdb=" O   SER B 916 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   TYR B 921 " --> pdb=" O   ASP B 917 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1015 through 1033
      removed outlier: 3.504A  pdb=" N   MET B1019 " --> pdb=" O   ASN B1015 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1052 through 1064
      removed outlier: 3.834A  pdb=" N   THR B1064 " --> pdb=" O   LEU B1060 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314
      removed outlier: 3.793A  pdb=" N   LEU A 310 " --> pdb=" O   ARG A 313 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329
    Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767
      removed outlier: 3.517A  pdb=" N   ILE A 726 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LEU A 695 " --> pdb=" O   VAL A 792 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   VAL A 791 " --> pdb=" O   LEU A 826 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A1072 " --> pdb=" O   VAL A 827 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   VAL A1070 " --> pdb=" O   LYS A 829 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   VAL A1039 " --> pdb=" O   LEU A1071 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   VAL A1073 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU A1041 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
      removed outlier: 8.442A  pdb=" N   LEU A1040 " --> pdb=" O   HIS A 845 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ASP A 847 " --> pdb=" O   LEU A1040 " (cutoff:3.500A)
      removed outlier: 8.705A  pdb=" N   ASN A1042 " --> pdb=" O   ASP A 847 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLU A 907 " --> pdb=" O   MET A 876 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   THR A 880 " --> pdb=" O   GLU A 909 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783
      removed outlier: 3.641A  pdb=" N   LEU A 783 " --> pdb=" O   MET A 786 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 314
      removed outlier: 3.650A  pdb=" N   LEU B 310 " --> pdb=" O   ARG B 313 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 329
    Processing sheet with id=AA7, first strand: chain 'B' and resid 761 through 767
      removed outlier: 6.795A  pdb=" N   THR B 725 " --> pdb=" O   PHE B 761 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   GLN B 763 " --> pdb=" O   THR B 725 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   VAL B 727 " --> pdb=" O   GLN B 763 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   VAL B 765 " --> pdb=" O   VAL B 727 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   SER B 729 " --> pdb=" O   VAL B 765 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   ALA B 767 " --> pdb=" O   SER B 729 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   ILE B 731 " --> pdb=" O   ALA B 767 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   VAL B 791 " --> pdb=" O   LEU B 826 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B1072 " --> pdb=" O   VAL B 827 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   VAL B1070 " --> pdb=" O   LYS B 829 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   VAL B1039 " --> pdb=" O   LEU B1071 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   VAL B1073 " --> pdb=" O   VAL B1039 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LEU B1041 " --> pdb=" O   VAL B1073 " (cutoff:3.500A)
      removed outlier: 8.515A  pdb=" N   LEU B1040 " --> pdb=" O   HIS B 845 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ASP B 847 " --> pdb=" O   LEU B1040 " (cutoff:3.500A)
      removed outlier: 8.700A  pdb=" N   ASN B1042 " --> pdb=" O   ASP B 847 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE B 846 " --> pdb=" O   ARG B 877 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   PHE B 879 " --> pdb=" O   ILE B 846 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   VAL B 848 " --> pdb=" O   PHE B 879 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   MET B 876 " --> pdb=" O   GLU B 907 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   GLU B 909 " --> pdb=" O   MET B 876 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ILE B 878 " --> pdb=" O   GLU B 909 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 783
      removed outlier: 3.578A  pdb=" N   LEU B 783 " --> pdb=" O   MET B 786 " (cutoff:3.500A)

    764 hydrogen bonds defined for protein.
    2211 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: 2.33

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4235
        1.35 -     1.47: 3479
        1.47 -     1.59: 5957
        1.59 -     1.72: 8
        1.72 -     1.84: 152
  Bond restraints: 13831
  Sorted by residual:
  bond pdb=" C4  ATP B1102 "
       pdb=" C5  ATP B1102 "
    ideal  model  delta    sigma   weight residual
    1.388  1.464 -0.076 1.00e-02 1.00e+04 5.71e+01
  bond pdb=" C4  ATP A1102 "
       pdb=" C5  ATP A1102 "
    ideal  model  delta    sigma   weight residual
    1.388  1.462 -0.074 1.00e-02 1.00e+04 5.47e+01
  bond pdb=" C5  ATP B1102 "
       pdb=" C6  ATP B1102 "
    ideal  model  delta    sigma   weight residual
    1.409  1.473 -0.064 1.00e-02 1.00e+04 4.08e+01
  bond pdb=" O1B ATP B1102 "
       pdb=" PB  ATP B1102 "
    ideal  model  delta    sigma   weight residual
    1.477  1.609 -0.132 2.20e-02 2.07e+03 3.58e+01
  bond pdb=" O1B ATP A1102 "
       pdb=" PB  ATP A1102 "
    ideal  model  delta    sigma   weight residual
    1.477  1.607 -0.130 2.20e-02 2.07e+03 3.48e+01
  ... (remaining 13826 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.79: 18388
        2.79 -     5.58: 384
        5.58 -     8.36: 51
        8.36 -    11.15: 17
       11.15 -    13.94: 4
  Bond angle restraints: 18844
  Sorted by residual:
  angle pdb=" PA  ATP A1102 "
        pdb=" O3A ATP A1102 "
        pdb=" PB  ATP A1102 "
      ideal   model   delta    sigma   weight residual
     136.83  122.89   13.94 1.00e+00 1.00e+00 1.94e+02
  angle pdb=" PA  ATP B1102 "
        pdb=" O3A ATP B1102 "
        pdb=" PB  ATP B1102 "
      ideal   model   delta    sigma   weight residual
     136.83  124.70   12.13 1.00e+00 1.00e+00 1.47e+02
  angle pdb=" C5  ATP B1102 "
        pdb=" C4  ATP B1102 "
        pdb=" N3  ATP B1102 "
      ideal   model   delta    sigma   weight residual
     126.80  118.38    8.42 1.00e+00 1.00e+00 7.08e+01
  angle pdb=" C5  ATP A1102 "
        pdb=" C4  ATP A1102 "
        pdb=" N3  ATP A1102 "
      ideal   model   delta    sigma   weight residual
     126.80  118.45    8.35 1.00e+00 1.00e+00 6.97e+01
  angle pdb=" N3  ATP B1102 "
        pdb=" C4  ATP B1102 "
        pdb=" N9  ATP B1102 "
      ideal   model   delta    sigma   weight residual
     127.04  135.12   -8.08 1.15e+00 7.59e-01 4.95e+01
  ... (remaining 18839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.48: 7549
       24.48 -    48.97: 596
       48.97 -    73.45: 63
       73.45 -    97.93: 23
       97.93 -   122.41: 25
  Dihedral angle restraints: 8256
    sinusoidal: 3245
      harmonic: 5011
  Sorted by residual:
  dihedral pdb=" CB  CYS A 343 "
           pdb=" SG  CYS A 343 "
           pdb=" SG  CYS A 353 "
           pdb=" CB  CYS A 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.12  -45.12     1      1.00e+01 1.00e-02 2.83e+01
  dihedral pdb=" CB  CYS B 343 "
           pdb=" SG  CYS B 343 "
           pdb=" SG  CYS B 353 "
           pdb=" CB  CYS B 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.12  -41.12     1      1.00e+01 1.00e-02 2.37e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C1  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C5  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   59.45 -122.41     1      3.00e+01 1.11e-03 1.64e+01
  ... (remaining 8253 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1563
       0.051 -    0.103: 541
       0.103 -    0.154: 103
       0.154 -    0.205: 17
       0.205 -    0.257: 5
  Chirality restraints: 2229
  Sorted by residual:
  chirality pdb=" CB  VAL A 881 "
            pdb=" CA  VAL A 881 "
            pdb=" CG1 VAL A 881 "
            pdb=" CG2 VAL A 881 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.53    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.52    0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 2226 not shown)

  Planarity restraints: 2330
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 137 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   LEU A 137 "    0.059 2.00e-02 2.50e+03
        pdb=" O   LEU A 137 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   PHE A 138 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 121 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.61e+00
        pdb=" C   LEU B 121 "    0.037 2.00e-02 2.50e+03
        pdb=" O   LEU B 121 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET B 122 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 408 "   -0.033 5.00e-02 4.00e+02   4.96e-02 3.93e+00
        pdb=" N   PRO B 409 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 409 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 409 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 2327 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1919
        2.74 -     3.28: 13369
        3.28 -     3.82: 21304
        3.82 -     4.36: 23058
        4.36 -     4.90: 41742
  Nonbonded interactions: 101392
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 314 "
            pdb=" O   VAL A 391 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" NE2 GLN A 152 "
            pdb=" OH  TYR A 384 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OG  SER B 430 "
            pdb=" OH  TYR B 466 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   GLY A 479 "
            pdb=" NH2 ARG A 483 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O   SER B 780 "
            pdb=" OG  SER B 780 "
     model   vdw
     2.254 3.040
  ... (remaining 101387 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 116 through 881 or resid 887 through 926 or resid 1014 thr \ 
ough 1102))
  selection = (chain 'B' and (resid 116 through 233 or resid 244 through 347 or (resid 348 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 349 through 912 o \ 
r (resid 913 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 
14 through 1019 or (resid 1020 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 1021 through 1102))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.800
  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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.650
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.132  13845  Z= 0.419
  Angle     :  1.024  13.940  18880  Z= 0.562
  Chirality :  0.053   0.257   2229
  Planarity :  0.005   0.050   2326
  Dihedral  : 18.348 122.414   5028
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 20.95 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.19), residues: 1731
  helix:  0.32 (0.16), residues: 953
  sheet: -1.90 (0.41), residues: 136
  loop : -2.74 (0.22), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 440 
 TYR   0.021   0.002   TYR A 356 
 PHE   0.026   0.003   PHE B 541 
 TRP   0.030   0.003   TRP B 795 
 HIS   0.011   0.002   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00869 (13831)
  covalent geometry    : angle       1.01383 (18844)
  SS BOND              : bond        0.00558 (    6)
  SS BOND              : angle       3.88512 (   12)
  hydrogen bonds       : bond        0.15785 (  764)
  hydrogen bonds       : angle       5.75474 ( 2211)
  link_BETA1-4         : bond        0.01538 (    4)
  link_BETA1-4         : angle       3.56861 (   12)
  link_NAG-ASN         : bond        0.00733 (    4)
  link_NAG-ASN         : angle       2.85943 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 307
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8251 (mtp) cc_final: 0.7775 (tmm)
REVERT: A  144 MET cc_start: 0.8485 (ttp) cc_final: 0.8037 (ptm)
REVERT: A  186 TYR cc_start: 0.8882 (t80) cc_final: 0.8590 (t80)
REVERT: A  188 MET cc_start: 0.7584 (mtm) cc_final: 0.7211 (ttt)
REVERT: A  313 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6262 (mtm-85)
REVERT: A  358 MET cc_start: 0.9423 (mpp) cc_final: 0.9108 (mpp)
REVERT: A  391 VAL cc_start: 0.8254 (t) cc_final: 0.7669 (t)
REVERT: A  630 MET cc_start: 0.8819 (ttp) cc_final: 0.8449 (ttp)
REVERT: A  658 GLU cc_start: 0.8283 (tt0) cc_final: 0.7922 (mm-30)
REVERT: A  752 MET cc_start: 0.9315 (tpp) cc_final: 0.8882 (tpp)
REVERT: A  859 MET cc_start: 0.9326 (mtp) cc_final: 0.8793 (mmp)
REVERT: A  878 ILE cc_start: 0.8829 (mt) cc_final: 0.8614 (mm)
REVERT: A 1074 ARG cc_start: 0.8646 (ttt90) cc_final: 0.8376 (ttt90)
REVERT: A 1078 ARG cc_start: 0.8653 (mtm110) cc_final: 0.8316 (ptm160)
REVERT: B  118 MET cc_start: 0.8444 (ptm) cc_final: 0.7770 (ptm)
REVERT: B  122 MET cc_start: 0.8997 (mtp) cc_final: 0.8205 (tmm)
REVERT: B  385 LEU cc_start: 0.9527 (mt) cc_final: 0.9058 (mt)
REVERT: B  419 SER cc_start: 0.8543 (t) cc_final: 0.7926 (p)
REVERT: B  563 LEU cc_start: 0.8774 (mp) cc_final: 0.8524 (tt)
REVERT: B  596 CYS cc_start: 0.8318 (m) cc_final: 0.8034 (t)
REVERT: B  630 MET cc_start: 0.9050 (ttp) cc_final: 0.8621 (ttm)
REVERT: B  659 LYS cc_start: 0.9087 (tttt) cc_final: 0.8728 (ttmm)
REVERT: B  696 VAL cc_start: 0.9062 (t) cc_final: 0.8849 (m)
REVERT: B  746 GLU cc_start: 0.8805 (tt0) cc_final: 0.8264 (tp30)
REVERT: B  750 LYS cc_start: 0.9389 (mttt) cc_final: 0.8569 (mttp)
REVERT: B  752 MET cc_start: 0.8794 (tpp) cc_final: 0.8564 (tpp)
REVERT: B  791 VAL cc_start: 0.9484 (t) cc_final: 0.9196 (m)
REVERT: B  813 ASP cc_start: 0.9114 (m-30) cc_final: 0.8845 (t0)
REVERT: B  857 MET cc_start: 0.8982 (ptm) cc_final: 0.8624 (pmm)
REVERT: B  874 CYS cc_start: 0.8415 (m) cc_final: 0.6985 (t)
REVERT: B 1055 ASN cc_start: 0.9231 (m110) cc_final: 0.8759 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 321
  average time/residue: 0.1163
  time to fit residues: 55.1235
Evaluate side-chains
  174 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  699 LYS
Chi-restraints excluded: chain A residue  903 ARG
Chi-restraints excluded: chain A residue 1021 THR
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  353 CYS
Chi-restraints excluded: chain B residue  427 PHE
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  699 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:   40.0000
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
A 344 HIS
A 521 GLN
A 655 GLN
A 732 GLN
A 751 ASN
B 130 GLN
B 152 GLN
B 250 ASN
B 344 HIS
B 655 GLN
B 717 GLN
B 732 GLN
B 747 GLN
B 751 ASN
B 763 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.095875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.070182 restraints weight = 38921.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.073140 restraints weight = 18647.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.075142 restraints weight = 11562.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.076549 restraints weight = 8402.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.077454 restraints weight = 6792.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13845  Z= 0.149
  Angle     :  0.686   9.481  18880  Z= 0.337
  Chirality :  0.044   0.235   2229
  Planarity :  0.004   0.048   2326
  Dihedral  : 12.782 104.337   2121
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 22.08 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.20), residues: 1731
  helix:  1.49 (0.17), residues: 952
  sheet: -1.08 (0.42), residues: 133
  loop : -2.33 (0.21), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 317 
 TYR   0.016   0.001   TYR A 292 
 PHE   0.018   0.002   PHE B 863 
 TRP   0.011   0.001   TRP B 143 
 HIS   0.005   0.001   HIS A 845 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (13831)
  covalent geometry    : angle       0.67676 (18844)
  SS BOND              : bond        0.00501 (    6)
  SS BOND              : angle       1.93483 (   12)
  hydrogen bonds       : bond        0.05338 (  764)
  hydrogen bonds       : angle       4.39407 ( 2211)
  link_BETA1-4         : bond        0.01166 (    4)
  link_BETA1-4         : angle       3.67555 (   12)
  link_NAG-ASN         : bond        0.00204 (    4)
  link_NAG-ASN         : angle       1.81192 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 217
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8197 (mtp) cc_final: 0.7802 (tmm)
REVERT: A  144 MET cc_start: 0.8263 (ttp) cc_final: 0.7933 (ptm)
REVERT: A  147 THR cc_start: 0.8488 (t) cc_final: 0.8236 (t)
REVERT: A  186 TYR cc_start: 0.8700 (t80) cc_final: 0.8294 (t80)
REVERT: A  188 MET cc_start: 0.7567 (mtm) cc_final: 0.7214 (ttt)
REVERT: A  358 MET cc_start: 0.9404 (mpp) cc_final: 0.9006 (mpp)
REVERT: A  484 ASP cc_start: 0.8373 (m-30) cc_final: 0.7781 (p0)
REVERT: A  542 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8353 (pp)
REVERT: A  631 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8435 (t80)
REVERT: A  658 GLU cc_start: 0.8404 (tt0) cc_final: 0.7996 (mm-30)
REVERT: A  752 MET cc_start: 0.9309 (tpp) cc_final: 0.8802 (tpp)
REVERT: A  753 MET cc_start: 0.9139 (ttp) cc_final: 0.8626 (ptm)
REVERT: A  848 VAL cc_start: 0.8685 (t) cc_final: 0.8389 (m)
REVERT: A  854 ASP cc_start: 0.8336 (m-30) cc_final: 0.8066 (m-30)
REVERT: A  859 MET cc_start: 0.9152 (mtp) cc_final: 0.8626 (mmp)
REVERT: A  864 LEU cc_start: 0.9359 (mt) cc_final: 0.9156 (mp)
REVERT: A 1078 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8204 (ptm160)
REVERT: B  353 CYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8330 (m)
REVERT: B  380 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8624 (tt)
REVERT: B  419 SER cc_start: 0.8488 (t) cc_final: 0.8150 (p)
REVERT: B  542 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8304 (pp)
REVERT: B  563 LEU cc_start: 0.8695 (mp) cc_final: 0.8491 (tt)
REVERT: B  576 MET cc_start: 0.8284 (mtp) cc_final: 0.7962 (mtp)
REVERT: B  587 MET cc_start: 0.8963 (tpt) cc_final: 0.8580 (tpt)
REVERT: B  623 MET cc_start: 0.9372 (tmm) cc_final: 0.8731 (tmm)
REVERT: B  630 MET cc_start: 0.8854 (ttp) cc_final: 0.8571 (ttm)
REVERT: B  659 LYS cc_start: 0.9071 (tttt) cc_final: 0.8680 (ttmm)
REVERT: B  693 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8159 (mm110)
REVERT: B  699 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7935 (tttt)
REVERT: B  712 LEU cc_start: 0.8813 (mt) cc_final: 0.8466 (mt)
REVERT: B  746 GLU cc_start: 0.8657 (tt0) cc_final: 0.7991 (tp30)
REVERT: B  750 LYS cc_start: 0.9392 (mttt) cc_final: 0.8513 (mttp)
REVERT: B  813 ASP cc_start: 0.9097 (m-30) cc_final: 0.8816 (t0)
REVERT: B  874 CYS cc_start: 0.8553 (m) cc_final: 0.7396 (t)
REVERT: B 1055 ASN cc_start: 0.9217 (m110) cc_final: 0.8775 (t0)
  outliers start: 60
  outliers final: 27
  residues processed: 260
  average time/residue: 0.0907
  time to fit residues: 38.2864
Evaluate side-chains
  201 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 168
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  480 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  631 PHE
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  343 CYS
Chi-restraints excluded: chain B residue  353 CYS
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  699 LYS
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 132 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0060
   chunk 100 optimal weight:    0.8980
   chunk 171 optimal weight:    9.9990
   chunk 116 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
A 717 GLN
A 868 HIS
B 763 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.096895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.071210 restraints weight = 39017.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.074222 restraints weight = 18537.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.076258 restraints weight = 11449.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.077695 restraints weight = 8296.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.078638 restraints weight = 6668.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13845  Z= 0.118
  Angle     :  0.630  10.704  18880  Z= 0.301
  Chirality :  0.042   0.224   2229
  Planarity :  0.004   0.053   2326
  Dihedral  : 11.660 101.592   2108
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 23.64 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.20), residues: 1731
  helix:  1.88 (0.17), residues: 950
  sheet: -0.64 (0.43), residues: 135
  loop : -2.03 (0.21), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.012   0.001   TYR A 292 
 PHE   0.015   0.001   PHE A 620 
 TRP   0.009   0.001   TRP B 143 
 HIS   0.006   0.001   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (13831)
  covalent geometry    : angle       0.62165 (18844)
  SS BOND              : bond        0.00232 (    6)
  SS BOND              : angle       1.62184 (   12)
  hydrogen bonds       : bond        0.04539 (  764)
  hydrogen bonds       : angle       4.02885 ( 2211)
  link_BETA1-4         : bond        0.01056 (    4)
  link_BETA1-4         : angle       3.53026 (   12)
  link_NAG-ASN         : bond        0.00062 (    4)
  link_NAG-ASN         : angle       1.54688 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 184
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8205 (mtp) cc_final: 0.7822 (tmm)
REVERT: A  144 MET cc_start: 0.8212 (ttp) cc_final: 0.7858 (ptm)
REVERT: A  147 THR cc_start: 0.8545 (t) cc_final: 0.8288 (t)
REVERT: A  188 MET cc_start: 0.7598 (mtm) cc_final: 0.7264 (ttm)
REVERT: A  358 MET cc_start: 0.9417 (mpp) cc_final: 0.9018 (mpp)
REVERT: A  376 LEU cc_start: 0.8844 (tp) cc_final: 0.8595 (tp)
REVERT: A  484 ASP cc_start: 0.8276 (m-30) cc_final: 0.7882 (p0)
REVERT: A  536 ASP cc_start: 0.7979 (t70) cc_final: 0.7758 (t0)
REVERT: A  658 GLU cc_start: 0.8402 (tt0) cc_final: 0.7946 (mm-30)
REVERT: A  752 MET cc_start: 0.9291 (tpp) cc_final: 0.8741 (tpp)
REVERT: A  791 VAL cc_start: 0.9006 (t) cc_final: 0.8737 (p)
REVERT: A  848 VAL cc_start: 0.8672 (t) cc_final: 0.8349 (m)
REVERT: A  854 ASP cc_start: 0.8194 (m-30) cc_final: 0.7987 (m-30)
REVERT: A  859 MET cc_start: 0.9087 (mtp) cc_final: 0.8653 (mmp)
REVERT: A  876 MET cc_start: 0.9087 (ttm) cc_final: 0.8838 (ttp)
REVERT: A 1043 MET cc_start: 0.9064 (ptt) cc_final: 0.8832 (pmm)
REVERT: A 1078 ARG cc_start: 0.8554 (mtm110) cc_final: 0.8224 (ptm160)
REVERT: B  390 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8643 (mm)
REVERT: B  542 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8166 (pp)
REVERT: B  576 MET cc_start: 0.8255 (mtp) cc_final: 0.7973 (mtp)
REVERT: B  587 MET cc_start: 0.8775 (tpt) cc_final: 0.8503 (tpt)
REVERT: B  630 MET cc_start: 0.8577 (ttp) cc_final: 0.8275 (ttm)
REVERT: B  659 LYS cc_start: 0.9021 (tttt) cc_final: 0.8657 (ttmm)
REVERT: B  693 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8118 (mm110)
REVERT: B  750 LYS cc_start: 0.9353 (mttt) cc_final: 0.9055 (mtmm)
REVERT: B  813 ASP cc_start: 0.9045 (m-30) cc_final: 0.8786 (t0)
REVERT: B  874 CYS cc_start: 0.8634 (m) cc_final: 0.7376 (t)
REVERT: B  900 TYR cc_start: 0.8972 (m-80) cc_final: 0.8476 (m-80)
REVERT: B 1055 ASN cc_start: 0.9168 (m110) cc_final: 0.8750 (t0)
  outliers start: 58
  outliers final: 32
  residues processed: 232
  average time/residue: 0.0897
  time to fit residues: 33.7360
Evaluate side-chains
  195 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 161
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  717 GLN
Chi-restraints excluded: chain A residue  781 CYS
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 145 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 152 optimal weight:    1.9990
   chunk 158 optimal weight:    5.9990
   chunk 78 optimal weight:   30.0000
   chunk 28 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0040
   chunk 59 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 76 optimal weight:   30.0000
   overall best weight:    2.0000

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

Flipped N/Q/H residues before XYZ refinement:
A 717 GLN
B 615 HIS
B 763 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.096906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.071201 restraints weight = 39869.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.074231 restraints weight = 18783.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.076299 restraints weight = 11563.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.077706 restraints weight = 8376.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.078566 restraints weight = 6743.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13845  Z= 0.143
  Angle     :  0.618  10.765  18880  Z= 0.297
  Chirality :  0.042   0.220   2229
  Planarity :  0.003   0.046   2326
  Dihedral  : 11.009  97.608   2101
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 25.27 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.20), residues: 1731
  helix:  2.00 (0.17), residues: 955
  sheet: -0.46 (0.46), residues: 120
  loop : -1.84 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1074 
 TYR   0.012   0.001   TYR A 292 
 PHE   0.019   0.001   PHE B1059 
 TRP   0.008   0.001   TRP B 143 
 HIS   0.005   0.001   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13831)
  covalent geometry    : angle       0.61047 (18844)
  SS BOND              : bond        0.00277 (    6)
  SS BOND              : angle       1.53700 (   12)
  hydrogen bonds       : bond        0.04449 (  764)
  hydrogen bonds       : angle       3.96130 ( 2211)
  link_BETA1-4         : bond        0.00857 (    4)
  link_BETA1-4         : angle       3.42029 (   12)
  link_NAG-ASN         : bond        0.00124 (    4)
  link_NAG-ASN         : angle       1.49963 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 162
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8237 (mtp) cc_final: 0.7814 (tmm)
REVERT: A  144 MET cc_start: 0.8217 (ttp) cc_final: 0.7887 (ptm)
REVERT: A  147 THR cc_start: 0.8575 (t) cc_final: 0.8328 (t)
REVERT: A  188 MET cc_start: 0.7536 (mtm) cc_final: 0.7318 (ttm)
REVERT: A  215 MET cc_start: 0.6733 (tpp) cc_final: 0.6512 (tpt)
REVERT: A  358 MET cc_start: 0.9426 (mpp) cc_final: 0.9157 (mpp)
REVERT: A  536 ASP cc_start: 0.8218 (t0) cc_final: 0.7996 (t0)
REVERT: A  658 GLU cc_start: 0.8431 (tt0) cc_final: 0.8045 (tp30)
REVERT: A  752 MET cc_start: 0.9304 (tpp) cc_final: 0.8927 (tpp)
REVERT: A  791 VAL cc_start: 0.8966 (t) cc_final: 0.8684 (p)
REVERT: A  859 MET cc_start: 0.9133 (mtp) cc_final: 0.8667 (mmp)
REVERT: A  876 MET cc_start: 0.9052 (ttm) cc_final: 0.8816 (ttp)
REVERT: A 1041 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7821 (pt)
REVERT: A 1042 ASN cc_start: 0.8161 (p0) cc_final: 0.7733 (p0)
REVERT: A 1043 MET cc_start: 0.9104 (ptt) cc_final: 0.8804 (pmm)
REVERT: A 1078 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8284 (ptm160)
REVERT: B  171 MET cc_start: 0.8868 (tpp) cc_final: 0.8620 (tpp)
REVERT: B  450 SER cc_start: 0.9381 (t) cc_final: 0.8779 (p)
REVERT: B  542 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8126 (pp)
REVERT: B  576 MET cc_start: 0.8289 (mtp) cc_final: 0.8002 (mtp)
REVERT: B  587 MET cc_start: 0.8765 (tpt) cc_final: 0.8486 (tpt)
REVERT: B  623 MET cc_start: 0.9402 (tmm) cc_final: 0.9187 (tmm)
REVERT: B  659 LYS cc_start: 0.8983 (tttt) cc_final: 0.8610 (ttmm)
REVERT: B  750 LYS cc_start: 0.9357 (mttt) cc_final: 0.9063 (mtmm)
REVERT: B  813 ASP cc_start: 0.9050 (m-30) cc_final: 0.8796 (t0)
REVERT: B  874 CYS cc_start: 0.8756 (m) cc_final: 0.7442 (t)
REVERT: B  900 TYR cc_start: 0.8974 (m-80) cc_final: 0.8452 (m-80)
REVERT: B 1055 ASN cc_start: 0.9181 (m110) cc_final: 0.8758 (t0)
  outliers start: 58
  outliers final: 44
  residues processed: 208
  average time/residue: 0.0917
  time to fit residues: 30.9826
Evaluate side-chains
  201 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 155
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  880 THR
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  574 LEU
Chi-restraints excluded: chain B residue  590 LEU
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain B residue  853 HIS
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 129 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 114 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 763 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 = 0.3569 r_free = 0.3569 target = 0.096634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.070618 restraints weight = 40239.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.073642 restraints weight = 18930.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.075706 restraints weight = 11676.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.077128 restraints weight = 8480.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.078100 restraints weight = 6841.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13845  Z= 0.152
  Angle     :  0.626  12.129  18880  Z= 0.299
  Chirality :  0.041   0.230   2229
  Planarity :  0.003   0.036   2326
  Dihedral  : 10.487  96.443   2101
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 25.05 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.20), residues: 1731
  helix:  2.06 (0.17), residues: 950
  sheet: -0.36 (0.46), residues: 122
  loop : -1.65 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.011   0.001   TYR B 649 
 PHE   0.018   0.001   PHE B 541 
 TRP   0.009   0.001   TRP A 690 
 HIS   0.005   0.001   HIS A 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (13831)
  covalent geometry    : angle       0.61724 (18844)
  SS BOND              : bond        0.00305 (    6)
  SS BOND              : angle       1.54205 (   12)
  hydrogen bonds       : bond        0.04462 (  764)
  hydrogen bonds       : angle       3.92103 ( 2211)
  link_BETA1-4         : bond        0.00766 (    4)
  link_BETA1-4         : angle       3.62687 (   12)
  link_NAG-ASN         : bond        0.00205 (    4)
  link_NAG-ASN         : angle       1.43413 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 162
  time to evaluate  : 0.518 
Fit side-chains
REVERT: A  122 MET cc_start: 0.8272 (mtp) cc_final: 0.7830 (tmm)
REVERT: A  144 MET cc_start: 0.8217 (ttp) cc_final: 0.7864 (ptm)
REVERT: A  147 THR cc_start: 0.8562 (t) cc_final: 0.8334 (t)
REVERT: A  156 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8413 (mp)
REVERT: A  160 CYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8046 (p)
REVERT: A  188 MET cc_start: 0.7654 (mtm) cc_final: 0.7317 (ttm)
REVERT: A  358 MET cc_start: 0.9461 (mpp) cc_final: 0.9196 (mpp)
REVERT: A  484 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7678 (p0)
REVERT: A  536 ASP cc_start: 0.8211 (t0) cc_final: 0.7993 (t0)
REVERT: A  630 MET cc_start: 0.8641 (tpp) cc_final: 0.8316 (tpp)
REVERT: A  658 GLU cc_start: 0.8433 (tt0) cc_final: 0.8042 (tp30)
REVERT: A  752 MET cc_start: 0.9312 (tpp) cc_final: 0.8922 (tpp)
REVERT: A  757 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8764 (mmmm)
REVERT: A  791 VAL cc_start: 0.8985 (t) cc_final: 0.8737 (p)
REVERT: A  806 ARG cc_start: 0.8578 (mmt90) cc_final: 0.8100 (mmp80)
REVERT: A  859 MET cc_start: 0.9182 (mtp) cc_final: 0.8683 (mmp)
REVERT: A  876 MET cc_start: 0.9063 (ttm) cc_final: 0.8836 (ttp)
REVERT: A 1041 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7871 (pt)
REVERT: A 1042 ASN cc_start: 0.8190 (p0) cc_final: 0.7779 (p0)
REVERT: A 1043 MET cc_start: 0.9132 (ptt) cc_final: 0.8810 (pmm)
REVERT: A 1078 ARG cc_start: 0.8662 (mtm110) cc_final: 0.8321 (ptm160)
REVERT: B  258 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8363 (t80)
REVERT: B  416 ILE cc_start: 0.9439 (tt) cc_final: 0.9107 (mm)
REVERT: B  542 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8234 (pp)
REVERT: B  576 MET cc_start: 0.8261 (mtp) cc_final: 0.7959 (mtp)
REVERT: B  587 MET cc_start: 0.8893 (tpt) cc_final: 0.8637 (tpt)
REVERT: B  623 MET cc_start: 0.9408 (tmm) cc_final: 0.9173 (tmm)
REVERT: B  630 MET cc_start: 0.8883 (ttm) cc_final: 0.8656 (ttm)
REVERT: B  659 LYS cc_start: 0.9007 (tttt) cc_final: 0.8633 (ttmm)
REVERT: B  750 LYS cc_start: 0.9393 (mttt) cc_final: 0.9070 (mtmm)
REVERT: B  813 ASP cc_start: 0.9057 (m-30) cc_final: 0.8797 (t0)
REVERT: B  874 CYS cc_start: 0.8774 (m) cc_final: 0.7510 (t)
REVERT: B 1055 ASN cc_start: 0.9194 (m110) cc_final: 0.8762 (t0)
REVERT: B 1057 MET cc_start: 0.9279 (tpp) cc_final: 0.9028 (tpp)
  outliers start: 66
  outliers final: 51
  residues processed: 214
  average time/residue: 0.0977
  time to fit residues: 33.1375
Evaluate side-chains
  209 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 152
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  880 THR
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  343 CYS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  574 LEU
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  643 LEU
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 141 optimal weight:    0.7980
   chunk 87 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 66 optimal weight:    6.9990
   chunk 157 optimal weight:    0.2980
   chunk 98 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 76 optimal weight:   30.0000
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 170 optimal weight:    6.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 763 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.096433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.070744 restraints weight = 40216.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.073722 restraints weight = 19148.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.075771 restraints weight = 11868.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.077185 restraints weight = 8626.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.078036 restraints weight = 6971.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13845  Z= 0.138
  Angle     :  0.594   9.194  18880  Z= 0.286
  Chirality :  0.041   0.224   2229
  Planarity :  0.003   0.037   2326
  Dihedral  :  9.206  92.372   2101
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 25.19 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.20), residues: 1731
  helix:  2.16 (0.17), residues: 956
  sheet: -0.37 (0.45), residues: 123
  loop : -1.56 (0.22), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 866 
 TYR   0.011   0.001   TYR B 649 
 PHE   0.020   0.001   PHE B1059 
 TRP   0.009   0.001   TRP B 143 
 HIS   0.004   0.001   HIS A 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (13831)
  covalent geometry    : angle       0.58200 (18844)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       1.49151 (   12)
  hydrogen bonds       : bond        0.04280 (  764)
  hydrogen bonds       : angle       3.83177 ( 2211)
  link_BETA1-4         : bond        0.00432 (    4)
  link_BETA1-4         : angle       4.32944 (   12)
  link_NAG-ASN         : bond        0.00305 (    4)
  link_NAG-ASN         : angle       1.46794 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 162
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8279 (mtp) cc_final: 0.7821 (tmm)
REVERT: A  144 MET cc_start: 0.8199 (ttp) cc_final: 0.7877 (ptm)
REVERT: A  147 THR cc_start: 0.8583 (t) cc_final: 0.8351 (t)
REVERT: A  156 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8414 (mp)
REVERT: A  160 CYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8027 (p)
REVERT: A  171 MET cc_start: 0.7290 (tpp) cc_final: 0.6999 (tpp)
REVERT: A  188 MET cc_start: 0.7706 (mtm) cc_final: 0.7457 (ttm)
REVERT: A  215 MET cc_start: 0.6839 (tpp) cc_final: 0.6435 (tpp)
REVERT: A  358 MET cc_start: 0.9473 (mpp) cc_final: 0.9211 (mpp)
REVERT: A  380 LEU cc_start: 0.9088 (tt) cc_final: 0.8879 (pp)
REVERT: A  484 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7504 (p0)
REVERT: A  630 MET cc_start: 0.8579 (tpp) cc_final: 0.8350 (tpp)
REVERT: A  658 GLU cc_start: 0.8418 (tt0) cc_final: 0.8041 (tp30)
REVERT: A  752 MET cc_start: 0.9322 (tpp) cc_final: 0.8919 (tpp)
REVERT: A  791 VAL cc_start: 0.8978 (t) cc_final: 0.8760 (p)
REVERT: A  859 MET cc_start: 0.9206 (mtp) cc_final: 0.8687 (mmp)
REVERT: A  876 MET cc_start: 0.9016 (ttm) cc_final: 0.8805 (ttp)
REVERT: A 1041 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7861 (pt)
REVERT: A 1042 ASN cc_start: 0.8194 (p0) cc_final: 0.7850 (p0)
REVERT: A 1043 MET cc_start: 0.9153 (ptt) cc_final: 0.8832 (pmm)
REVERT: A 1078 ARG cc_start: 0.8691 (mtm110) cc_final: 0.8352 (ptm160)
REVERT: B  258 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8322 (t80)
REVERT: B  416 ILE cc_start: 0.9448 (tt) cc_final: 0.9152 (mm)
REVERT: B  542 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8281 (pp)
REVERT: B  576 MET cc_start: 0.8252 (mtp) cc_final: 0.7952 (mtp)
REVERT: B  587 MET cc_start: 0.8890 (tpt) cc_final: 0.8615 (tpt)
REVERT: B  591 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8791 (m-80)
REVERT: B  623 MET cc_start: 0.9389 (tmm) cc_final: 0.9119 (tmm)
REVERT: B  659 LYS cc_start: 0.8983 (tttt) cc_final: 0.8613 (ttmm)
REVERT: B  750 LYS cc_start: 0.9395 (mttt) cc_final: 0.9036 (mtmm)
REVERT: B  781 CYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8323 (m)
REVERT: B  813 ASP cc_start: 0.9048 (m-30) cc_final: 0.8780 (t0)
REVERT: B 1043 MET cc_start: 0.9026 (ptm) cc_final: 0.8567 (tmm)
REVERT: B 1055 ASN cc_start: 0.9205 (m110) cc_final: 0.8772 (t0)
  outliers start: 70
  outliers final: 50
  residues processed: 219
  average time/residue: 0.0876
  time to fit residues: 31.2188
Evaluate side-chains
  211 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 153
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  781 CYS
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  343 CYS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  574 LEU
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  643 LEU
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  781 CYS
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 136 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 126 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 113 optimal weight:   10.0000
   chunk 163 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 112 optimal weight:    1.9990
   chunk 168 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3563 r_free = 0.3563 target = 0.096092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.070510 restraints weight = 40492.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.073472 restraints weight = 19182.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.075523 restraints weight = 11878.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.076881 restraints weight = 8630.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.077848 restraints weight = 6980.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13845  Z= 0.138
  Angle     :  0.603   8.792  18880  Z= 0.290
  Chirality :  0.041   0.253   2229
  Planarity :  0.003   0.038   2326
  Dihedral  :  8.656  87.504   2101
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 26.11 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.21), residues: 1731
  helix:  2.18 (0.17), residues: 957
  sheet: -0.36 (0.46), residues: 117
  loop : -1.42 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 317 
 TYR   0.011   0.001   TYR B 649 
 PHE   0.027   0.001   PHE B1059 
 TRP   0.009   0.001   TRP B 143 
 HIS   0.004   0.001   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (13831)
  covalent geometry    : angle       0.59583 (18844)
  SS BOND              : bond        0.00348 (    6)
  SS BOND              : angle       1.55221 (   12)
  hydrogen bonds       : bond        0.04260 (  764)
  hydrogen bonds       : angle       3.82595 ( 2211)
  link_BETA1-4         : bond        0.00855 (    4)
  link_BETA1-4         : angle       3.24034 (   12)
  link_NAG-ASN         : bond        0.00188 (    4)
  link_NAG-ASN         : angle       1.30735 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 167
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8290 (mtp) cc_final: 0.7832 (tmm)
REVERT: A  144 MET cc_start: 0.8202 (ttp) cc_final: 0.7873 (ptm)
REVERT: A  147 THR cc_start: 0.8587 (t) cc_final: 0.8355 (t)
REVERT: A  156 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8420 (mp)
REVERT: A  160 CYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8065 (p)
REVERT: A  172 SER cc_start: 0.8757 (t) cc_final: 0.8237 (p)
REVERT: A  188 MET cc_start: 0.7688 (mtm) cc_final: 0.7395 (ttm)
REVERT: A  309 MET cc_start: 0.8734 (mmm) cc_final: 0.8503 (tpp)
REVERT: A  358 MET cc_start: 0.9472 (mpp) cc_final: 0.9215 (mpp)
REVERT: A  484 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7417 (p0)
REVERT: A  630 MET cc_start: 0.8792 (tpp) cc_final: 0.8438 (tpp)
REVERT: A  658 GLU cc_start: 0.8388 (tt0) cc_final: 0.7923 (mm-30)
REVERT: A  752 MET cc_start: 0.9328 (tpp) cc_final: 0.8920 (tpp)
REVERT: A  791 VAL cc_start: 0.9000 (t) cc_final: 0.8795 (p)
REVERT: A  859 MET cc_start: 0.9213 (mtp) cc_final: 0.8639 (mmp)
REVERT: A  876 MET cc_start: 0.9053 (ttm) cc_final: 0.8852 (ttp)
REVERT: A 1041 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7932 (pt)
REVERT: A 1042 ASN cc_start: 0.8130 (p0) cc_final: 0.7822 (p0)
REVERT: A 1043 MET cc_start: 0.9153 (ptt) cc_final: 0.8814 (pmm)
REVERT: A 1078 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8370 (ptm160)
REVERT: B  258 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8312 (t80)
REVERT: B  416 ILE cc_start: 0.9428 (tt) cc_final: 0.9147 (mm)
REVERT: B  419 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8071 (p)
REVERT: B  542 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8289 (pp)
REVERT: B  576 MET cc_start: 0.8248 (mtp) cc_final: 0.7945 (mtp)
REVERT: B  587 MET cc_start: 0.8937 (tpt) cc_final: 0.8685 (tpt)
REVERT: B  591 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8818 (m-80)
REVERT: B  623 MET cc_start: 0.9391 (tmm) cc_final: 0.9122 (tmm)
REVERT: B  659 LYS cc_start: 0.8972 (tttt) cc_final: 0.8610 (ttmm)
REVERT: B  750 LYS cc_start: 0.9373 (mttt) cc_final: 0.9006 (mtmm)
REVERT: B  781 CYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8342 (m)
REVERT: B  813 ASP cc_start: 0.9045 (m-30) cc_final: 0.8795 (t0)
REVERT: B 1055 ASN cc_start: 0.9206 (m110) cc_final: 0.8429 (t0)
REVERT: B 1059 PHE cc_start: 0.9214 (t80) cc_final: 0.8803 (t80)
  outliers start: 68
  outliers final: 52
  residues processed: 222
  average time/residue: 0.0860
  time to fit residues: 31.2819
Evaluate side-chains
  219 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 158
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  781 CYS
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  343 CYS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  419 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  574 LEU
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  634 SER
Chi-restraints excluded: chain B residue  643 LEU
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  781 CYS
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 93 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 68 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0870
   chunk 97 optimal weight:    0.8980
   chunk 123 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
B 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.097998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.072609 restraints weight = 39613.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.075658 restraints weight = 18714.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.077668 restraints weight = 11541.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.079144 restraints weight = 8389.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.080003 restraints weight = 6743.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13845  Z= 0.107
  Angle     :  0.609  13.649  18880  Z= 0.285
  Chirality :  0.041   0.236   2229
  Planarity :  0.003   0.039   2326
  Dihedral  :  8.299  82.068   2101
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 28.03 %
    Favored  : 69.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.21), residues: 1731
  helix:  2.24 (0.17), residues: 956
  sheet: -0.23 (0.47), residues: 117
  loop : -1.37 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 816 
 TYR   0.015   0.001   TYR B1056 
 PHE   0.024   0.001   PHE B1059 
 TRP   0.009   0.001   TRP B 635 
 HIS   0.005   0.001   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (13831)
  covalent geometry    : angle       0.60212 (18844)
  SS BOND              : bond        0.00210 (    6)
  SS BOND              : angle       1.36440 (   12)
  hydrogen bonds       : bond        0.03885 (  764)
  hydrogen bonds       : angle       3.74737 ( 2211)
  link_BETA1-4         : bond        0.00658 (    4)
  link_BETA1-4         : angle       3.27626 (   12)
  link_NAG-ASN         : bond        0.00064 (    4)
  link_NAG-ASN         : angle       1.06731 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 183
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8239 (mtp) cc_final: 0.7791 (tmm)
REVERT: A  144 MET cc_start: 0.8170 (ttp) cc_final: 0.7883 (ptm)
REVERT: A  147 THR cc_start: 0.8565 (t) cc_final: 0.8336 (t)
REVERT: A  160 CYS cc_start: 0.8730 (m) cc_final: 0.8046 (p)
REVERT: A  215 MET cc_start: 0.6623 (tpp) cc_final: 0.6236 (mmt)
REVERT: A  309 MET cc_start: 0.8741 (mmm) cc_final: 0.8532 (tpp)
REVERT: A  358 MET cc_start: 0.9468 (mpp) cc_final: 0.9231 (mpp)
REVERT: A  380 LEU cc_start: 0.9025 (tt) cc_final: 0.8800 (pp)
REVERT: A  435 MET cc_start: 0.8878 (mmt) cc_final: 0.8659 (mmm)
REVERT: A  630 MET cc_start: 0.8750 (tpp) cc_final: 0.8401 (tpp)
REVERT: A  658 GLU cc_start: 0.8381 (tt0) cc_final: 0.7913 (mm-30)
REVERT: A  752 MET cc_start: 0.9318 (tpp) cc_final: 0.8891 (tpp)
REVERT: A  859 MET cc_start: 0.9209 (mtp) cc_final: 0.8633 (mmp)
REVERT: A  876 MET cc_start: 0.8979 (ttm) cc_final: 0.8774 (ttp)
REVERT: A 1041 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7840 (pt)
REVERT: A 1042 ASN cc_start: 0.8068 (p0) cc_final: 0.7766 (p0)
REVERT: A 1043 MET cc_start: 0.9104 (ptt) cc_final: 0.8854 (pmm)
REVERT: A 1078 ARG cc_start: 0.8691 (mtm110) cc_final: 0.8355 (ptm160)
REVERT: B  258 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8385 (t80)
REVERT: B  390 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8967 (mm)
REVERT: B  416 ILE cc_start: 0.9399 (tt) cc_final: 0.9134 (mm)
REVERT: B  419 SER cc_start: 0.8250 (t) cc_final: 0.8011 (p)
REVERT: B  450 SER cc_start: 0.9353 (t) cc_final: 0.8849 (p)
REVERT: B  521 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8032 (tm-30)
REVERT: B  542 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8251 (pp)
REVERT: B  576 MET cc_start: 0.8220 (mtp) cc_final: 0.7919 (mtp)
REVERT: B  587 MET cc_start: 0.8896 (tpt) cc_final: 0.8654 (tpt)
REVERT: B  591 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8781 (m-80)
REVERT: B  623 MET cc_start: 0.9364 (tmm) cc_final: 0.9133 (tmm)
REVERT: B  659 LYS cc_start: 0.9002 (tttt) cc_final: 0.8613 (ttmm)
REVERT: B  746 GLU cc_start: 0.8569 (tt0) cc_final: 0.8270 (tm-30)
REVERT: B  750 LYS cc_start: 0.9357 (mttt) cc_final: 0.8447 (mttp)
REVERT: B  781 CYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8203 (m)
REVERT: B  813 ASP cc_start: 0.9013 (m-30) cc_final: 0.8746 (t0)
REVERT: B 1043 MET cc_start: 0.9106 (ttp) cc_final: 0.8839 (tmm)
REVERT: B 1055 ASN cc_start: 0.8954 (m110) cc_final: 0.8460 (t0)
  outliers start: 42
  outliers final: 29
  residues processed: 219
  average time/residue: 0.0887
  time to fit residues: 31.4508
Evaluate side-chains
  199 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  343 CYS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  781 CYS
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 147 optimal weight:    0.3980
   chunk 138 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 148 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3603 r_free = 0.3603 target = 0.098273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.073072 restraints weight = 40343.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.076138 restraints weight = 19006.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.078220 restraints weight = 11671.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.079637 restraints weight = 8421.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.080495 restraints weight = 6766.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13845  Z= 0.109
  Angle     :  0.601  10.099  18880  Z= 0.283
  Chirality :  0.041   0.256   2229
  Planarity :  0.003   0.040   2326
  Dihedral  :  7.894  77.722   2099
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 28.52 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.21), residues: 1731
  helix:  2.24 (0.17), residues: 956
  sheet: -0.13 (0.46), residues: 117
  loop : -1.28 (0.23), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1074 
 TYR   0.011   0.001   TYR B 649 
 PHE   0.015   0.001   PHE B 428 
 TRP   0.008   0.001   TRP A 616 
 HIS   0.005   0.001   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (13831)
  covalent geometry    : angle       0.59513 (18844)
  SS BOND              : bond        0.00236 (    6)
  SS BOND              : angle       1.29905 (   12)
  hydrogen bonds       : bond        0.03809 (  764)
  hydrogen bonds       : angle       3.72120 ( 2211)
  link_BETA1-4         : bond        0.00642 (    4)
  link_BETA1-4         : angle       3.16800 (   12)
  link_NAG-ASN         : bond        0.00089 (    4)
  link_NAG-ASN         : angle       1.05005 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 168
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8255 (mtp) cc_final: 0.7819 (tmm)
REVERT: A  144 MET cc_start: 0.8179 (ttp) cc_final: 0.7905 (ptm)
REVERT: A  147 THR cc_start: 0.8574 (t) cc_final: 0.8345 (t)
REVERT: A  156 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8316 (mp)
REVERT: A  160 CYS cc_start: 0.8719 (m) cc_final: 0.8026 (p)
REVERT: A  215 MET cc_start: 0.6566 (tpp) cc_final: 0.6166 (mmt)
REVERT: A  309 MET cc_start: 0.8766 (mmm) cc_final: 0.8563 (tpp)
REVERT: A  313 ARG cc_start: 0.6939 (mtm180) cc_final: 0.6638 (mtm-85)
REVERT: A  358 MET cc_start: 0.9478 (mpp) cc_final: 0.9235 (mpp)
REVERT: A  630 MET cc_start: 0.8763 (tpp) cc_final: 0.8431 (tpp)
REVERT: A  636 TYR cc_start: 0.7863 (p90) cc_final: 0.7616 (p90)
REVERT: A  658 GLU cc_start: 0.8343 (tt0) cc_final: 0.7900 (mm-30)
REVERT: A  752 MET cc_start: 0.9321 (tpp) cc_final: 0.8890 (tpp)
REVERT: A  859 MET cc_start: 0.9217 (mtp) cc_final: 0.8635 (mmp)
REVERT: A  876 MET cc_start: 0.8975 (ttm) cc_final: 0.8747 (ttp)
REVERT: A 1041 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7871 (pt)
REVERT: A 1042 ASN cc_start: 0.8038 (p0) cc_final: 0.7740 (p0)
REVERT: A 1043 MET cc_start: 0.9105 (ptt) cc_final: 0.8875 (pmm)
REVERT: A 1078 ARG cc_start: 0.8663 (mtm110) cc_final: 0.8327 (ptm160)
REVERT: B  258 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8447 (t80)
REVERT: B  416 ILE cc_start: 0.9409 (tt) cc_final: 0.9154 (mm)
REVERT: B  419 SER cc_start: 0.8261 (t) cc_final: 0.8036 (p)
REVERT: B  450 SER cc_start: 0.9354 (t) cc_final: 0.8865 (p)
REVERT: B  521 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8035 (tm-30)
REVERT: B  542 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8234 (pp)
REVERT: B  576 MET cc_start: 0.8192 (mtp) cc_final: 0.7892 (mtp)
REVERT: B  587 MET cc_start: 0.8901 (tpt) cc_final: 0.8629 (tpt)
REVERT: B  591 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8810 (m-80)
REVERT: B  623 MET cc_start: 0.9378 (tmm) cc_final: 0.9131 (tmm)
REVERT: B  659 LYS cc_start: 0.9002 (tttt) cc_final: 0.8606 (ttmm)
REVERT: B  781 CYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8171 (m)
REVERT: B  813 ASP cc_start: 0.8986 (m-30) cc_final: 0.8705 (t0)
REVERT: B 1043 MET cc_start: 0.9053 (ttp) cc_final: 0.8769 (tmm)
REVERT: B 1055 ASN cc_start: 0.8960 (m110) cc_final: 0.8479 (t0)
  outliers start: 41
  outliers final: 32
  residues processed: 200
  average time/residue: 0.0989
  time to fit residues: 31.6386
Evaluate side-chains
  204 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 166
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  642 MET
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue 1041 LEU
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  343 CYS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  781 CYS
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 168 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 162 optimal weight:    0.5980
   chunk 15 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 134 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 109 optimal weight:    8.9990
   overall best weight:    3.3188

-------------------------------------------------------------------------------
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 = 0.3551 r_free = 0.3551 target = 0.095094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.069354 restraints weight = 40581.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.072289 restraints weight = 19378.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.074221 restraints weight = 12065.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.075631 restraints weight = 8822.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.076575 restraints weight = 7134.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13845  Z= 0.198
  Angle     :  0.676  11.822  18880  Z= 0.325
  Chirality :  0.043   0.260   2229
  Planarity :  0.003   0.038   2326
  Dihedral  :  7.829  74.264   2099
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 28.52 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.21), residues: 1731
  helix:  2.21 (0.17), residues: 954
  sheet: -0.34 (0.43), residues: 131
  loop : -1.26 (0.23), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1074 
 TYR   0.012   0.001   TYR B 649 
 PHE   0.022   0.001   PHE B1059 
 TRP   0.013   0.001   TRP B 795 
 HIS   0.006   0.001   HIS A 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (13831)
  covalent geometry    : angle       0.66993 (18844)
  SS BOND              : bond        0.00356 (    6)
  SS BOND              : angle       1.60600 (   12)
  hydrogen bonds       : bond        0.04449 (  764)
  hydrogen bonds       : angle       3.90135 ( 2211)
  link_BETA1-4         : bond        0.00622 (    4)
  link_BETA1-4         : angle       3.12518 (   12)
  link_NAG-ASN         : bond        0.00286 (    4)
  link_NAG-ASN         : angle       1.10488 (   12)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 158
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8317 (mtp) cc_final: 0.7797 (tmm)
REVERT: A  144 MET cc_start: 0.8240 (ttp) cc_final: 0.7893 (ptm)
REVERT: A  147 THR cc_start: 0.8610 (t) cc_final: 0.8388 (t)
REVERT: A  156 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8316 (mp)
REVERT: A  160 CYS cc_start: 0.8767 (m) cc_final: 0.8091 (p)
REVERT: A  215 MET cc_start: 0.6725 (tpp) cc_final: 0.6374 (tpp)
REVERT: A  313 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6565 (mtm-85)
REVERT: A  358 MET cc_start: 0.9494 (mpp) cc_final: 0.9256 (mpp)
REVERT: A  630 MET cc_start: 0.8790 (tpp) cc_final: 0.8453 (tpp)
REVERT: A  636 TYR cc_start: 0.7989 (p90) cc_final: 0.7735 (p90)
REVERT: A  658 GLU cc_start: 0.8382 (tt0) cc_final: 0.8054 (tp30)
REVERT: A  752 MET cc_start: 0.9325 (tpp) cc_final: 0.8904 (tpp)
REVERT: A  859 MET cc_start: 0.9264 (mtp) cc_final: 0.8677 (mmp)
REVERT: A  876 MET cc_start: 0.9052 (ttm) cc_final: 0.8832 (ttp)
REVERT: A 1078 ARG cc_start: 0.8738 (mtm110) cc_final: 0.8394 (ptm160)
REVERT: B  258 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8256 (t80)
REVERT: B  416 ILE cc_start: 0.9427 (tt) cc_final: 0.9171 (mm)
REVERT: B  419 SER cc_start: 0.8457 (t) cc_final: 0.8246 (p)
REVERT: B  450 SER cc_start: 0.9449 (t) cc_final: 0.8915 (p)
REVERT: B  542 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8314 (pp)
REVERT: B  576 MET cc_start: 0.8229 (mtp) cc_final: 0.7910 (mtp)
REVERT: B  587 MET cc_start: 0.8938 (tpt) cc_final: 0.8619 (tpt)
REVERT: B  623 MET cc_start: 0.9413 (tmm) cc_final: 0.9114 (tmm)
REVERT: B  630 MET cc_start: 0.8948 (ttm) cc_final: 0.8739 (ttm)
REVERT: B  659 LYS cc_start: 0.8981 (tttt) cc_final: 0.8633 (ttmm)
REVERT: B  781 CYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8283 (m)
REVERT: B  813 ASP cc_start: 0.9045 (m-30) cc_final: 0.8790 (t0)
REVERT: B 1043 MET cc_start: 0.9118 (ttp) cc_final: 0.8811 (tmm)
REVERT: B 1055 ASN cc_start: 0.8980 (m110) cc_final: 0.8520 (t0)
  outliers start: 45
  outliers final: 35
  residues processed: 193
  average time/residue: 0.0942
  time to fit residues: 28.9664
Evaluate side-chains
  192 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 153
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  781 CYS
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  258 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  342 PHE
Chi-restraints excluded: chain B residue  343 CYS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  430 SER
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  643 LEU
Chi-restraints excluded: chain B residue  781 CYS
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain B residue  853 HIS
Chi-restraints excluded: chain B residue  910 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0270
   chunk 147 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 52 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0270
   chunk 88 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9990
   overall best weight:    0.7900

-------------------------------------------------------------------------------
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 = 0.3603 r_free = 0.3603 target = 0.098232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.072735 restraints weight = 40057.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.075785 restraints weight = 18969.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.077863 restraints weight = 11724.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.079305 restraints weight = 8497.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.080255 restraints weight = 6834.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  13845  Z= 0.111
  Angle     :  0.640  11.901  18880  Z= 0.299
  Chirality :  0.041   0.274   2229
  Planarity :  0.003   0.040   2326
  Dihedral  :  7.513  69.692   2099
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 29.23 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.21), residues: 1731
  helix:  2.27 (0.17), residues: 953
  sheet: -0.28 (0.44), residues: 132
  loop : -1.18 (0.23), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1074 
 TYR   0.011   0.001   TYR B1056 
 PHE   0.017   0.001   PHE B 428 
 TRP   0.011   0.001   TRP B 635 
 HIS   0.004   0.001   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (13831)
  covalent geometry    : angle       0.63405 (18844)
  SS BOND              : bond        0.00212 (    6)
  SS BOND              : angle       1.34963 (   12)
  hydrogen bonds       : bond        0.03908 (  764)
  hydrogen bonds       : angle       3.73944 ( 2211)
  link_BETA1-4         : bond        0.00798 (    4)
  link_BETA1-4         : angle       3.23332 (   12)
  link_NAG-ASN         : bond        0.00108 (    4)
  link_NAG-ASN         : angle       1.02818 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2430.87 seconds
wall clock time: 42 minutes 42.71 seconds (2562.71 seconds total)