Starting phenix.real_space_refine
on Tue Jun 10 11:42:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w4a_32299/06_2025/7w4a_32299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w4a_32299/06_2025/7w4a_32299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w4a_32299/06_2025/7w4a_32299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w4a_32299/06_2025/7w4a_32299.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w4a_32299/06_2025/7w4a_32299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w4a_32299/06_2025/7w4a_32299.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1623 atoms to isotropic.
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: 9
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     Mg      1      5.21       5
     S      64      5.16       5
     Na      1      4.78       5
     Be      1      3.05       5
     C    6318      2.51       5
     N    1638      2.21       5
     O    1827      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9855
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 984, 7642
          Classifications: {'peptide': 984}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 47, 'TRANS': 936}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
    Chain: "B"
      Number of atoms: 2076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2076
          Classifications: {'peptide': 261}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 4, 'PTRANS': 17, 'TRANS': 239}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 1, ' NA': 1, '8CK': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 96
          Unusual residues: {'NAG': 3, 'PCW': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 6.39, per 1000 atoms: 0.65
  Number of scatterers: 9855
  At special positions: 0
  Unit cell: (118.064, 91.744, 170.704, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     S      64     16.00
     P       1     15.00
     Mg      1     11.99
     Na      1     11.00
     F       4      9.00
     O    1827      8.00
     N    1638      7.00
     C    6318      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 201 " - pdb=" SG  CYS B 262 " 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
    NAG-ASN
      " NAG B 301 " - " ASN B  99 "
      " NAG B 302 " - " ASN B 130 "
      " NAG B 303 " - " ASN B 161 "
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2330

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 9 sheets defined
      51.0% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 55
      removed outlier: 3.536A  pdb=" N   GLN A  54 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 65
    Processing helix  chain 'A' and resid 73 through 85
    Processing helix  chain 'A' and resid 96 through 105
    Processing helix  chain 'A' and resid 107 through 130
    Processing helix  chain 'A' and resid 135 through 168
      removed outlier: 4.006A  pdb=" N   LEU A 139 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 171
      No H-bonds generated for 'chain 'A' and resid 169 through 171'
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 274 through 286
    Processing helix  chain 'A' and resid 291 through 323
    Processing helix  chain 'A' and resid 325 through 340
    Processing helix  chain 'A' and resid 343 through 363
      removed outlier: 4.440A  pdb=" N   ALA A 347 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LYS A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 379
      removed outlier: 3.540A  pdb=" N   ALA A 372 " --> pdb=" O   ASN A 369 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLU A 374 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   LEU A 376 " --> pdb=" O   VAL A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 438
    Processing helix  chain 'A' and resid 459 through 473
    Processing helix  chain 'A' and resid 475 through 483
      removed outlier: 3.829A  pdb=" N   GLU A 481 " --> pdb=" O   MET A 477 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A 482 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   PHE A 483 " --> pdb=" O   TYR A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 524
    Processing helix  chain 'A' and resid 540 through 556
    Processing helix  chain 'A' and resid 607 through 618
    Processing helix  chain 'A' and resid 629 through 640
    Processing helix  chain 'A' and resid 649 through 658
    Processing helix  chain 'A' and resid 665 through 669
    Processing helix  chain 'A' and resid 675 through 682
    Processing helix  chain 'A' and resid 683 through 694
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 727 through 729
      No H-bonds generated for 'chain 'A' and resid 727 through 729'
    Processing helix  chain 'A' and resid 730 through 737
    Processing helix  chain 'A' and resid 748 through 755
    Processing helix  chain 'A' and resid 765 through 791
      removed outlier: 3.795A  pdb=" N   THR A 769 " --> pdb=" O   ALA A 765 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   LYS A 791 " --> pdb=" O   TYR A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 806
      Proline residue:  A 798  - end of helix
    Processing helix  chain 'A' and resid 812 through 822
    Processing helix  chain 'A' and resid 824 through 831
      removed outlier: 3.700A  pdb=" N   SER A 828 " --> pdb=" O   ASP A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 855 through 865
    Processing helix  chain 'A' and resid 865 through 886
    Processing helix  chain 'A' and resid 888 through 893
      removed outlier: 3.532A  pdb=" N   VAL A 893 " --> pdb=" O   PRO A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 900
    Processing helix  chain 'A' and resid 916 through 947
      removed outlier: 3.729A  pdb=" N   ALA A 941 " --> pdb=" O   MET A 937 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 944 " --> pdb=" O   ILE A 940 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 980
    Processing helix  chain 'A' and resid 983 through 988
      removed outlier: 3.682A  pdb=" N   ILE A 987 " --> pdb=" O   GLY A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1000
    Processing helix  chain 'A' and resid 1001 through 1022
    Processing helix  chain 'A' and resid 1025 through 1032
    Processing helix  chain 'B' and resid 33 through 66
    Processing helix  chain 'B' and resid 102 through 119
      removed outlier: 4.448A  pdb=" N   TRP B 106 " --> pdb=" O   ASP B 102 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLY B 108 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   LEU B 109 " --> pdb=" O   THR B 105 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   GLY B 119 " --> pdb=" O   ARG B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 4.109A  pdb=" N   GLU B 126 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 164
      removed outlier: 6.253A  pdb=" N   ASN B 161 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLY B 164 " --> pdb=" O   ASN B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 223
      removed outlier: 3.809A  pdb=" N   THR B 223 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
      removed outlier: 3.556A  pdb=" N   PHE B 229 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189
      removed outlier: 3.546A  pdb=" N   ARG A 182 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   CYS A 258 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASP A 223 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   THR A 262 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   GLY A 219 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   GLN A 264 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   ALA A 217 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   LEU A 266 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU A 215 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL A 268 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   ARG A 213 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   CYS A 220 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   ASN A 224 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   GLU A 232 " --> pdb=" O   ASN A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 189
      removed outlier: 3.546A  pdb=" N   ARG A 182 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   CYS A 258 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASP A 223 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   THR A 262 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   GLY A 219 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   GLN A 264 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   ALA A 217 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   LEU A 266 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU A 215 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL A 268 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   ARG A 213 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367
      removed outlier: 6.138A  pdb=" N   GLY A 740 " --> pdb=" O   MET A 757 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU A 759 " --> pdb=" O   GLY A 740 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ALA A 742 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   VAL A 721 " --> pdb=" O   ILE A 739 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   VAL A 741 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   VAL A 723 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   MET A 743 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   GLY A 725 " --> pdb=" O   MET A 743 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   VAL A 381 " --> pdb=" O   ALA A 722 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   THR A 724 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   CYS A 383 " --> pdb=" O   THR A 724 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   VAL A 622 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 8.342A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   MET A 624 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   CYS A 672 " --> pdb=" O   VAL A 698 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408
      removed outlier: 3.562A  pdb=" N   THR A 396 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   SER A 599 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   PHE A 402 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 10.024A  pdb=" N   ALA A 595 " --> pdb=" O   PHE A 402 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   PHE A 564 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU A 562 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   SER A 599 " --> pdb=" O   ARG A 560 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ARG A 560 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   CYS A 487 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408
      removed outlier: 3.562A  pdb=" N   THR A 396 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   SER A 599 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   PHE A 402 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 10.024A  pdb=" N   ALA A 595 " --> pdb=" O   PHE A 402 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   LEU A 592 " --> pdb=" O   CYS A 527 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLY A 596 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908
    Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85
      removed outlier: 3.576A  pdb=" N   VAL B 245 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 99

    527 hydrogen bonds defined for protein.
    1497 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.18

  Time building geometry restraints manager: 3.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3142
        1.34 -     1.46: 1780
        1.46 -     1.58: 5049
        1.58 -     1.70: 2
        1.70 -     1.82: 95
  Bond restraints: 10068
  Sorted by residual:
  bond pdb=" F3  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.529  1.763 -0.234 2.00e-02 2.50e+03 1.36e+02
  bond pdb=" F2  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.535  1.754 -0.219 2.00e-02 2.50e+03 1.19e+02
  bond pdb=" F1  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.542  1.753 -0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" CG  BFD A 385 "
       pdb=" OD1 BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.269  1.450 -0.181 2.00e-02 2.50e+03 8.15e+01
  bond pdb=" C31 PCW B 304 "
       pdb=" O2  PCW B 304 "
    ideal  model  delta    sigma   weight residual
    1.333  1.454 -0.121 2.00e-02 2.50e+03 3.68e+01
  ... (remaining 10063 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 13603
        3.37 -     6.74: 62
        6.74 -    10.11: 11
       10.11 -    13.48: 1
       13.48 -    16.86: 4
  Bond angle restraints: 13681
  Sorted by residual:
  angle pdb=" F2  BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F3  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     112.60   95.74   16.86 3.00e+00 1.11e-01 3.16e+01
  angle pdb=" OD1 BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F1  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     102.38  118.72  -16.34 3.00e+00 1.11e-01 2.97e+01
  angle pdb=" F1  BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F3  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     111.29   95.71   15.58 3.00e+00 1.11e-01 2.70e+01
  angle pdb=" C   ASN A 792 "
        pdb=" N   ILE A 793 "
        pdb=" CA  ILE A 793 "
      ideal   model   delta    sigma   weight residual
     120.24  123.49   -3.25 6.30e-01 2.52e+00 2.67e+01
  angle pdb=" OD1 BFD A 385 "
        pdb="BE   BFD A 385 "
        pdb=" F3  BFD A 385 "
      ideal   model   delta    sigma   weight residual
     109.93   95.90   14.03 3.00e+00 1.11e-01 2.19e+01
  ... (remaining 13676 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.41: 5728
       22.41 -    44.81: 315
       44.81 -    67.22: 31
       67.22 -    89.62: 15
       89.62 -   112.03: 3
  Dihedral angle restraints: 6092
    sinusoidal: 2475
      harmonic: 3617
  Sorted by residual:
  dihedral pdb=" CB  CYS B 131 "
           pdb=" SG  CYS B 131 "
           pdb=" SG  CYS B 152 "
           pdb=" CB  CYS B 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.85   55.15     1      1.00e+01 1.00e-02 4.11e+01
  dihedral pdb=" C3  NAG B 302 "
           pdb=" C1  NAG B 302 "
           pdb=" C2  NAG B 302 "
           pdb=" O5  NAG B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.55   56.48 -112.03     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" N2  NAG B 302 "
           pdb=" C1  NAG B 302 "
           pdb=" C2  NAG B 302 "
           pdb=" O5  NAG B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -67.58 -110.61     1      3.00e+01 1.11e-03 1.44e+01
  ... (remaining 6089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1250
       0.053 -    0.106: 256
       0.106 -    0.158: 39
       0.158 -    0.211: 2
       0.211 -    0.264: 2
  Chirality restraints: 1549
  Sorted by residual:
  chirality pdb=" C1  NAG B 302 "
            pdb=" ND2 ASN B 130 "
            pdb=" C2  NAG B 302 "
            pdb=" O5  NAG B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CB  VAL A 930 "
            pdb=" CA  VAL A 930 "
            pdb=" CG1 VAL A 930 "
            pdb=" CG2 VAL A 930 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C2  PCW B 304 "
            pdb=" C1  PCW B 304 "
            pdb=" C3  PCW B 304 "
            pdb=" O2  PCW B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.52    0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 1546 not shown)

  Planarity restraints: 1757
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 232 "   -0.041 5.00e-02 4.00e+02   6.22e-02 6.19e+00
        pdb=" N   PRO A 233 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 233 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 233 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  99 "    0.001 2.00e-02 2.50e+03   1.92e-02 4.62e+00
        pdb=" CG  ASN B  99 "   -0.024 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  99 "    0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  99 "   -0.020 2.00e-02 2.50e+03
        pdb=" C1  NAG B 301 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 237 "   -0.034 5.00e-02 4.00e+02   5.27e-02 4.44e+00
        pdb=" N   PRO A 238 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 238 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 238 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1754 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 74
        2.62 -     3.19: 8723
        3.19 -     3.76: 15535
        3.76 -     4.33: 21460
        4.33 -     4.90: 35355
  Nonbonded interactions: 81147
  Sorted by model distance:
  nonbonded pdb=" F2  BFD A 385 "
            pdb="MG    MG A1103 "
     model   vdw
     2.048 2.120
  nonbonded pdb=" OD2 BFD A 385 "
            pdb="MG    MG A1103 "
     model   vdw
     2.082 2.170
  nonbonded pdb=" ND2 ASN A 792 "
            pdb=" O   HOH A1201 "
     model   vdw
     2.146 3.120
  nonbonded pdb=" OH  TYR A1011 "
            pdb=" OH  TYR B  43 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O   SER A 244 "
            pdb=" OG1 THR A 248 "
     model   vdw
     2.240 3.040
  ... (remaining 81142 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.740
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:14.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.234  10074  Z= 0.279
  Angle     :  0.718  16.855  13696  Z= 0.345
  Chirality :  0.044   0.264   1549
  Planarity :  0.004   0.062   1754
  Dihedral  : 13.796 112.026   3753
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.24), residues: 1238
  helix:  1.76 (0.21), residues: 575
  sheet: -0.01 (0.37), residues: 162
  loop :  0.21 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 427 
 HIS   0.009   0.001   HIS B 114 
 PHE   0.030   0.002   PHE A 124 
 TYR   0.018   0.001   TYR A 802 
 ARG   0.008   0.000   ARG A 844 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00419 (    3)
  link_NAG-ASN         : angle       3.55352 (    9)
  hydrogen bonds       : bond        0.13589 (  508)
  hydrogen bonds       : angle       5.56355 ( 1497)
  SS BOND              : bond        0.00158 (    3)
  SS BOND              : angle       0.70251 (    6)
  covalent geometry    : bond        0.00571 (10068)
  covalent geometry    : angle       0.71250 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  140 TYR cc_start: 0.6553 (m-10) cc_final: 0.6270 (m-10)
REVERT: A  213 ARG cc_start: 0.5596 (ttt-90) cc_final: 0.5284 (ttt180)
REVERT: A  220 CYS cc_start: 0.6849 (t) cc_final: 0.6577 (t)
REVERT: A  260 GLU cc_start: 0.5871 (mt-10) cc_final: 0.5612 (mt-10)
REVERT: A  314 THR cc_start: 0.6909 (t) cc_final: 0.6619 (p)
REVERT: A  320 MET cc_start: 0.6875 (mmp) cc_final: 0.6515 (mmp)
REVERT: A  333 PHE cc_start: 0.7257 (t80) cc_final: 0.6890 (t80)
REVERT: A  369 ASN cc_start: 0.7437 (p0) cc_final: 0.7182 (p0)
REVERT: A  425 GLU cc_start: 0.4301 (pm20) cc_final: 0.3772 (tm-30)
REVERT: A  585 MET cc_start: -0.1063 (mmt) cc_final: -0.1434 (mmt)
REVERT: A  652 ASP cc_start: 0.5905 (m-30) cc_final: 0.5649 (m-30)
REVERT: A  743 MET cc_start: 0.8061 (mmm) cc_final: 0.7789 (mpp)
REVERT: A  970 PHE cc_start: 0.7261 (t80) cc_final: 0.7056 (t80)
REVERT: B  147 HIS cc_start: 0.6754 (t-90) cc_final: 0.6450 (t-170)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 1.2450
  time to fit residues: 184.4826
Evaluate side-chains
  108 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
A 706 GLN
A 924 GLN
A 986 ASN
B 146 ASN
B 289 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.179289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.131026 restraints weight = 11338.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.64
r_work: 0.3176 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10074  Z= 0.158
  Angle     :  0.587   6.261  13696  Z= 0.302
  Chirality :  0.045   0.262   1549
  Planarity :  0.005   0.062   1754
  Dihedral  :  8.182  93.404   1480
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  6.54 %
    Favored  : 91.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.24), residues: 1238
  helix:  1.82 (0.21), residues: 564
  sheet: -0.06 (0.37), residues: 162
  loop :  0.17 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 998 
 HIS   0.007   0.001   HIS B 227 
 PHE   0.018   0.002   PHE A 932 
 TYR   0.019   0.002   TYR A 802 
 ARG   0.004   0.001   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00589 (    3)
  link_NAG-ASN         : angle       2.33785 (    9)
  hydrogen bonds       : bond        0.04996 (  508)
  hydrogen bonds       : angle       4.69942 ( 1497)
  SS BOND              : bond        0.00346 (    3)
  SS BOND              : angle       0.94304 (    6)
  covalent geometry    : bond        0.00373 (10068)
  covalent geometry    : angle       0.58402 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7219 (m-10) cc_final: 0.6807 (m-10)
REVERT: A  193 GLN cc_start: 0.6251 (mm-40) cc_final: 0.5680 (mm-40)
REVERT: A  213 ARG cc_start: 0.5848 (ttt-90) cc_final: 0.5509 (ttt180)
REVERT: A  260 GLU cc_start: 0.6188 (mt-10) cc_final: 0.5865 (mt-10)
REVERT: A  320 MET cc_start: 0.6825 (mmp) cc_final: 0.6592 (mmp)
REVERT: A  333 PHE cc_start: 0.7399 (t80) cc_final: 0.7053 (t80)
REVERT: A  425 GLU cc_start: 0.4244 (pm20) cc_final: 0.3761 (tm-30)
REVERT: A  516 MET cc_start: 0.4087 (tmt) cc_final: 0.3727 (tmt)
REVERT: A  652 ASP cc_start: 0.5948 (m-30) cc_final: 0.5681 (m-30)
REVERT: A  986 ASN cc_start: 0.6635 (m-40) cc_final: 0.6415 (m110)
REVERT: B  114 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.6413 (t-90)
REVERT: B  135 LYS cc_start: 0.7566 (ptpp) cc_final: 0.7323 (ptpp)
REVERT: B  147 HIS cc_start: 0.6932 (t-90) cc_final: 0.6575 (t-170)
REVERT: B  258 VAL cc_start: 0.7808 (p) cc_final: 0.7522 (m)
  outliers start: 19
  outliers final: 7
  residues processed: 127
  average time/residue: 1.2007
  time to fit residues: 165.1112
Evaluate side-chains
  121 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  906 ASP
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 108 optimal weight:    0.1980
   chunk 102 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
B 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.180374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.131027 restraints weight = 11576.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.63
r_work: 0.3242 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10074  Z= 0.112
  Angle     :  0.511   7.911  13696  Z= 0.259
  Chirality :  0.042   0.192   1549
  Planarity :  0.004   0.057   1754
  Dihedral  :  7.661  88.128   1480
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.38 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.24), residues: 1238
  helix:  2.11 (0.22), residues: 565
  sheet:  0.07 (0.38), residues: 162
  loop :  0.21 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 915 
 HIS   0.005   0.001   HIS B 227 
 PHE   0.015   0.001   PHE A 970 
 TYR   0.015   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00410 (    3)
  link_NAG-ASN         : angle       2.08803 (    9)
  hydrogen bonds       : bond        0.04173 (  508)
  hydrogen bonds       : angle       4.45046 ( 1497)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       0.70132 (    6)
  covalent geometry    : bond        0.00248 (10068)
  covalent geometry    : angle       0.50819 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7127 (m-10) cc_final: 0.6715 (m-10)
REVERT: A  193 GLN cc_start: 0.6393 (mm-40) cc_final: 0.5727 (mm-40)
REVERT: A  213 ARG cc_start: 0.5878 (ttt-90) cc_final: 0.5553 (ttt180)
REVERT: A  260 GLU cc_start: 0.6193 (mt-10) cc_final: 0.5903 (mt-10)
REVERT: A  333 PHE cc_start: 0.7382 (t80) cc_final: 0.7103 (t80)
REVERT: A  425 GLU cc_start: 0.4323 (pm20) cc_final: 0.3778 (tm-30)
REVERT: A  516 MET cc_start: 0.4291 (tmt) cc_final: 0.4049 (tmt)
REVERT: A  652 ASP cc_start: 0.5967 (m-30) cc_final: 0.5696 (m-30)
REVERT: A  686 GLU cc_start: 0.5871 (tp30) cc_final: 0.5653 (tp30)
REVERT: A  986 ASN cc_start: 0.6506 (m-40) cc_final: 0.6276 (m110)
REVERT: B  114 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.6344 (t-90)
REVERT: B  135 LYS cc_start: 0.7557 (ptpp) cc_final: 0.7287 (ptpp)
REVERT: B  147 HIS cc_start: 0.6930 (t-90) cc_final: 0.6579 (t-170)
REVERT: B  193 ASN cc_start: 0.6662 (m-40) cc_final: 0.6445 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 129
  average time/residue: 1.1386
  time to fit residues: 159.1650
Evaluate side-chains
  116 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
B 289 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.179298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.120668 restraints weight = 11428.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.92
r_work: 0.3146 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10074  Z= 0.146
  Angle     :  0.562   9.399  13696  Z= 0.285
  Chirality :  0.044   0.240   1549
  Planarity :  0.005   0.060   1754
  Dihedral  :  7.718  83.809   1480
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.18 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.24), residues: 1238
  helix:  1.99 (0.21), residues: 564
  sheet:  0.02 (0.38), residues: 162
  loop :  0.14 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 998 
 HIS   0.005   0.001   HIS B 227 
 PHE   0.017   0.002   PHE A 932 
 TYR   0.018   0.002   TYR A 802 
 ARG   0.003   0.000   ARG A  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00432 (    3)
  link_NAG-ASN         : angle       2.13728 (    9)
  hydrogen bonds       : bond        0.04699 (  508)
  hydrogen bonds       : angle       4.50915 ( 1497)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       0.85579 (    6)
  covalent geometry    : bond        0.00344 (10068)
  covalent geometry    : angle       0.55923 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7245 (m-10) cc_final: 0.6815 (m-10)
REVERT: A  193 GLN cc_start: 0.6402 (mm-40) cc_final: 0.5692 (mm-40)
REVERT: A  213 ARG cc_start: 0.5885 (ttt-90) cc_final: 0.5626 (ttt180)
REVERT: A  260 GLU cc_start: 0.6455 (mt-10) cc_final: 0.6155 (mt-10)
REVERT: A  320 MET cc_start: 0.6678 (mmp) cc_final: 0.6292 (mmt)
REVERT: A  333 PHE cc_start: 0.7395 (t80) cc_final: 0.7131 (t80)
REVERT: A  425 GLU cc_start: 0.4410 (pm20) cc_final: 0.3841 (tm-30)
REVERT: A  516 MET cc_start: 0.4254 (tmt) cc_final: 0.3974 (tmt)
REVERT: A  652 ASP cc_start: 0.5947 (m-30) cc_final: 0.5706 (m-30)
REVERT: A  696 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7128 (mt-10)
REVERT: A  986 ASN cc_start: 0.6628 (m-40) cc_final: 0.6363 (m110)
REVERT: B  114 HIS cc_start: 0.6716 (OUTLIER) cc_final: 0.6348 (t-90)
REVERT: B  135 LYS cc_start: 0.7587 (ptpp) cc_final: 0.7291 (ptpp)
REVERT: B  147 HIS cc_start: 0.6964 (t-90) cc_final: 0.6559 (t-170)
REVERT: B  193 ASN cc_start: 0.6678 (m-40) cc_final: 0.6400 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 126
  average time/residue: 1.1494
  time to fit residues: 156.8173
Evaluate side-chains
  119 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  906 ASP
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 87 optimal weight:    1.9990
   chunk 98 optimal weight:    8.9990
   chunk 95 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    1.1964

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
B 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.179638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.120226 restraints weight = 11445.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.74
r_work: 0.3169 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10074  Z= 0.130
  Angle     :  0.535   8.270  13696  Z= 0.271
  Chirality :  0.043   0.212   1549
  Planarity :  0.004   0.059   1754
  Dihedral  :  7.581  81.364   1480
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.23 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.24), residues: 1238
  helix:  2.06 (0.21), residues: 564
  sheet: -0.01 (0.38), residues: 162
  loop :  0.14 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.019   0.001   PHE A 970 
 TYR   0.017   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00442 (    3)
  link_NAG-ASN         : angle       2.21341 (    9)
  hydrogen bonds       : bond        0.04432 (  508)
  hydrogen bonds       : angle       4.41135 ( 1497)
  SS BOND              : bond        0.00275 (    3)
  SS BOND              : angle       0.76628 (    6)
  covalent geometry    : bond        0.00303 (10068)
  covalent geometry    : angle       0.53177 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.5900 (OUTLIER) cc_final: 0.5551 (m-30)
REVERT: A  140 TYR cc_start: 0.7169 (m-10) cc_final: 0.6730 (m-10)
REVERT: A  193 GLN cc_start: 0.6396 (mm-40) cc_final: 0.5705 (mm-40)
REVERT: A  213 ARG cc_start: 0.5811 (ttt-90) cc_final: 0.5575 (ttt180)
REVERT: A  260 GLU cc_start: 0.6401 (mt-10) cc_final: 0.6051 (mt-10)
REVERT: A  320 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6400 (mmt)
REVERT: A  333 PHE cc_start: 0.7383 (t80) cc_final: 0.7116 (t80)
REVERT: A  425 GLU cc_start: 0.4405 (pm20) cc_final: 0.3865 (tm-30)
REVERT: A  516 MET cc_start: 0.4198 (tmt) cc_final: 0.3970 (tmt)
REVERT: A  652 ASP cc_start: 0.5923 (m-30) cc_final: 0.5692 (m-30)
REVERT: A  696 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7071 (mt-10)
REVERT: A  986 ASN cc_start: 0.6599 (m-40) cc_final: 0.6331 (m110)
REVERT: B  114 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.6308 (t-90)
REVERT: B  126 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5907 (mm-30)
REVERT: B  135 LYS cc_start: 0.7504 (ptpp) cc_final: 0.7201 (ptpp)
REVERT: B  147 HIS cc_start: 0.6932 (t-90) cc_final: 0.6554 (t-170)
REVERT: B  193 ASN cc_start: 0.6726 (m-40) cc_final: 0.6459 (t0)
  outliers start: 24
  outliers final: 14
  residues processed: 130
  average time/residue: 1.0941
  time to fit residues: 154.0252
Evaluate side-chains
  125 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0770
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 114 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.1744

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

Flipped N/Q/H residues before XYZ refinement:
B 289 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.179632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124761 restraints weight = 11503.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 1.94
r_work: 0.3148 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10074  Z= 0.131
  Angle     :  0.541   9.754  13696  Z= 0.273
  Chirality :  0.043   0.203   1549
  Planarity :  0.004   0.058   1754
  Dihedral  :  7.515  79.459   1480
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.89 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.24), residues: 1238
  helix:  2.06 (0.21), residues: 570
  sheet: -0.03 (0.39), residues: 162
  loop :  0.11 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.016   0.001   PHE A 932 
 TYR   0.017   0.001   TYR A 802 
 ARG   0.002   0.000   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00442 (    3)
  link_NAG-ASN         : angle       2.26773 (    9)
  hydrogen bonds       : bond        0.04418 (  508)
  hydrogen bonds       : angle       4.37389 ( 1497)
  SS BOND              : bond        0.00271 (    3)
  SS BOND              : angle       0.75982 (    6)
  covalent geometry    : bond        0.00305 (10068)
  covalent geometry    : angle       0.53830 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7274 (m-10) cc_final: 0.6805 (m-10)
REVERT: A  193 GLN cc_start: 0.6470 (mm-40) cc_final: 0.5788 (mm-40)
REVERT: A  213 ARG cc_start: 0.5895 (ttt-90) cc_final: 0.5663 (ttt180)
REVERT: A  260 GLU cc_start: 0.6502 (mt-10) cc_final: 0.6184 (mt-10)
REVERT: A  320 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6422 (mmt)
REVERT: A  333 PHE cc_start: 0.7456 (t80) cc_final: 0.7210 (t80)
REVERT: A  425 GLU cc_start: 0.4460 (pm20) cc_final: 0.3927 (tm-30)
REVERT: A  652 ASP cc_start: 0.5992 (m-30) cc_final: 0.5766 (m-30)
REVERT: A  686 GLU cc_start: 0.5790 (mp0) cc_final: 0.5506 (mp0)
REVERT: A  696 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7149 (mt-10)
REVERT: A  986 ASN cc_start: 0.6653 (m-40) cc_final: 0.6359 (m110)
REVERT: B  114 HIS cc_start: 0.6750 (OUTLIER) cc_final: 0.6396 (t-90)
REVERT: B  126 GLU cc_start: 0.6255 (mm-30) cc_final: 0.5962 (mm-30)
REVERT: B  135 LYS cc_start: 0.7563 (ptpp) cc_final: 0.7260 (ptpp)
REVERT: B  147 HIS cc_start: 0.6961 (t-90) cc_final: 0.6574 (t-170)
REVERT: B  193 ASN cc_start: 0.6704 (m-40) cc_final: 0.6430 (t0)
  outliers start: 24
  outliers final: 17
  residues processed: 132
  average time/residue: 1.1555
  time to fit residues: 165.6666
Evaluate side-chains
  129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  906 ASP
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 64 optimal weight:    0.5980
   chunk 94 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 123 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0570
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.180632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.126169 restraints weight = 11568.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.82
r_work: 0.3182 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10074  Z= 0.109
  Angle     :  0.529   9.134  13696  Z= 0.263
  Chirality :  0.042   0.174   1549
  Planarity :  0.004   0.057   1754
  Dihedral  :  7.404  78.062   1480
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.36 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.24), residues: 1238
  helix:  2.21 (0.22), residues: 565
  sheet:  0.05 (0.39), residues: 162
  loop :  0.16 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 401 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.022   0.001   PHE A 970 
 TYR   0.018   0.001   TYR B  60 
 ARG   0.002   0.000   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01000 (    3)
  link_NAG-ASN         : angle       2.86468 (    9)
  hydrogen bonds       : bond        0.03964 (  508)
  hydrogen bonds       : angle       4.27030 ( 1497)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       0.62915 (    6)
  covalent geometry    : bond        0.00237 (10068)
  covalent geometry    : angle       0.52350 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 ASP cc_start: 0.5936 (OUTLIER) cc_final: 0.5586 (m-30)
REVERT: A  140 TYR cc_start: 0.7206 (m-10) cc_final: 0.6772 (m-10)
REVERT: A  193 GLN cc_start: 0.6448 (mm-40) cc_final: 0.5767 (mm-40)
REVERT: A  213 ARG cc_start: 0.5843 (ttt-90) cc_final: 0.5619 (ttt180)
REVERT: A  260 GLU cc_start: 0.6406 (mt-10) cc_final: 0.6107 (mt-10)
REVERT: A  320 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6394 (mmt)
REVERT: A  333 PHE cc_start: 0.7389 (t80) cc_final: 0.7172 (t80)
REVERT: A  425 GLU cc_start: 0.4304 (pm20) cc_final: 0.3809 (tm-30)
REVERT: A  516 MET cc_start: 0.4083 (tmt) cc_final: 0.3730 (tmt)
REVERT: A  652 ASP cc_start: 0.5945 (m-30) cc_final: 0.5691 (m-30)
REVERT: A  686 GLU cc_start: 0.5717 (mp0) cc_final: 0.5391 (tp30)
REVERT: A  696 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7104 (mt-10)
REVERT: A  986 ASN cc_start: 0.6492 (m-40) cc_final: 0.6206 (m110)
REVERT: B  109 LEU cc_start: 0.6639 (mt) cc_final: 0.6404 (mm)
REVERT: B  114 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6398 (t-90)
REVERT: B  126 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5857 (mm-30)
REVERT: B  135 LYS cc_start: 0.7498 (ptpp) cc_final: 0.7194 (ptpp)
REVERT: B  147 HIS cc_start: 0.6943 (t-90) cc_final: 0.6560 (t-170)
REVERT: B  193 ASN cc_start: 0.6734 (m-40) cc_final: 0.6481 (t0)
  outliers start: 22
  outliers final: 13
  residues processed: 135
  average time/residue: 1.2743
  time to fit residues: 186.3328
Evaluate side-chains
  132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 119 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0870
   chunk 8 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0070
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 898 GLN
A 971 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.181019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.125405 restraints weight = 11572.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.07
r_work: 0.3194 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10074  Z= 0.106
  Angle     :  0.522  11.406  13696  Z= 0.259
  Chirality :  0.042   0.168   1549
  Planarity :  0.004   0.057   1754
  Dihedral  :  7.133  76.440   1480
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.03 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.24), residues: 1238
  helix:  2.27 (0.22), residues: 565
  sheet:  0.11 (0.39), residues: 162
  loop :  0.18 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 401 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 161 
 TYR   0.015   0.001   TYR A 802 
 ARG   0.002   0.000   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00803 (    3)
  link_NAG-ASN         : angle       2.16557 (    9)
  hydrogen bonds       : bond        0.03833 (  508)
  hydrogen bonds       : angle       4.18526 ( 1497)
  SS BOND              : bond        0.00187 (    3)
  SS BOND              : angle       0.59624 (    6)
  covalent geometry    : bond        0.00236 (10068)
  covalent geometry    : angle       0.51904 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.5930 (OUTLIER) cc_final: 0.5524 (m-30)
REVERT: A  140 TYR cc_start: 0.7217 (m-10) cc_final: 0.6694 (m-10)
REVERT: A  193 GLN cc_start: 0.6324 (mm-40) cc_final: 0.5733 (mm-40)
REVERT: A  213 ARG cc_start: 0.5829 (ttt-90) cc_final: 0.5598 (ttt180)
REVERT: A  260 GLU cc_start: 0.6434 (mt-10) cc_final: 0.6092 (mt-10)
REVERT: A  320 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6336 (mmt)
REVERT: A  333 PHE cc_start: 0.7395 (t80) cc_final: 0.7176 (t80)
REVERT: A  425 GLU cc_start: 0.4342 (pm20) cc_final: 0.3836 (tm-30)
REVERT: A  516 MET cc_start: 0.4205 (tmt) cc_final: 0.3825 (tmt)
REVERT: A  652 ASP cc_start: 0.5973 (m-30) cc_final: 0.5723 (m-30)
REVERT: A  686 GLU cc_start: 0.5732 (mp0) cc_final: 0.5321 (mp0)
REVERT: A  696 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7150 (mt-10)
REVERT: A  738 ASP cc_start: 0.8056 (m-30) cc_final: 0.7787 (m-30)
REVERT: A  986 ASN cc_start: 0.6377 (m-40) cc_final: 0.6085 (m110)
REVERT: B  109 LEU cc_start: 0.6643 (mt) cc_final: 0.6423 (mm)
REVERT: B  114 HIS cc_start: 0.6745 (OUTLIER) cc_final: 0.6379 (t-90)
REVERT: B  147 HIS cc_start: 0.6961 (t-90) cc_final: 0.6551 (t-170)
REVERT: B  193 ASN cc_start: 0.6709 (m-40) cc_final: 0.6491 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 132
  average time/residue: 1.1525
  time to fit residues: 165.3369
Evaluate side-chains
  129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0000
   chunk 103 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 111 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 369 ASN
A 971 GLN
B 289 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.181037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127293 restraints weight = 11598.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.87
r_work: 0.3179 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10074  Z= 0.109
  Angle     :  0.527  10.695  13696  Z= 0.263
  Chirality :  0.042   0.167   1549
  Planarity :  0.004   0.057   1754
  Dihedral  :  7.091  74.999   1480
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.31 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.24), residues: 1238
  helix:  2.25 (0.22), residues: 565
  sheet:  0.13 (0.39), residues: 162
  loop :  0.18 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 915 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 932 
 TYR   0.019   0.001   TYR B  60 
 ARG   0.002   0.000   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00584 (    3)
  link_NAG-ASN         : angle       2.46881 (    9)
  hydrogen bonds       : bond        0.03882 (  508)
  hydrogen bonds       : angle       4.19107 ( 1497)
  SS BOND              : bond        0.00194 (    3)
  SS BOND              : angle       0.77617 (    6)
  covalent geometry    : bond        0.00247 (10068)
  covalent geometry    : angle       0.52290 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 2.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7233 (m-10) cc_final: 0.6701 (m-10)
REVERT: A  193 GLN cc_start: 0.6325 (mm-40) cc_final: 0.5748 (mm-40)
REVERT: A  213 ARG cc_start: 0.5824 (ttt-90) cc_final: 0.5601 (ttt180)
REVERT: A  260 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6141 (mt-10)
REVERT: A  320 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6319 (mmt)
REVERT: A  333 PHE cc_start: 0.7381 (t80) cc_final: 0.7171 (t80)
REVERT: A  425 GLU cc_start: 0.4355 (pm20) cc_final: 0.3845 (tm-30)
REVERT: A  516 MET cc_start: 0.4197 (tmt) cc_final: 0.3864 (tmt)
REVERT: A  652 ASP cc_start: 0.5977 (m-30) cc_final: 0.5731 (m-30)
REVERT: A  686 GLU cc_start: 0.5722 (mp0) cc_final: 0.5286 (mp0)
REVERT: A  696 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7172 (mt-10)
REVERT: A  738 ASP cc_start: 0.8045 (m-30) cc_final: 0.7778 (m-30)
REVERT: A  986 ASN cc_start: 0.6467 (m-40) cc_final: 0.6168 (m110)
REVERT: B  109 LEU cc_start: 0.6665 (mt) cc_final: 0.6438 (mm)
REVERT: B  114 HIS cc_start: 0.6726 (OUTLIER) cc_final: 0.6354 (t-90)
REVERT: B  147 HIS cc_start: 0.6976 (t-90) cc_final: 0.6586 (t-170)
  outliers start: 18
  outliers final: 14
  residues processed: 125
  average time/residue: 1.1171
  time to fit residues: 151.6482
Evaluate side-chains
  129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  302 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 66 optimal weight:    0.0770
   chunk 26 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0050
   chunk 119 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.4552

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

Flipped N/Q/H residues before XYZ refinement:
A 369 ASN
B 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.181843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.127534 restraints weight = 11562.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.97
r_work: 0.3192 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10074  Z= 0.101
  Angle     :  0.528  10.523  13696  Z= 0.258
  Chirality :  0.042   0.187   1549
  Planarity :  0.004   0.056   1754
  Dihedral  :  6.892  72.846   1480
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.60 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.24), residues: 1238
  helix:  2.31 (0.21), residues: 576
  sheet:  0.18 (0.39), residues: 162
  loop :  0.23 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 106 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 161 
 TYR   0.013   0.001   TYR A 802 
 ARG   0.002   0.000   ARG A 278 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00323 (    3)
  link_NAG-ASN         : angle       5.00594 (    9)
  hydrogen bonds       : bond        0.03596 (  508)
  hydrogen bonds       : angle       4.12857 ( 1497)
  SS BOND              : bond        0.00136 (    3)
  SS BOND              : angle       0.68060 (    6)
  covalent geometry    : bond        0.00221 (10068)
  covalent geometry    : angle       0.51225 (13681)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 1.119 
Fit side-chains
REVERT: A  140 TYR cc_start: 0.7203 (m-10) cc_final: 0.6683 (m-10)
REVERT: A  193 GLN cc_start: 0.6308 (mm-40) cc_final: 0.5735 (mm-40)
REVERT: A  260 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6073 (mt-10)
REVERT: A  320 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6363 (mmt)
REVERT: A  333 PHE cc_start: 0.7388 (t80) cc_final: 0.7182 (t80)
REVERT: A  425 GLU cc_start: 0.4273 (pm20) cc_final: 0.3752 (tm-30)
REVERT: A  516 MET cc_start: 0.4140 (tmt) cc_final: 0.3819 (tmt)
REVERT: A  652 ASP cc_start: 0.5916 (m-30) cc_final: 0.5681 (m-30)
REVERT: A  686 GLU cc_start: 0.5704 (mp0) cc_final: 0.5260 (mp0)
REVERT: A  696 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7119 (mt-10)
REVERT: A  738 ASP cc_start: 0.7999 (m-30) cc_final: 0.7744 (m-30)
REVERT: A  838 SER cc_start: 0.6796 (p) cc_final: 0.6468 (m)
REVERT: A  986 ASN cc_start: 0.6289 (m-40) cc_final: 0.5987 (m110)
REVERT: B  109 LEU cc_start: 0.6657 (mt) cc_final: 0.6400 (mm)
REVERT: B  114 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.6314 (t-90)
REVERT: B  147 HIS cc_start: 0.6947 (t-90) cc_final: 0.6568 (t-170)
REVERT: B  258 VAL cc_start: 0.7828 (p) cc_final: 0.7542 (t)
REVERT: B  267 GLU cc_start: 0.7197 (pt0) cc_final: 0.6586 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 130
  average time/residue: 1.0296
  time to fit residues: 145.9492
Evaluate side-chains
  123 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  114 HIS
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  250 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 123 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 415 GLN
B 289 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.179768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.124845 restraints weight = 11517.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.06
r_work: 0.3156 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10074  Z= 0.139
  Angle     :  0.582  10.541  13696  Z= 0.290
  Chirality :  0.044   0.223   1549
  Planarity :  0.005   0.058   1754
  Dihedral  :  7.382  73.325   1480
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.07 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1238
  helix:  2.17 (0.21), residues: 565
  sheet:  0.06 (0.39), residues: 162
  loop :  0.12 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 106 
 HIS   0.005   0.001   HIS B 227 
 PHE   0.018   0.002   PHE A 970 
 TYR   0.020   0.002   TYR B  60 
 ARG   0.008   0.000   ARG A 182 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00304 (    3)
  link_NAG-ASN         : angle       4.50370 (    9)
  hydrogen bonds       : bond        0.04404 (  508)
  hydrogen bonds       : angle       4.35502 ( 1497)
  SS BOND              : bond        0.00336 (    3)
  SS BOND              : angle       1.04395 (    6)
  covalent geometry    : bond        0.00331 (10068)
  covalent geometry    : angle       0.57032 (13681)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10159.97 seconds
wall clock time: 175 minutes 1.60 seconds (10501.60 seconds total)