Starting phenix.real_space_refine
on Tue Jul 29 07:03:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ijv_35500/07_2025/8ijv_35500.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ijv_35500/07_2025/8ijv_35500.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ijv_35500/07_2025/8ijv_35500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ijv_35500/07_2025/8ijv_35500.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ijv_35500/07_2025/8ijv_35500.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ijv_35500/07_2025/8ijv_35500.cif"
  }
  resolution = 2.1
  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=  -0.002 sd=   0.094
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 9
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      1      5.21       5
     S      65      5.16       5
     Cl      4      4.86       5
     Be      1      3.05       5
     C    6570      2.51       5
     N    1654      2.21       5
     O    2229      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10532
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 983, 7631
          Classifications: {'peptide': 983}
          Link IDs: {'PTRANS': 47, 'TRANS': 935}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2142
          Classifications: {'peptide': 268}
          Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 238
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 6, 216
          Unusual residues: {' MG': 1, 'PCW': 4, 'PWI': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 6, 216
          Unusual residues: {' MG': 1, 'PCW': 4, 'PWI': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 189
    Chain: "B"
      Number of atoms: 152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 152
          Unusual residues: {'CLR': 2, 'NAG': 3, 'PCW': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          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: 255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 255
          Classifications: {'water': 255}
          Link IDs: {None: 254}
    Chain: "B"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 114
          Classifications: {'water': 114}
          Link IDs: {None: 113}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C01APWI A1106 " occ=0.46
      ... (42 atoms not shown)
      pdb="CL2 BPWI A1106 " occ=0.54
  Time building chain proxies: 7.90, per 1000 atoms: 0.75
  Number of scatterers: 10532
  At special positions: 0
  Unit cell: (81.216, 97.76, 174.464, 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)
     Cl      4     17.00
     S      65     16.00
     P       5     15.00
     Mg      1     11.99
     F       3      9.00
     O    2229      8.00
     N    1654      7.00
     C    6570      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 302 " - " ASN B  99 "
      " NAG B 303 " - " ASN B 130 "
      " NAG B 304 " - " ASN B 161 "
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2340

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      50.2% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 84
    Processing helix  chain 'A' and resid 96 through 106
      removed outlier: 3.614A  pdb=" N   LYS A 100 " --> pdb=" O   PRO A  96 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE A 101 " --> pdb=" O   GLU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 129
    Processing helix  chain 'A' and resid 135 through 170
      removed outlier: 3.989A  pdb=" N   LEU A 139 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   PHE A 170 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 274 through 285
    Processing helix  chain 'A' and resid 291 through 322
    Processing helix  chain 'A' and resid 325 through 340
    Processing helix  chain 'A' and resid 344 through 362
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 374 through 379
      removed outlier: 3.561A  pdb=" N   SER A 378 " --> pdb=" O   GLU A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 437
    Processing helix  chain 'A' and resid 450 through 454
    Processing helix  chain 'A' and resid 459 through 473
    Processing helix  chain 'A' and resid 475 through 483
    Processing helix  chain 'A' and resid 519 through 526
      removed outlier: 3.664A  pdb=" N   ARG A 526 " --> pdb=" O   ARG A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 557
    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 660 through 664
    Processing helix  chain 'A' and resid 665 through 669
    Processing helix  chain 'A' and resid 676 through 682
      removed outlier: 3.580A  pdb=" N   ASP A 681 " --> pdb=" O   MET A 677 " (cutoff:3.500A)
    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: 4.072A  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 820
    Processing helix  chain 'A' and resid 824 through 831
      removed outlier: 3.608A  pdb=" N   LEU A 831 " --> pdb=" O   PRO A 827 " (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 839 through 843
    Processing helix  chain 'A' and resid 855 through 865
    Processing helix  chain 'A' and resid 865 through 885
    Processing helix  chain 'A' and resid 888 through 893
    Processing helix  chain 'A' and resid 895 through 901
    Processing helix  chain 'A' and resid 916 through 946
      removed outlier: 3.622A  pdb=" N   ALA A 941 " --> pdb=" O   MET A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 961 through 981
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 994 through 1000
      removed outlier: 3.861A  pdb=" N   TRP A 998 " --> pdb=" O   ARG A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1001 through 1022
    Processing helix  chain 'A' and resid 1025 through 1032
    Processing helix  chain 'B' and resid 34 through 66
    Processing helix  chain 'B' and resid 102 through 119
      removed outlier: 4.240A  pdb=" N   TRP B 106 " --> pdb=" O   ASP B 102 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLY B 108 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   LEU B 109 " --> pdb=" O   THR B 105 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   GLY B 119 " --> pdb=" O   ARG B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 163
      removed outlier: 6.664A  pdb=" N   ASN B 161 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 223
      removed outlier: 4.117A  pdb=" N   THR B 223 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 11.763A  pdb=" N   GLN A 177 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
      removed outlier: 9.456A  pdb=" N   LYS A 203 " --> pdb=" O   GLN A 177 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   MET A 257 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LYS A 221 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY A 261 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   GLY A 219 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ALA A 217 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   GLY A 265 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU A 215 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   VAL A 267 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ARG A 213 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   CYS A 220 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 11.763A  pdb=" N   GLN A 177 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
      removed outlier: 9.456A  pdb=" N   LYS A 203 " --> pdb=" O   GLN A 177 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   THR A 179 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LEU A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   MET A 257 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LYS A 221 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY A 261 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   GLY A 219 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ALA A 217 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   GLY A 265 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU A 215 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   VAL A 267 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ARG A 213 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367
      removed outlier: 6.323A  pdb=" N   GLY A 740 " --> pdb=" O   MET A 757 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   LEU A 759 " --> pdb=" O   GLY A 740 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ALA A 742 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL A 721 " --> pdb=" O   ILE A 739 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   VAL A 741 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   VAL A 723 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   MET A 743 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   GLY A 725 " --> pdb=" O   MET A 743 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   VAL A 622 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   MET A 624 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.334A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   HIS A 399 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   PHE A 564 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   LEU A 562 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   SER A 599 " --> pdb=" O   ARG A 560 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ARG A 560 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   HIS A 512 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   PHE A 497 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   PHE A 491 " --> pdb=" O   PHE A 497 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   CYS A 487 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   THR A 503 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   LYS A 485 " --> pdb=" O   THR A 503 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408
      removed outlier: 5.334A  pdb=" N   VAL A 397 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ILE A 601 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   HIS A 399 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   SER A 529 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
      removed outlier: 8.473A  pdb=" N   GLY A 596 " --> pdb=" O   SER A 529 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442
      removed outlier: 3.697A  pdb=" N   ALA A 441 " --> pdb=" O   ILE A 457 " (cutoff:3.500A)
    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 28 through 29
    Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 85
    Processing sheet with id=AB1, first strand: chain 'B' and resid 94 through 99
      removed outlier: 4.493A  pdb=" N   LEU B  94 " --> pdb=" O   GLU B 283 " (cutoff:3.500A)

    533 hydrogen bonds defined for protein.
    1509 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: 4.02

  Time building geometry restraints manager: 3.45 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1623
        1.29 -     1.42: 2593
        1.42 -     1.55: 6056
        1.55 -     1.68: 17
        1.68 -     1.82: 101
  Bond restraints: 10390
  Sorted by residual:
  bond pdb=" F3  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.529  1.764 -0.235 2.00e-02 2.50e+03 1.38e+02
  bond pdb=" F2  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.535  1.753 -0.218 2.00e-02 2.50e+03 1.18e+02
  bond pdb=" F1  BFD A 385 "
       pdb="BE   BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.542  1.752 -0.210 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" CG  BFD A 385 "
       pdb=" OD1 BFD A 385 "
    ideal  model  delta    sigma   weight residual
    1.269  1.447 -0.178 2.00e-02 2.50e+03 7.89e+01
  bond pdb=" C17APWI A1106 "
       pdb=" N01APWI A1106 "
    ideal  model  delta    sigma   weight residual
    1.466  1.292  0.174 2.00e-02 2.50e+03 7.56e+01
  ... (remaining 10385 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.50: 14001
        5.50 -    10.99: 64
       10.99 -    16.49: 9
       16.49 -    21.98: 3
       21.98 -    27.48: 5
  Bond angle restraints: 14082
  Sorted by residual:
  angle pdb=" C19 CLR B 306 "
        pdb=" C10 CLR B 306 "
        pdb=" C9  CLR B 306 "
      ideal   model   delta    sigma   weight residual
     111.86   84.38   27.48 3.00e+00 1.11e-01 8.39e+01
  angle pdb=" C1  CLR B 306 "
        pdb=" C10 CLR B 306 "
        pdb=" C19 CLR B 306 "
      ideal   model   delta    sigma   weight residual
     109.60   82.90   26.70 3.00e+00 1.11e-01 7.92e+01
  angle pdb=" C5  PCW A1104 "
        pdb=" N   PCW A1104 "
        pdb=" C8  PCW A1104 "
      ideal   model   delta    sigma   weight residual
     111.64   86.86   24.78 3.00e+00 1.11e-01 6.82e+01
  angle pdb=" C19 CLR B 306 "
        pdb=" C10 CLR B 306 "
        pdb=" C5  CLR B 306 "
      ideal   model   delta    sigma   weight residual
     108.37   83.64   24.73 3.00e+00 1.11e-01 6.79e+01
  angle pdb=" C6  PCW A1104 "
        pdb=" N   PCW A1104 "
        pdb=" C8  PCW A1104 "
      ideal   model   delta    sigma   weight residual
     109.11   86.89   22.22 3.00e+00 1.11e-01 5.48e+01
  ... (remaining 14077 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 6119
       35.95 -    71.90: 265
       71.90 -   107.85: 24
      107.85 -   143.81: 6
      143.81 -   179.76: 6
  Dihedral angle restraints: 6420
    sinusoidal: 2787
      harmonic: 3633
  Sorted by residual:
  dihedral pdb=" C13BPWI A1106 "
           pdb=" C14BPWI A1106 "
           pdb=" O01BPWI A1106 "
           pdb=" C15BPWI A1106 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -179.86   -0.10 -179.76     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C19 CLR B 306 "
           pdb=" C10 CLR B 306 "
           pdb=" C5  CLR B 306 "
           pdb=" C6  CLR B 306 "
      ideal   model   delta sinusoidal    sigma   weight residual
     252.42   74.68  177.74     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C11 CLR B 306 "
           pdb=" C10 CLR B 306 "
           pdb=" C9  CLR B 306 "
           pdb=" C19 CLR B 306 "
      ideal   model   delta sinusoidal    sigma   weight residual
      51.90 -124.69  176.59     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 6417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.358: 1573
       0.358 -    0.716: 0
       0.716 -    1.074: 0
       1.074 -    1.432: 0
       1.432 -    1.790: 1
  Chirality restraints: 1574
  Sorted by residual:
  chirality pdb=" C10 CLR B 306 "
            pdb=" C1  CLR B 306 "
            pdb=" C5  CLR B 306 "
            pdb=" C9  CLR B 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -1.06   -1.79 2.00e-01 2.50e+01 8.01e+01
  chirality pdb=" C1  NAG B 303 "
            pdb=" ND2 ASN B 130 "
            pdb=" C2  NAG B 303 "
            pdb=" O5  NAG B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.74    0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" C1  NAG B 302 "
            pdb=" ND2 ASN B  99 "
            pdb=" C2  NAG B 302 "
            pdb=" O5  NAG B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1571 not shown)

  Planarity restraints: 1780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 130 "    0.216 2.00e-02 2.50e+03   1.94e-01 4.71e+02
        pdb=" CG  ASN B 130 "   -0.082 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 130 "   -0.148 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 130 "   -0.230 2.00e-02 2.50e+03
        pdb=" C1  NAG B 303 "    0.244 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C01APWI A1106 "    0.006 2.00e-02 2.50e+03   5.57e-02 6.98e+01
        pdb=" C07APWI A1106 "    0.000 2.00e-02 2.50e+03
        pdb=" C08APWI A1106 "    0.048 2.00e-02 2.50e+03
        pdb=" C09APWI A1106 "    0.101 2.00e-02 2.50e+03
        pdb=" C10APWI A1106 "    0.043 2.00e-02 2.50e+03
        pdb=" C11APWI A1106 "   -0.014 2.00e-02 2.50e+03
        pdb=" C12APWI A1106 "   -0.027 2.00e-02 2.50e+03
        pdb=" C13APWI A1106 "   -0.089 2.00e-02 2.50e+03
        pdb="CL2 APWI A1106 "   -0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C01APWI A1106 "   -0.028 2.00e-02 2.50e+03   4.56e-02 4.16e+01
        pdb=" C02APWI A1106 "   -0.045 2.00e-02 2.50e+03
        pdb=" C03APWI A1106 "   -0.016 2.00e-02 2.50e+03
        pdb=" C04APWI A1106 "   -0.001 2.00e-02 2.50e+03
        pdb=" C05APWI A1106 "   -0.026 2.00e-02 2.50e+03
        pdb=" C06APWI A1106 "   -0.036 2.00e-02 2.50e+03
        pdb=" C07APWI A1106 "    0.089 2.00e-02 2.50e+03
        pdb="CL1 APWI A1106 "    0.062 2.00e-02 2.50e+03
  ... (remaining 1777 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 129
        2.56 -     3.14: 8347
        3.14 -     3.73: 17964
        3.73 -     4.31: 25929
        4.31 -     4.90: 39940
  Nonbonded interactions: 92309
  Sorted by model distance:
  nonbonded pdb=" O   THR A 387 "
            pdb="MG    MG A1102 "
     model   vdw
     1.973 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O   HOH A1204 "
     model   vdw
     2.021 2.170
  nonbonded pdb=" F2  BFD A 385 "
            pdb="MG    MG A1102 "
     model   vdw
     2.104 2.120
  nonbonded pdb=" CE  LYS B 135 "
            pdb=" O   HOH B 463 "
     model   vdw
     2.141 3.440
  nonbonded pdb=" F1  BFD A 385 "
            pdb=" OG1 THR A 626 "
     model   vdw
     2.152 2.990
  ... (remaining 92304 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=0.46 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:             4.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     29.970
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.423  10396  Z= 0.450
  Angle     :  1.142  29.579  14097  Z= 0.484
  Chirality :  0.066   1.790   1574
  Planarity :  0.006   0.125   1777
  Dihedral  : 20.105 179.758   4071
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.78 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.17 (0.24), residues: 1244
  helix:  1.65 (0.22), residues: 579
  sheet:  0.43 (0.41), residues: 155
  loop : -0.04 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 997 
 HIS   0.003   0.001   HIS B 227 
 PHE   0.022   0.002   PHE A 333 
 TYR   0.017   0.001   TYR A 802 
 ARG   0.006   0.000   ARG A1020 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.24432 (    3)
  link_NAG-ASN         : angle      12.39495 (    9)
  hydrogen bonds       : bond        0.12070 (  510)
  hydrogen bonds       : angle       5.55949 ( 1509)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       0.62786 (    6)
  covalent geometry    : bond        0.00786 (10390)
  covalent geometry    : angle       1.09833 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 29
  outliers final: 29
  residues processed: 145
  average time/residue: 1.4081
  time to fit residues: 218.2683
Evaluate side-chains
  145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  495 ASN
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  508 ARG
Chi-restraints excluded: chain A residue  525 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 97 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    0.4980
   chunk 72 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.169427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.121960 restraints weight = 9398.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 1.59
r_work: 0.3153 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.0541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10396  Z= 0.128
  Angle     :  0.705  31.047  14097  Z= 0.323
  Chirality :  0.063   1.800   1574
  Planarity :  0.005   0.057   1777
  Dihedral  : 17.619 176.881   1831
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 15.52 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.33 (0.24), residues: 1244
  helix:  1.80 (0.22), residues: 587
  sheet:  0.48 (0.41), residues: 154
  loop : -0.01 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.003   0.001   HIS B 227 
 PHE   0.014   0.001   PHE A 161 
 TYR   0.020   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00765 (    3)
  link_NAG-ASN         : angle       3.08155 (    9)
  hydrogen bonds       : bond        0.04711 (  510)
  hydrogen bonds       : angle       4.46358 ( 1509)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       0.68194 (    6)
  covalent geometry    : bond        0.00270 (10390)
  covalent geometry    : angle       0.70126 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.7898 (mp10) cc_final: 0.7668 (mm-40)
REVERT: A  247 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7383 (mm-30)
REVERT: A  505 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5488 (tp30)
REVERT: A  835 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7858 (mttp)
REVERT: A  844 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7915 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8719 (mmtp) cc_final: 0.8147 (mmmt)
REVERT: B  135 LYS cc_start: 0.7665 (tptm) cc_final: 0.7201 (mmpt)
  outliers start: 40
  outliers final: 21
  residues processed: 144
  average time/residue: 1.6060
  time to fit residues: 247.5290
Evaluate side-chains
  135 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 2.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  162 LYS
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  201 GLU
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  505 GLU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0970
   chunk 59 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0470
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.169718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.122745 restraints weight = 9761.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.66
r_work: 0.3157 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.0629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10396  Z= 0.120
  Angle     :  0.690  30.739  14097  Z= 0.314
  Chirality :  0.063   1.814   1574
  Planarity :  0.004   0.054   1777
  Dihedral  : 17.445 176.791   1809
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.62 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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: 1244
  helix:  1.95 (0.22), residues: 581
  sheet:  0.75 (0.41), residues: 149
  loop : -0.08 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.024   0.001   PHE A 970 
 TYR   0.021   0.001   TYR A 802 
 ARG   0.004   0.000   ARG A 511 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00486 (    3)
  link_NAG-ASN         : angle       2.70148 (    9)
  hydrogen bonds       : bond        0.04479 (  510)
  hydrogen bonds       : angle       4.37297 ( 1509)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       0.53531 (    6)
  covalent geometry    : bond        0.00253 (10390)
  covalent geometry    : angle       0.68681 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.7891 (mp10) cc_final: 0.7640 (mm-40)
REVERT: A  247 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7384 (mm-30)
REVERT: A  689 GLU cc_start: 0.7924 (tp30) cc_final: 0.7685 (tp30)
REVERT: A  835 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7812 (mttp)
REVERT: A  844 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7881 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8707 (mmtp) cc_final: 0.8102 (mmmt)
REVERT: B  135 LYS cc_start: 0.7612 (tptm) cc_final: 0.7110 (mmpt)
  outliers start: 34
  outliers final: 23
  residues processed: 140
  average time/residue: 1.6250
  time to fit residues: 242.7725
Evaluate side-chains
  137 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 99 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 43 optimal weight:   10.0000
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.169694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.122308 restraints weight = 8820.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.41
r_work: 0.3177 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.0629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.140  10396  Z= 0.141
  Angle     :  0.717  30.739  14097  Z= 0.321
  Chirality :  0.064   1.814   1574
  Planarity :  0.004   0.054   1777
  Dihedral  : 17.437 176.791   1808
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.37 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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: 1244
  helix:  1.95 (0.22), residues: 581
  sheet:  0.75 (0.41), residues: 149
  loop : -0.08 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.024   0.001   PHE A 970 
 TYR   0.021   0.001   TYR A 802 
 ARG   0.004   0.000   ARG A 511 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.08843 (    3)
  link_NAG-ASN         : angle       8.13300 (    9)
  hydrogen bonds       : bond        0.04479 (  510)
  hydrogen bonds       : angle       4.37297 ( 1509)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       0.53531 (    6)
  covalent geometry    : bond        0.00253 (10390)
  covalent geometry    : angle       0.68681 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 1.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.7897 (mp10) cc_final: 0.7645 (mm-40)
REVERT: A  247 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7368 (mm-30)
REVERT: A  689 GLU cc_start: 0.7882 (tp30) cc_final: 0.7634 (tp30)
REVERT: A  835 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7797 (mttp)
REVERT: A  844 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7840 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8090 (mmmt)
REVERT: B  135 LYS cc_start: 0.7590 (tptm) cc_final: 0.7099 (mmpt)
  outliers start: 26
  outliers final: 23
  residues processed: 131
  average time/residue: 2.0843
  time to fit residues: 294.2325
Evaluate side-chains
  137 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 94 optimal weight:    0.6980
   chunk 61 optimal weight:    0.2980
   chunk 38 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.169378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.122779 restraints weight = 9741.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.62
r_work: 0.3149 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.0649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10396  Z= 0.127
  Angle     :  0.699  30.777  14097  Z= 0.318
  Chirality :  0.064   1.815   1574
  Planarity :  0.004   0.053   1777
  Dihedral  : 17.317 176.587   1808
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.52 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.43 (0.24), residues: 1244
  helix:  1.95 (0.22), residues: 581
  sheet:  0.70 (0.41), residues: 150
  loop : -0.09 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 315 
 TYR   0.020   0.001   TYR A 802 
 ARG   0.002   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00725 (    3)
  link_NAG-ASN         : angle       2.59156 (    9)
  hydrogen bonds       : bond        0.04590 (  510)
  hydrogen bonds       : angle       4.32892 ( 1509)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       0.53731 (    6)
  covalent geometry    : bond        0.00271 (10390)
  covalent geometry    : angle       0.69618 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.7852 (mp10) cc_final: 0.7588 (mm-40)
REVERT: A  247 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7422 (mm-30)
REVERT: A  289 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.6643 (mp0)
REVERT: A  835 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.7793 (mttp)
REVERT: A  844 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7892 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8101 (mmmt)
REVERT: B  135 LYS cc_start: 0.7653 (tptm) cc_final: 0.7105 (mmpt)
  outliers start: 35
  outliers final: 25
  residues processed: 140
  average time/residue: 1.6247
  time to fit residues: 243.3292
Evaluate side-chains
  138 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  525 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 110 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0980
   chunk 115 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 121 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.169360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.122137 restraints weight = 10904.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.77
r_work: 0.3149 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.0667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087  10396  Z= 0.133
  Angle     :  0.704  30.777  14097  Z= 0.319
  Chirality :  0.063   1.815   1574
  Planarity :  0.004   0.053   1777
  Dihedral  : 17.308 176.587   1804
  Min Nonbonded Distance : 1.242

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.27 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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:  1.43 (0.24), residues: 1244
  helix:  1.95 (0.22), residues: 581
  sheet:  0.70 (0.41), residues: 150
  loop : -0.09 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.013   0.001   PHE A 315 
 TYR   0.020   0.001   TYR A 802 
 ARG   0.002   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05029 (    3)
  link_NAG-ASN         : angle       4.22942 (    9)
  hydrogen bonds       : bond        0.04590 (  510)
  hydrogen bonds       : angle       4.32892 ( 1509)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       0.53731 (    6)
  covalent geometry    : bond        0.00271 (10390)
  covalent geometry    : angle       0.69618 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.7848 (mp10) cc_final: 0.7585 (mm-40)
REVERT: A  247 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7418 (mm-30)
REVERT: A  289 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.6646 (mp0)
REVERT: A  835 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7797 (mttp)
REVERT: A  844 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7898 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8710 (mmtp) cc_final: 0.8096 (mmmt)
REVERT: B  135 LYS cc_start: 0.7662 (tptm) cc_final: 0.7106 (mmpt)
  outliers start: 29
  outliers final: 25
  residues processed: 133
  average time/residue: 1.5240
  time to fit residues: 216.1655
Evaluate side-chains
  138 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  525 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 110 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0970
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN
** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.169579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.122296 restraints weight = 11053.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.79
r_work: 0.3148 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.0701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10396  Z= 0.124
  Angle     :  0.694  30.735  14097  Z= 0.317
  Chirality :  0.064   1.815   1574
  Planarity :  0.004   0.052   1777
  Dihedral  : 17.257 176.611   1804
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.09 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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: 1244
  helix:  1.96 (0.22), residues: 581
  sheet:  0.71 (0.41), residues: 150
  loop : -0.08 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.026   0.001   PHE A 970 
 TYR   0.020   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00719 (    3)
  link_NAG-ASN         : angle       2.65358 (    9)
  hydrogen bonds       : bond        0.04525 (  510)
  hydrogen bonds       : angle       4.29630 ( 1509)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       0.51971 (    6)
  covalent geometry    : bond        0.00265 (10390)
  covalent geometry    : angle       0.69132 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ASN cc_start: 0.6196 (OUTLIER) cc_final: 0.5793 (m-40)
REVERT: A   60 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5266 (mp)
REVERT: A  247 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7415 (mm-30)
REVERT: A  453 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7854 (mttp)
REVERT: A  505 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5557 (pt0)
REVERT: A  835 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7847 (mttp)
REVERT: A  844 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7879 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8105 (mmmt)
REVERT: B  135 LYS cc_start: 0.7653 (tptm) cc_final: 0.7100 (mmpt)
  outliers start: 33
  outliers final: 23
  residues processed: 138
  average time/residue: 1.7860
  time to fit residues: 264.2229
Evaluate side-chains
  140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  453 LYS
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  505 GLU
Chi-restraints excluded: chain A residue  525 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 104 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 101 optimal weight:    0.5980
   chunk 91 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN
** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.169556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.122297 restraints weight = 13194.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.98
r_work: 0.3132 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.0685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093  10396  Z= 0.132
  Angle     :  0.700  30.735  14097  Z= 0.318
  Chirality :  0.063   1.815   1574
  Planarity :  0.004   0.052   1777
  Dihedral  : 17.256 176.611   1804
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.37 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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: 1244
  helix:  1.96 (0.22), residues: 581
  sheet:  0.71 (0.41), residues: 150
  loop : -0.08 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.026   0.001   PHE A 970 
 TYR   0.020   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05370 (    3)
  link_NAG-ASN         : angle       4.38379 (    9)
  hydrogen bonds       : bond        0.04525 (  510)
  hydrogen bonds       : angle       4.29629 ( 1509)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       0.51966 (    6)
  covalent geometry    : bond        0.00265 (10390)
  covalent geometry    : angle       0.69129 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 2.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ASN cc_start: 0.6185 (OUTLIER) cc_final: 0.5777 (m-40)
REVERT: A   60 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5241 (mp)
REVERT: A  247 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7430 (mm-30)
REVERT: A  453 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7850 (mttp)
REVERT: A  505 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5554 (pt0)
REVERT: A  835 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7847 (mttp)
REVERT: A  844 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7901 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8100 (mmmt)
REVERT: B  135 LYS cc_start: 0.7665 (tptm) cc_final: 0.7100 (mmpt)
  outliers start: 30
  outliers final: 23
  residues processed: 134
  average time/residue: 2.1339
  time to fit residues: 305.5362
Evaluate side-chains
  140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 1.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  453 LYS
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  505 GLU
Chi-restraints excluded: chain A residue  525 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN
** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.169556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122003 restraints weight = 10147.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.80
r_work: 0.3148 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.0685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093  10396  Z= 0.133
  Angle     :  0.700  30.735  14097  Z= 0.318
  Chirality :  0.063   1.815   1574
  Planarity :  0.004   0.052   1777
  Dihedral  : 17.256 176.611   1804
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.37 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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: 1244
  helix:  1.96 (0.22), residues: 581
  sheet:  0.71 (0.41), residues: 150
  loop : -0.08 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.026   0.001   PHE A 970 
 TYR   0.020   0.001   TYR A 802 
 ARG   0.003   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05397 (    3)
  link_NAG-ASN         : angle       4.39756 (    9)
  hydrogen bonds       : bond        0.04525 (  510)
  hydrogen bonds       : angle       4.29629 ( 1509)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       0.51966 (    6)
  covalent geometry    : bond        0.00265 (10390)
  covalent geometry    : angle       0.69129 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ASN cc_start: 0.6209 (OUTLIER) cc_final: 0.5811 (m-40)
REVERT: A   60 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5300 (mp)
REVERT: A  247 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7423 (mm-30)
REVERT: A  453 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7868 (mttp)
REVERT: A  505 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5570 (pt0)
REVERT: A  835 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7862 (mttp)
REVERT: A  844 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7886 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8722 (mmtp) cc_final: 0.8120 (mmmt)
REVERT: B  135 LYS cc_start: 0.7660 (tptm) cc_final: 0.7117 (mmpt)
  outliers start: 30
  outliers final: 23
  residues processed: 134
  average time/residue: 1.5746
  time to fit residues: 225.3667
Evaluate side-chains
  140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  453 LYS
Chi-restraints excluded: chain A residue  481 GLU
Chi-restraints excluded: chain A residue  505 GLU
Chi-restraints excluded: chain A residue  525 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 97 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 96 optimal weight:    0.0170
   chunk 35 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN
** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.169884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.122265 restraints weight = 8626.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.32
r_work: 0.3176 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.0715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10396  Z= 0.119
  Angle     :  0.692  30.683  14097  Z= 0.314
  Chirality :  0.063   1.813   1574
  Planarity :  0.004   0.052   1777
  Dihedral  : 17.141 176.525   1804
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.37 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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: 1244
  helix:  1.96 (0.22), residues: 581
  sheet:  0.77 (0.41), residues: 148
  loop : -0.09 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.003   0.001   HIS B 227 
 PHE   0.014   0.001   PHE A 161 
 TYR   0.020   0.001   TYR A 802 
 ARG   0.004   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00570 (    3)
  link_NAG-ASN         : angle       3.06391 (    9)
  hydrogen bonds       : bond        0.04423 (  510)
  hydrogen bonds       : angle       4.26028 ( 1509)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.51235 (    6)
  covalent geometry    : bond        0.00254 (10390)
  covalent geometry    : angle       0.68780 (14082)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 ASN cc_start: 0.6220 (OUTLIER) cc_final: 0.5834 (m-40)
REVERT: A   60 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5363 (mp)
REVERT: A  130 GLU cc_start: 0.5884 (pp20) cc_final: 0.5486 (pp20)
REVERT: A  237 SER cc_start: 0.7670 (OUTLIER) cc_final: 0.7336 (t)
REVERT: A  247 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7399 (mm-30)
REVERT: A  453 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7883 (mttp)
REVERT: A  505 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5588 (pt0)
REVERT: A  689 GLU cc_start: 0.7876 (tp30) cc_final: 0.7603 (tp30)
REVERT: A  835 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7877 (mttp)
REVERT: A  844 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7841 (mtt-85)
REVERT: B   78 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8121 (mmmt)
REVERT: B  135 LYS cc_start: 0.7637 (tptm) cc_final: 0.7119 (mmpt)
  outliers start: 31
  outliers final: 21
  residues processed: 136
  average time/residue: 1.5115
  time to fit residues: 219.4087
Evaluate side-chains
  141 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASN
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  453 LYS
Chi-restraints excluded: chain A residue  505 GLU
Chi-restraints excluded: chain A residue  525 GLU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  680 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  835 LYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  890 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  261 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0010
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 109 optimal weight:    0.0270
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.5446

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

Flipped N/Q/H residues before XYZ refinement:
A 665 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.169874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.122255 restraints weight = 8645.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.30
r_work: 0.3173 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.0744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091  10396  Z= 0.127
  Angle     :  0.697  30.683  14097  Z= 0.316
  Chirality :  0.063   1.813   1574
  Planarity :  0.004   0.052   1777
  Dihedral  : 17.069 176.525   1800
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.46 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.80 %
    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: 1244
  helix:  1.96 (0.22), residues: 581
  sheet:  0.77 (0.41), residues: 148
  loop : -0.09 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 997 
 HIS   0.003   0.001   HIS B 227 
 PHE   0.014   0.001   PHE A 161 
 TYR   0.020   0.001   TYR A 802 
 ARG   0.004   0.000   ARG A 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05287 (    3)
  link_NAG-ASN         : angle       4.43613 (    9)
  hydrogen bonds       : bond        0.04423 (  510)
  hydrogen bonds       : angle       4.26028 ( 1509)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.51234 (    6)
  covalent geometry    : bond        0.00254 (10390)
  covalent geometry    : angle       0.68779 (14082)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14584.06 seconds
wall clock time: 256 minutes 22.32 seconds (15382.32 seconds total)