Starting phenix.real_space_refine
on Tue May 13 22:47:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bfq_44503/05_2025/9bfq_44503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bfq_44503/05_2025/9bfq_44503.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bfq_44503/05_2025/9bfq_44503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bfq_44503/05_2025/9bfq_44503.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bfq_44503/05_2025/9bfq_44503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bfq_44503/05_2025/9bfq_44503.cif"
  }
  resolution = 3.09
  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=   0.003 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    6985      2.51       5
     N    1884      2.21       5
     O    2036      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10958
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1000, 7992
          Classifications: {'peptide': 1000}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 927}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 2896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2896
          Classifications: {'peptide': 365}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 9, 'TRANS': 355}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 7.32, per 1000 atoms: 0.67
  Number of scatterers: 10958
  At special positions: 0
  Unit cell: (85.49, 112.88, 162.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    2036      8.00
     N    1884      7.00
     C    6985      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 257 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 253 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 239 " - pdb=" SG  CYS A 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 270 " - pdb=" SG  CYS A 290 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 286 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 387 " - pdb=" SG  CYS A 393 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 981 " - pdb=" SG  CYS A 991 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 112 " - pdb=" SG  CYS B 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 282 " - pdb=" SG  CYS B 501 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 403 " 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 A2601 " - " ASN A 966 "
      " NAG A2602 " - " ASN A 505 "
      " NAG B 601 " - " ASN B 183 "
      " NAG B 602 " - " ASN B 474 "
      " NAG B 603 " - " ASN B 485 "
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2578

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 23 sheets defined
      16.7% alpha, 29.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 208 through 227
    Processing helix  chain 'A' and resid 248 through 258
      removed outlier: 3.540A  pdb=" N   ARG A 252 " --> pdb=" O   CYS A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 266
      removed outlier: 3.562A  pdb=" N   LEU A 264 " --> pdb=" O   TRP A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 274
    Processing helix  chain 'A' and resid 283 through 305
      removed outlier: 3.886A  pdb=" N   ILE A 305 " --> pdb=" O   GLN A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 312
      removed outlier: 3.520A  pdb=" N   VAL A 309 " --> pdb=" O   ILE A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1070
      removed outlier: 3.629A  pdb=" N   GLU A1069 " --> pdb=" O   THR A1066 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ALA A1070 " --> pdb=" O   PRO A1067 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1066 through 1070'
    Processing helix  chain 'A' and resid 1172 through 1176
      removed outlier: 3.979A  pdb=" N   SER A1176 " --> pdb=" O   ASP A1173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 115
    Processing helix  chain 'B' and resid 131 through 134
    Processing helix  chain 'B' and resid 151 through 166
      removed outlier: 4.155A  pdb=" N   ALA B 155 " --> pdb=" O   ASP B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 201
      removed outlier: 3.684A  pdb=" N   LEU B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 218
    Processing helix  chain 'B' and resid 218 through 226
    Processing helix  chain 'B' and resid 234 through 238
      removed outlier: 3.694A  pdb=" N   ALA B 237 " --> pdb=" O   GLY B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 249
    Processing helix  chain 'B' and resid 265 through 278
      removed outlier: 3.858A  pdb=" N   TYR B 269 " --> pdb=" O   THR B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 326
      removed outlier: 3.504A  pdb=" N   LEU B 323 " --> pdb=" O   ASP B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 388
      removed outlier: 4.463A  pdb=" N   SER B 373 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 414
      removed outlier: 4.029A  pdb=" N   TRP B 413 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 431
    Processing helix  chain 'B' and resid 494 through 499
    Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 317
      removed outlier: 4.050A  pdb=" N   LEU A 329 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 381
    Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 381
    Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 448
      removed outlier: 6.667A  pdb=" N   HIS A 457 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LEU A 446 " --> pdb=" O   ALA A 455 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ALA A 455 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 489
      removed outlier: 3.504A  pdb=" N   GLY A 524 " --> pdb=" O   LEU A 508 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 568
      removed outlier: 6.707A  pdb=" N   VAL A 552 " --> pdb=" O   ILE A 566 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA A 810 " --> pdb=" O   VAL A 547 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 576 through 578
      removed outlier: 4.031A  pdb=" N   LEU A 594 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 624 through 631
      removed outlier: 6.164A  pdb=" N   GLU A 642 " --> pdb=" O   PRO A 625 " (cutoff:3.500A)
      removed outlier: 5.525A  pdb=" N   ILE A 653 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLU A 668 " --> pdb=" O   ILE A 653 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   SER A 655 " --> pdb=" O   VAL A 666 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   VAL A 666 " --> pdb=" O   SER A 655 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 676 through 680
      removed outlier: 4.416A  pdb=" N   GLN A 676 " --> pdb=" O   ARG A 689 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   TRP A 688 " --> pdb=" O   TRP A 695 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A 694 " --> pdb=" O   LEU A 707 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 716 through 719
      removed outlier: 3.701A  pdb=" N   ILE A 724 " --> pdb=" O   GLN A 719 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE A 735 " --> pdb=" O   LEU A 748 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 776 through 779
      removed outlier: 3.671A  pdb=" N   ALA A 798 " --> pdb=" O   LEU A 786 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 832 through 835
    Processing sheet with id=AB4, first strand: chain 'A' and resid 917 through 920
      removed outlier: 5.876A  pdb=" N   TYR A 863 " --> pdb=" O   ASN A 880 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ILE B 466 " --> pdb=" O   TYR B 479 " (cutoff:3.500A)
      removed outlier: 10.058A  pdb=" N   TYR B 481 " --> pdb=" O   ARG B 464 " (cutoff:3.500A)
      removed outlier: 12.349A  pdb=" N   ARG B 464 " --> pdb=" O   TYR B 481 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   MET B 444 " --> pdb=" O   ILE B 466 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   SER B 468 " --> pdb=" O   PHE B 442 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   PHE B 442 " --> pdb=" O   SER B 468 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ALA B 330 " --> pdb=" O   LYS B 447 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU B 310 " --> pdb=" O   PHE B 331 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   LEU B 333 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   SER B 312 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   GLU B 335 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ASN B 291 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   PHE B 311 " --> pdb=" O   ASN B 291 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   TYR B 293 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   VAL B 313 " --> pdb=" O   TYR B 293 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   MET B 295 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   SER B 258 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   ILE B 294 " --> pdb=" O   SER B 258 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   GLU B 260 " --> pdb=" O   ILE B 294 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   PHE B 296 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ALA B 262 " --> pdb=" O   PHE B 296 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 949 through 954
      removed outlier: 5.041A  pdb=" N   VAL A 938 " --> pdb=" O   GLN A 951 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   SER A 937 " --> pdb=" O   SER A 933 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA A1180 " --> pdb=" O   ALA A 932 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 963 through 964
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1000 through 1006
      removed outlier: 4.649A  pdb=" N   SER A1002 " --> pdb=" O   THR A1015 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR A1015 " --> pdb=" O   SER A1002 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A1011 " --> pdb=" O   ASP A1006 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1042 through 1045
      removed outlier: 3.625A  pdb=" N   TYR A1074 " --> pdb=" O   LEU A1060 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1089
      removed outlier: 6.537A  pdb=" N   LEU A1098 " --> pdb=" O   ALA A1084 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   PHE A1086 " --> pdb=" O   PHE A1096 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   PHE A1096 " --> pdb=" O   PHE A1086 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   LEU A1088 " --> pdb=" O   GLN A1094 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   GLN A1094 " --> pdb=" O   LEU A1088 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   TRP A1097 " --> pdb=" O   TYR A1108 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ARG A1109 " --> pdb=" O   MET A1121 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   MET A1121 " --> pdb=" O   ARG A1109 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1137 through 1139
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1207 through 1208
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1242 through 1248
    Processing sheet with id=AC4, first strand: chain 'B' and resid 136 through 139
      removed outlier: 3.774A  pdb=" N   LEU B 139 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL B 143 " --> pdb=" O   GLY B 175 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ARG B 177 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LEU B 145 " --> pdb=" O   ARG B 177 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   ILE B 179 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   VAL B 147 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   VAL B 144 " --> pdb=" O   GLY B 207 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   PHE B 209 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   SER B 146 " --> pdb=" O   PHE B 209 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 338 through 339

    390 hydrogen bonds defined for protein.
    1053 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: 5.01

  Time building geometry restraints manager: 2.77 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: 1815
        1.29 -     1.42: 2950
        1.42 -     1.55: 6355
        1.55 -     1.69: 21
        1.69 -     1.82: 84
  Bond restraints: 11225
  Sorted by residual:
  bond pdb=" CA  SER B 488 "
       pdb=" CB  SER B 488 "
    ideal  model  delta    sigma   weight residual
    1.535  1.359  0.176 1.90e-02 2.77e+03 8.61e+01
  bond pdb=" C   HIS B 480 "
       pdb=" O   HIS B 480 "
    ideal  model  delta    sigma   weight residual
    1.235  1.159  0.076 1.23e-02 6.61e+03 3.85e+01
  bond pdb=" C   LEU B 489 "
       pdb=" O   LEU B 489 "
    ideal  model  delta    sigma   weight residual
    1.236  1.178  0.058 1.14e-02 7.69e+03 2.55e+01
  bond pdb=" C   SER B 488 "
       pdb=" O   SER B 488 "
    ideal  model  delta    sigma   weight residual
    1.234  1.171  0.062 1.24e-02 6.50e+03 2.53e+01
  bond pdb=" C   THR B 487 "
       pdb=" O   THR B 487 "
    ideal  model  delta    sigma   weight residual
    1.236  1.189  0.047 1.29e-02 6.01e+03 1.33e+01
  ... (remaining 11220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.12: 14999
        4.12 -     8.24: 243
        8.24 -    12.36: 16
       12.36 -    16.48: 2
       16.48 -    20.59: 2
  Bond angle restraints: 15262
  Sorted by residual:
  angle pdb=" C   ASP B 484 "
        pdb=" CA  ASP B 484 "
        pdb=" CB  ASP B 484 "
      ideal   model   delta    sigma   weight residual
     110.35  129.02  -18.67 1.91e+00 2.74e-01 9.56e+01
  angle pdb=" CG1 ILE A 305 "
        pdb=" CB  ILE A 305 "
        pdb=" CG2 ILE A 305 "
      ideal   model   delta    sigma   weight residual
     110.70   90.11   20.59 3.00e+00 1.11e-01 4.71e+01
  angle pdb=" CA  HIS B 480 "
        pdb=" CB  HIS B 480 "
        pdb=" CG  HIS B 480 "
      ideal   model   delta    sigma   weight residual
     113.80  120.41   -6.61 1.00e+00 1.00e+00 4.37e+01
  angle pdb=" N   ASP B 484 "
        pdb=" CA  ASP B 484 "
        pdb=" C   ASP B 484 "
      ideal   model   delta    sigma   weight residual
     113.29  100.71   12.58 2.00e+00 2.50e-01 3.96e+01
  angle pdb=" C   ASN B 485 "
        pdb=" CA  ASN B 485 "
        pdb=" CB  ASN B 485 "
      ideal   model   delta    sigma   weight residual
     111.89  120.61   -8.72 1.42e+00 4.96e-01 3.77e+01
  ... (remaining 15257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 6146
       17.95 -    35.90: 542
       35.90 -    53.85: 89
       53.85 -    71.80: 18
       71.80 -    89.75: 7
  Dihedral angle restraints: 6802
    sinusoidal: 2832
      harmonic: 3970
  Sorted by residual:
  dihedral pdb=" C   ASP B 484 "
           pdb=" N   ASP B 484 "
           pdb=" CA  ASP B 484 "
           pdb=" CB  ASP B 484 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.03   18.43     0      2.50e+00 1.60e-01 5.44e+01
  dihedral pdb=" CB  CYS B 282 "
           pdb=" SG  CYS B 282 "
           pdb=" SG  CYS B 501 "
           pdb=" CB  CYS B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   35.28   57.72     1      1.00e+01 1.00e-02 4.47e+01
  dihedral pdb=" C   ASN B 485 "
           pdb=" N   ASN B 485 "
           pdb=" CA  ASN B 485 "
           pdb=" CB  ASN B 485 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.50   13.90     0      2.50e+00 1.60e-01 3.09e+01
  ... (remaining 6799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1548
       0.112 -    0.224: 124
       0.224 -    0.336: 14
       0.336 -    0.448: 4
       0.448 -    0.560: 3
  Chirality restraints: 1693
  Sorted by residual:
  chirality pdb=" CA  ASP B 484 "
            pdb=" N   ASP B 484 "
            pdb=" C   ASP B 484 "
            pdb=" CB  ASP B 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.84e+00
  chirality pdb=" CA  ASN B 485 "
            pdb=" N   ASN B 485 "
            pdb=" C   ASN B 485 "
            pdb=" CB  ASN B 485 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CB  VAL B 162 "
            pdb=" CA  VAL B 162 "
            pdb=" CG1 VAL B 162 "
            pdb=" CG2 VAL B 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.46 2.00e-01 2.50e+01 5.29e+00
  ... (remaining 1690 not shown)

  Planarity restraints: 1974
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A2602 "   -0.335 2.00e-02 2.50e+03   2.85e-01 1.02e+03
        pdb=" C7  NAG A2602 "    0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG A2602 "   -0.004 2.00e-02 2.50e+03
        pdb=" N2  NAG A2602 "    0.487 2.00e-02 2.50e+03
        pdb=" O7  NAG A2602 "   -0.227 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 230 "    0.034 2.00e-02 2.50e+03   3.01e-02 2.26e+01
        pdb=" CG  TRP B 230 "   -0.080 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 230 "    0.038 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 230 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 230 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 230 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 230 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 230 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 230 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 230 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 370 "   -0.023 2.00e-02 2.50e+03   3.15e-02 1.73e+01
        pdb=" CG  PHE B 370 "    0.072 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 370 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 370 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 370 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 370 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 370 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1971 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 3442
        2.85 -     3.36: 7947
        3.36 -     3.88: 18363
        3.88 -     4.39: 20217
        4.39 -     4.90: 35711
  Nonbonded interactions: 85680
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 246 "
            pdb=" OH  TYR B 478 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   LYS A 250 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" O   GLY B 253 "
            pdb=" OG1 THR B 493 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" OG  SER A1225 "
            pdb=" O   GLY A1227 "
     model   vdw
     2.384 3.040
  nonbonded pdb=" O   MET A1199 "
            pdb=" OG  SER A1223 "
     model   vdw
     2.385 3.040
  ... (remaining 85675 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.710
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     28.430
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
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      :  0.008   0.176  11240  Z= 0.381
  Angle     :  1.244  20.595  15297  Z= 0.675
  Chirality :  0.071   0.560   1693
  Planarity :  0.012   0.285   1969
  Dihedral  : 13.922  89.751   4194
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.51 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -2.70 (0.20), residues: 1333
  helix: -4.06 (0.17), residues: 209
  sheet: -0.65 (0.23), residues: 496
  loop : -1.86 (0.20), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.080   0.003   TRP B 230 
 HIS   0.024   0.003   HIS A 529 
 PHE   0.072   0.005   PHE B 370 
 TYR   0.024   0.003   TYR A1013 
 ARG   0.020   0.001   ARG B 317 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00883 (    5)
  link_NAG-ASN         : angle       4.21321 (   15)
  hydrogen bonds       : bond        0.22441 (  382)
  hydrogen bonds       : angle       9.45304 ( 1053)
  SS BOND              : bond        0.00528 (   10)
  SS BOND              : angle       1.36674 (   20)
  covalent geometry    : bond        0.00762 (11225)
  covalent geometry    : angle       1.23767 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 ASP cc_start: 0.6894 (m-30) cc_final: 0.6623 (m-30)
REVERT: A  550 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7570 (mtp180)
REVERT: A  565 MET cc_start: 0.7978 (tpp) cc_final: 0.7683 (mmm)
REVERT: A  642 GLU cc_start: 0.6978 (tt0) cc_final: 0.6344 (tm-30)
REVERT: A  682 LEU cc_start: 0.8626 (tp) cc_final: 0.8393 (tt)
REVERT: A  890 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7745 (mtp180)
REVERT: A  928 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7564 (mtm110)
REVERT: A  935 GLN cc_start: 0.7972 (tt0) cc_final: 0.7680 (mp-120)
REVERT: A  949 GLU cc_start: 0.7693 (tt0) cc_final: 0.7274 (mt-10)
REVERT: A 1194 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7532 (mp0)
REVERT: A 1264 GLN cc_start: 0.8170 (mt0) cc_final: 0.7160 (tt0)
REVERT: B  164 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7487 (mm-40)
REVERT: B  266 LEU cc_start: 0.7846 (tp) cc_final: 0.7545 (tt)
REVERT: B  277 ARG cc_start: 0.7300 (mtm110) cc_final: 0.7012 (ttp80)
REVERT: B  447 LYS cc_start: 0.7669 (tttt) cc_final: 0.7364 (ttpp)
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2668
  time to fit residues: 70.9836
Evaluate side-chains
  159 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 712 GLN
A 726 HIS
B 245 HIS
B 291 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.169617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.138507 restraints weight = 12064.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 1.87
r_work: 0.3321 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11240  Z= 0.184
  Angle     :  0.628   6.262  15297  Z= 0.317
  Chirality :  0.044   0.158   1693
  Planarity :  0.006   0.056   1969
  Dihedral  :  5.712  59.333   1578
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.05 %
    Favored  : 92.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -1.71 (0.21), residues: 1333
  helix: -1.79 (0.30), residues: 205
  sheet: -0.38 (0.23), residues: 481
  loop : -1.44 (0.21), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 688 
 HIS   0.009   0.001   HIS A 459 
 PHE   0.018   0.002   PHE B 495 
 TYR   0.015   0.002   TYR B 227 
 ARG   0.004   0.001   ARG B 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00419 (    5)
  link_NAG-ASN         : angle       2.63237 (   15)
  hydrogen bonds       : bond        0.04391 (  382)
  hydrogen bonds       : angle       6.19679 ( 1053)
  SS BOND              : bond        0.00317 (   10)
  SS BOND              : angle       0.70769 (   20)
  covalent geometry    : bond        0.00436 (11225)
  covalent geometry    : angle       0.62238 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 177
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 ASP cc_start: 0.7015 (m-30) cc_final: 0.6805 (m-30)
REVERT: A  549 ARG cc_start: 0.8105 (mmt180) cc_final: 0.7870 (mmp80)
REVERT: A  550 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7681 (mtp180)
REVERT: A  642 GLU cc_start: 0.6991 (tt0) cc_final: 0.6471 (tm-30)
REVERT: A  682 LEU cc_start: 0.8648 (tp) cc_final: 0.8442 (tt)
REVERT: A  890 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7620 (mtp180)
REVERT: A  928 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7598 (mtm110)
REVERT: A  997 LEU cc_start: 0.8463 (mt) cc_final: 0.8226 (mp)
REVERT: A 1046 ASP cc_start: 0.8206 (t0) cc_final: 0.7946 (t0)
REVERT: A 1134 ASP cc_start: 0.7242 (t0) cc_final: 0.6972 (t70)
REVERT: A 1264 GLN cc_start: 0.8259 (mt0) cc_final: 0.7220 (tt0)
REVERT: B  266 LEU cc_start: 0.7731 (tp) cc_final: 0.7505 (tt)
REVERT: B  434 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7567 (mtm180)
  outliers start: 8
  outliers final: 3
  residues processed: 182
  average time/residue: 0.2250
  time to fit residues: 58.6037
Evaluate side-chains
  155 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 152
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain B residue  291 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0070
   chunk 29 optimal weight:    0.0470
   chunk 99 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0270
   chunk 115 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0970
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.1552

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
A 712 GLN
A 935 GLN
B 298 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.173551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.142033 restraints weight = 12148.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.92
r_work: 0.3362 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11240  Z= 0.093
  Angle     :  0.535   9.048  15297  Z= 0.266
  Chirality :  0.041   0.178   1693
  Planarity :  0.004   0.046   1969
  Dihedral  :  5.110  57.506   1578
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.51 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -1.09 (0.21), residues: 1333
  helix: -0.52 (0.35), residues: 205
  sheet: -0.17 (0.23), residues: 472
  loop : -1.16 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1014 
 HIS   0.006   0.001   HIS A 459 
 PHE   0.016   0.001   PHE A 876 
 TYR   0.011   0.001   TYR B 227 
 ARG   0.005   0.000   ARG B 483 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00251 (    5)
  link_NAG-ASN         : angle       2.25046 (   15)
  hydrogen bonds       : bond        0.03407 (  382)
  hydrogen bonds       : angle       5.55126 ( 1053)
  SS BOND              : bond        0.00249 (   10)
  SS BOND              : angle       0.49620 (   20)
  covalent geometry    : bond        0.00208 (11225)
  covalent geometry    : angle       0.53060 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 168
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 ASP cc_start: 0.7010 (m-30) cc_final: 0.6707 (m-30)
REVERT: A  228 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6811 (pt0)
REVERT: A  550 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7565 (mtp180)
REVERT: A  642 GLU cc_start: 0.6771 (tt0) cc_final: 0.6474 (tm-30)
REVERT: A  715 TRP cc_start: 0.8775 (t-100) cc_final: 0.8550 (t-100)
REVERT: A  890 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7605 (mtp180)
REVERT: A  928 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7502 (mtm110)
REVERT: A  997 LEU cc_start: 0.8452 (mt) cc_final: 0.8244 (mp)
REVERT: A 1134 ASP cc_start: 0.7141 (t0) cc_final: 0.6892 (t0)
REVERT: A 1156 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7750 (mmt-90)
REVERT: A 1264 GLN cc_start: 0.8196 (mt0) cc_final: 0.7101 (tt0)
  outliers start: 7
  outliers final: 3
  residues processed: 171
  average time/residue: 0.2235
  time to fit residues: 54.5594
Evaluate side-chains
  160 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 156
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1248 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 2 optimal weight:    0.2980
   chunk 76 optimal weight:    0.1980
   chunk 32 optimal weight:    0.0170
   chunk 125 optimal weight:    0.0970
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.2216

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

Flipped N/Q/H residues before XYZ refinement:
A 697 GLN
A 700 HIS
A 712 GLN
A 719 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.171590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.140291 restraints weight = 12056.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.86
r_work: 0.3382 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11240  Z= 0.093
  Angle     :  0.513   7.486  15297  Z= 0.254
  Chirality :  0.041   0.170   1693
  Planarity :  0.004   0.040   1969
  Dihedral  :  4.790  57.026   1578
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.95 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -0.67 (0.22), residues: 1333
  helix:  0.31 (0.37), residues: 211
  sheet: -0.07 (0.23), residues: 481
  loop : -0.93 (0.23), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1147 
 HIS   0.006   0.001   HIS A 459 
 PHE   0.014   0.001   PHE A 876 
 TYR   0.009   0.001   TYR A1108 
 ARG   0.003   0.000   ARG B 483 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    5)
  link_NAG-ASN         : angle       2.00105 (   15)
  hydrogen bonds       : bond        0.03071 (  382)
  hydrogen bonds       : angle       5.14832 ( 1053)
  SS BOND              : bond        0.00241 (   10)
  SS BOND              : angle       0.49363 (   20)
  covalent geometry    : bond        0.00212 (11225)
  covalent geometry    : angle       0.50926 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ASP cc_start: 0.6960 (m-30) cc_final: 0.6652 (m-30)
REVERT: A  228 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6708 (pt0)
REVERT: A  599 PHE cc_start: 0.6571 (p90) cc_final: 0.6265 (p90)
REVERT: A  642 GLU cc_start: 0.6708 (tt0) cc_final: 0.6416 (tm-30)
REVERT: A  715 TRP cc_start: 0.8786 (t-100) cc_final: 0.8533 (t-100)
REVERT: A  890 ARG cc_start: 0.7918 (ttm170) cc_final: 0.7595 (mtp180)
REVERT: A  928 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7470 (mtm110)
REVERT: A 1134 ASP cc_start: 0.7119 (t0) cc_final: 0.6871 (t0)
REVERT: A 1156 ARG cc_start: 0.8000 (mmt90) cc_final: 0.7769 (mmt-90)
REVERT: A 1264 GLN cc_start: 0.8151 (mt0) cc_final: 0.7104 (tt0)
REVERT: B  190 LEU cc_start: 0.6607 (mt) cc_final: 0.6361 (mp)
REVERT: B  206 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6998 (mtm)
  outliers start: 13
  outliers final: 6
  residues processed: 174
  average time/residue: 0.2381
  time to fit residues: 58.5337
Evaluate side-chains
  166 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1061 SER
Chi-restraints excluded: chain A residue 1248 LEU
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  278 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 72 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 65 optimal weight:    0.3980
   chunk 121 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 51 optimal weight:    0.0870
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
A 712 GLN
A1229 HIS
A1284 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.170174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.138822 restraints weight = 12128.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.84
r_work: 0.3349 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11240  Z= 0.125
  Angle     :  0.528   8.866  15297  Z= 0.262
  Chirality :  0.042   0.169   1693
  Planarity :  0.004   0.036   1969
  Dihedral  :  4.778  57.231   1578
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.22 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -0.51 (0.23), residues: 1333
  helix:  0.62 (0.36), residues: 211
  sheet: -0.18 (0.23), residues: 514
  loop : -0.72 (0.24), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 809 
 HIS   0.007   0.001   HIS A 459 
 PHE   0.017   0.001   PHE B 495 
 TYR   0.010   0.001   TYR A1054 
 ARG   0.005   0.000   ARG A 549 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00237 (    5)
  link_NAG-ASN         : angle       1.97623 (   15)
  hydrogen bonds       : bond        0.03141 (  382)
  hydrogen bonds       : angle       5.09233 ( 1053)
  SS BOND              : bond        0.00234 (   10)
  SS BOND              : angle       0.58200 (   20)
  covalent geometry    : bond        0.00297 (11225)
  covalent geometry    : angle       0.52469 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 ASP cc_start: 0.6947 (m-30) cc_final: 0.6633 (m-30)
REVERT: A  228 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6797 (pt0)
REVERT: A  599 PHE cc_start: 0.6611 (p90) cc_final: 0.6269 (p90)
REVERT: A  809 TRP cc_start: 0.8150 (p-90) cc_final: 0.7772 (p-90)
REVERT: A  928 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7439 (mtm110)
REVERT: A 1134 ASP cc_start: 0.7096 (t0) cc_final: 0.6853 (t0)
REVERT: A 1156 ARG cc_start: 0.8041 (mmt90) cc_final: 0.7754 (mmt-90)
REVERT: A 1264 GLN cc_start: 0.8129 (mt0) cc_final: 0.7096 (tt0)
REVERT: B  190 LEU cc_start: 0.6688 (mt) cc_final: 0.6364 (mp)
REVERT: B  206 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7075 (mtm)
REVERT: B  290 ASP cc_start: 0.6014 (m-30) cc_final: 0.5731 (t0)
REVERT: B  447 LYS cc_start: 0.7536 (tttt) cc_final: 0.7322 (ttpp)
  outliers start: 15
  outliers final: 7
  residues processed: 175
  average time/residue: 0.2451
  time to fit residues: 61.0409
Evaluate side-chains
  172 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  529 HIS
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1061 SER
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  278 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 134 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 589 ASN
A 712 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.166782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.134295 restraints weight = 12190.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.94
r_work: 0.3310 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  11240  Z= 0.217
  Angle     :  0.610   9.147  15297  Z= 0.303
  Chirality :  0.044   0.168   1693
  Planarity :  0.005   0.042   1969
  Dihedral  :  5.125  57.562   1578
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.65 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -0.62 (0.23), residues: 1333
  helix:  0.50 (0.35), residues: 217
  sheet: -0.33 (0.23), residues: 511
  loop : -0.69 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 931 
 HIS   0.007   0.001   HIS A 459 
 PHE   0.025   0.002   PHE B 495 
 TYR   0.016   0.002   TYR A 261 
 ARG   0.011   0.001   ARG A 550 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00331 (    5)
  link_NAG-ASN         : angle       2.27142 (   15)
  hydrogen bonds       : bond        0.03527 (  382)
  hydrogen bonds       : angle       5.31332 ( 1053)
  SS BOND              : bond        0.00286 (   10)
  SS BOND              : angle       0.82762 (   20)
  covalent geometry    : bond        0.00527 (11225)
  covalent geometry    : angle       0.60596 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A  219 ASP cc_start: 0.7266 (m-30) cc_final: 0.6903 (m-30)
REVERT: A  261 TYR cc_start: 0.8313 (t80) cc_final: 0.8080 (t80)
REVERT: A  331 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7910 (mm)
REVERT: A  809 TRP cc_start: 0.8225 (p-90) cc_final: 0.7941 (p-90)
REVERT: A  928 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7560 (mtm180)
REVERT: A  998 GLN cc_start: 0.8446 (mt0) cc_final: 0.8038 (mp10)
REVERT: A 1134 ASP cc_start: 0.7537 (t0) cc_final: 0.7266 (t0)
REVERT: A 1264 GLN cc_start: 0.8312 (mt0) cc_final: 0.7188 (tt0)
REVERT: B  206 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7397 (mtm)
REVERT: B  264 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6718 (mt-10)
REVERT: B  274 GLU cc_start: 0.7747 (tp30) cc_final: 0.7207 (tp30)
REVERT: B  278 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7650 (mp10)
  outliers start: 19
  outliers final: 13
  residues processed: 172
  average time/residue: 0.2390
  time to fit residues: 59.3813
Evaluate side-chains
  174 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  529 HIS
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  861 TRP
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1061 SER
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain B residue  278 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 115 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 95 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 132 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 120 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
A 712 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.166210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.134112 restraints weight = 12336.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.96
r_work: 0.3309 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11240  Z= 0.164
  Angle     :  0.562   9.329  15297  Z= 0.279
  Chirality :  0.043   0.173   1693
  Planarity :  0.004   0.033   1969
  Dihedral  :  4.975  57.542   1578
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.58 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -0.51 (0.23), residues: 1333
  helix:  0.74 (0.36), residues: 217
  sheet: -0.36 (0.23), residues: 512
  loop : -0.59 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 554 
 HIS   0.006   0.001   HIS A 459 
 PHE   0.020   0.002   PHE A 876 
 TYR   0.013   0.001   TYR A1233 
 ARG   0.004   0.000   ARG A 549 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00277 (    5)
  link_NAG-ASN         : angle       2.09075 (   15)
  hydrogen bonds       : bond        0.03245 (  382)
  hydrogen bonds       : angle       5.20659 ( 1053)
  SS BOND              : bond        0.00273 (   10)
  SS BOND              : angle       0.73120 (   20)
  covalent geometry    : bond        0.00399 (11225)
  covalent geometry    : angle       0.55848 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 1.123 
Fit side-chains
REVERT: A  219 ASP cc_start: 0.7032 (m-30) cc_final: 0.6636 (m-30)
REVERT: A  261 TYR cc_start: 0.8247 (t80) cc_final: 0.7958 (t80)
REVERT: A  331 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7853 (mm)
REVERT: A  738 ILE cc_start: 0.7641 (mp) cc_final: 0.7358 (mm)
REVERT: A  928 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7394 (mtm180)
REVERT: A  998 GLN cc_start: 0.8243 (mt0) cc_final: 0.7978 (mp10)
REVERT: A 1134 ASP cc_start: 0.7157 (t0) cc_final: 0.6897 (t0)
REVERT: A 1264 GLN cc_start: 0.8158 (mt0) cc_final: 0.7081 (tt0)
REVERT: A 1284 GLN cc_start: 0.7814 (mt0) cc_final: 0.7348 (tp40)
REVERT: B  206 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7264 (mtm)
REVERT: B  264 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6671 (mt-10)
  outliers start: 18
  outliers final: 13
  residues processed: 175
  average time/residue: 0.2351
  time to fit residues: 58.7802
Evaluate side-chains
  177 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 162
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  529 HIS
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  861 TRP
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1061 SER
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  487 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 133 optimal weight:    0.0370
   chunk 53 optimal weight:    0.9980
   chunk 7 optimal weight:    0.3980
   chunk 79 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0270
   chunk 37 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.4116

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
A 697 GLN
A 712 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.167833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.136201 restraints weight = 12238.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 1.85
r_work: 0.3347 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11240  Z= 0.122
  Angle     :  0.535   8.537  15297  Z= 0.266
  Chirality :  0.042   0.164   1693
  Planarity :  0.004   0.079   1969
  Dihedral  :  4.828  57.365   1578
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 13.67 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -0.36 (0.23), residues: 1333
  helix:  0.99 (0.36), residues: 217
  sheet: -0.26 (0.23), residues: 511
  loop : -0.56 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 931 
 HIS   0.006   0.001   HIS A 459 
 PHE   0.019   0.001   PHE A 876 
 TYR   0.012   0.001   TYR A1054 
 ARG   0.004   0.000   ARG A1156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00231 (    5)
  link_NAG-ASN         : angle       1.97535 (   15)
  hydrogen bonds       : bond        0.03063 (  382)
  hydrogen bonds       : angle       5.11833 ( 1053)
  SS BOND              : bond        0.00261 (   10)
  SS BOND              : angle       0.65085 (   20)
  covalent geometry    : bond        0.00293 (11225)
  covalent geometry    : angle       0.53158 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 ASP cc_start: 0.6987 (m-30) cc_final: 0.6602 (m-30)
REVERT: A  228 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6970 (pt0)
REVERT: A  261 TYR cc_start: 0.8218 (t80) cc_final: 0.7857 (t80)
REVERT: A  331 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7827 (mm)
REVERT: A  928 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7363 (mtm180)
REVERT: A 1134 ASP cc_start: 0.7098 (t0) cc_final: 0.6827 (t0)
REVERT: A 1264 GLN cc_start: 0.8125 (mt0) cc_final: 0.6869 (tm-30)
REVERT: B  206 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7273 (mtm)
REVERT: B  264 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6622 (mt-10)
  outliers start: 16
  outliers final: 9
  residues processed: 176
  average time/residue: 0.2453
  time to fit residues: 60.7551
Evaluate side-chains
  171 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  861 TRP
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1061 SER
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  487 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 86 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0870
   chunk 133 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 121 optimal weight:    0.6980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 244 ASN
A 697 GLN
A 712 GLN
A 719 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.167342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.134941 restraints weight = 12251.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.98
r_work: 0.3415 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11240  Z= 0.143
  Angle     :  0.556   9.294  15297  Z= 0.276
  Chirality :  0.042   0.182   1693
  Planarity :  0.004   0.068   1969
  Dihedral  :  4.834  57.202   1578
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 14.18 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -0.32 (0.23), residues: 1333
  helix:  1.09 (0.36), residues: 217
  sheet: -0.25 (0.23), residues: 511
  loop : -0.54 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 809 
 HIS   0.006   0.001   HIS A 459 
 PHE   0.019   0.001   PHE A 876 
 TYR   0.013   0.001   TYR A1054 
 ARG   0.003   0.000   ARG B 483 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00242 (    5)
  link_NAG-ASN         : angle       1.98840 (   15)
  hydrogen bonds       : bond        0.03173 (  382)
  hydrogen bonds       : angle       5.11475 ( 1053)
  SS BOND              : bond        0.00259 (   10)
  SS BOND              : angle       0.69269 (   20)
  covalent geometry    : bond        0.00346 (11225)
  covalent geometry    : angle       0.55303 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 1.144 
Fit side-chains
REVERT: A  219 ASP cc_start: 0.7041 (m-30) cc_final: 0.6648 (m-30)
REVERT: A  228 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6932 (pt0)
REVERT: A  261 TYR cc_start: 0.8247 (t80) cc_final: 0.7883 (t80)
REVERT: A  317 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6731 (mt-10)
REVERT: A  331 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7862 (mm)
REVERT: A  738 ILE cc_start: 0.7482 (mp) cc_final: 0.7257 (mm)
REVERT: A  928 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7376 (mtm180)
REVERT: A 1134 ASP cc_start: 0.7216 (t0) cc_final: 0.6921 (t0)
REVERT: A 1264 GLN cc_start: 0.8100 (mt0) cc_final: 0.6855 (tm-30)
REVERT: B  206 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7314 (mtm)
REVERT: B  264 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6603 (mt-10)
REVERT: B  278 GLN cc_start: 0.7682 (mp10) cc_final: 0.7094 (mp10)
  outliers start: 16
  outliers final: 11
  residues processed: 169
  average time/residue: 0.2268
  time to fit residues: 54.8821
Evaluate side-chains
  168 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  861 TRP
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1061 SER
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  487 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    0.2980
   chunk 99 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 90 optimal weight:    0.4980
   chunk 134 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 712 GLN
A 999 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.166669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.134085 restraints weight = 12186.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 1.84
r_work: 0.3384 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11240  Z= 0.160
  Angle     :  0.570   9.230  15297  Z= 0.283
  Chirality :  0.042   0.178   1693
  Planarity :  0.004   0.061   1969
  Dihedral  :  4.891  57.280   1578
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.35 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -0.29 (0.23), residues: 1333
  helix:  1.10 (0.37), residues: 217
  sheet: -0.29 (0.23), residues: 510
  loop : -0.45 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 809 
 HIS   0.006   0.001   HIS A 459 
 PHE   0.020   0.002   PHE B 495 
 TYR   0.033   0.002   TYR A 351 
 ARG   0.003   0.000   ARG B 483 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00260 (    5)
  link_NAG-ASN         : angle       1.99782 (   15)
  hydrogen bonds       : bond        0.03248 (  382)
  hydrogen bonds       : angle       5.17325 ( 1053)
  SS BOND              : bond        0.00270 (   10)
  SS BOND              : angle       0.74617 (   20)
  covalent geometry    : bond        0.00388 (11225)
  covalent geometry    : angle       0.56682 (15262)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 1.105 
Fit side-chains
REVERT: A  219 ASP cc_start: 0.7065 (m-30) cc_final: 0.6672 (m-30)
REVERT: A  317 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6746 (mt-10)
REVERT: A  331 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7896 (mm)
REVERT: A  565 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7485 (mmm)
REVERT: A  575 ASP cc_start: 0.6287 (t70) cc_final: 0.5961 (t70)
REVERT: A  928 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7412 (mtm180)
REVERT: A 1134 ASP cc_start: 0.7264 (t0) cc_final: 0.6970 (t0)
REVERT: A 1264 GLN cc_start: 0.8134 (mt0) cc_final: 0.6834 (tp40)
REVERT: B  206 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7315 (mtm)
REVERT: B  264 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6640 (mt-10)
REVERT: B  278 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7143 (mp10)
  outliers start: 17
  outliers final: 11
  residues processed: 168
  average time/residue: 0.2260
  time to fit residues: 55.0891
Evaluate side-chains
  171 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  861 TRP
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1061 SER
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  278 GLN
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  487 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 131 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 130 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 712 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.165007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.131831 restraints weight = 12168.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 1.95
r_work: 0.3374 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  11240  Z= 0.184
  Angle     :  0.601  15.172  15297  Z= 0.295
  Chirality :  0.043   0.260   1693
  Planarity :  0.005   0.057   1969
  Dihedral  :  4.967  57.165   1578
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.69 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    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: -0.31 (0.23), residues: 1333
  helix:  1.06 (0.36), residues: 217
  sheet: -0.28 (0.23), residues: 502
  loop : -0.48 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 809 
 HIS   0.006   0.001   HIS A 459 
 PHE   0.021   0.002   PHE B 495 
 TYR   0.030   0.002   TYR A 351 
 ARG   0.004   0.000   ARG A1154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00293 (    5)
  link_NAG-ASN         : angle       2.04287 (   15)
  hydrogen bonds       : bond        0.03318 (  382)
  hydrogen bonds       : angle       5.24808 ( 1053)
  SS BOND              : bond        0.00284 (   10)
  SS BOND              : angle       0.80102 (   20)
  covalent geometry    : bond        0.00452 (11225)
  covalent geometry    : angle       0.59777 (15262)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5520.28 seconds
wall clock time: 96 minutes 15.32 seconds (5775.32 seconds total)