Starting phenix.real_space_refine
on Tue Nov 18 13:28:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qex_4539/11_2025/6qex_4539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qex_4539/11_2025/6qex_4539.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qex_4539/11_2025/6qex_4539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qex_4539/11_2025/6qex_4539.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qex_4539/11_2025/6qex_4539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qex_4539/11_2025/6qex_4539.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 526 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      53      5.16       5
     C    8648      2.51       5
     N    2131      2.21       5
     O    2417      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 83 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13251
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1182, 9191
          Classifications: {'peptide': 1182}
          Link IDs: {'PTRANS': 27, 'TRANS': 1154}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1713
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 220, 1710
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206}
      Conformer: "B"
        Number of residues, atoms: 220, 1710
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206}
          bond proxies already assigned to first conformer: 1747
    Chain: "C"
      Number of atoms: 1717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1717
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211}
    Chain: "A"
      Number of atoms: 630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 630
          Unusual residues: {'3PE': 2, 'CLR': 16, 'NAG': 3, 'TA1': 1}
          Classifications: {'undetermined': 22}
          Link IDs: {None: 21}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.13, per 1000 atoms: 0.24
  Number of scatterers: 13251
  At special positions: 0
  Unit cell: (89.04, 101.64, 210, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      53     16.00
     P       2     15.00
     O    2417      8.00
     N    2131      7.00
     C    8648      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 140 " - pdb=" SG ACYS B 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 140 " - pdb=" SG BCYS B 200 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 220 " - pdb=" SG  CYS C 137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 149 " - pdb=" SG  CYS C 204 " 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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A  91 "
      " NAG A1302 " - " ASN A  94 "
      " NAG A1303 " - " ASN A  99 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 616.0 milliseconds
  

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3004

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      51.8% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 40
      removed outlier: 4.107A  pdb=" N   PHE A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 63
      removed outlier: 3.698A  pdb=" N   VAL A  52 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA A  58 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 93
      removed outlier: 3.756A  pdb=" N   VAL A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASP A  87 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   LEU A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   MET A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A  91 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ILE A  92 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   THR A  93 " --> pdb=" O   MET A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 156
      removed outlier: 3.972A  pdb=" N   LEU A 107 " --> pdb=" O   PHE A 103 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   THR A 112 " --> pdb=" O   GLU A 108 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ARG A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 166
    Processing helix  chain 'A' and resid 168 through 186
      removed outlier: 3.681A  pdb=" N   ASN A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 211
      removed outlier: 3.528A  pdb=" N   PHE A 194 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLY A 211 " --> pdb=" O   GLY A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 238
      removed outlier: 3.674A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL A 217 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      Proline residue:  A 223  - end of helix
      removed outlier: 3.520A  pdb=" N   SER A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 248
      removed outlier: 3.684A  pdb=" N   LEU A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 260
      removed outlier: 3.614A  pdb=" N   ALA A 254 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 268
    Processing helix  chain 'A' and resid 269 through 323
      removed outlier: 3.672A  pdb=" N   GLU A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   GLU A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 348
      removed outlier: 3.562A  pdb=" N   VAL A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 371
      removed outlier: 4.128A  pdb=" N   ILE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLU A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   GLU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ILE A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 441
      removed outlier: 3.686A  pdb=" N   GLN A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.875A  pdb=" N   THR A 460 " --> pdb=" O   ASP A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 469
      removed outlier: 3.836A  pdb=" N   ILE A 469 " --> pdb=" O   PHE A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 490
    Processing helix  chain 'A' and resid 496 through 508
    Processing helix  chain 'A' and resid 510 through 516
    Processing helix  chain 'A' and resid 525 through 529
      removed outlier: 3.736A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 546
    Processing helix  chain 'A' and resid 562 through 576
      removed outlier: 3.525A  pdb=" N   GLU A 566 " --> pdb=" O   ASP A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 619
      removed outlier: 3.534A  pdb=" N   LYS A 619 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 700 through 705
      removed outlier: 3.721A  pdb=" N   LEU A 705 " --> pdb=" O   LYS A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 723
      removed outlier: 3.946A  pdb=" N   PHE A 711 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY A 723 " --> pdb=" O   ILE A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 739
    Processing helix  chain 'A' and resid 744 through 798
      removed outlier: 4.304A  pdb=" N   LEU A 760 " --> pdb=" O   SER A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 805
      removed outlier: 3.606A  pdb=" N   PHE A 804 " --> pdb=" O   ASP A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 820
    Processing helix  chain 'A' and resid 829 through 854
      removed outlier: 4.913A  pdb=" N   THR A 845 " --> pdb=" O   ALA A 841 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   GLY A 846 " --> pdb=" O   ASN A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 880
      Proline residue:  A 866  - end of helix
      removed outlier: 3.785A  pdb=" N   GLU A 875 " --> pdb=" O   ALA A 871 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER A 880 " --> pdb=" O   MET A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 894
      removed outlier: 3.918A  pdb=" N   LYS A 888 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 903
      removed outlier: 3.998A  pdb=" N   THR A 898 " --> pdb=" O   GLY A 894 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A 903 " --> pdb=" O   GLU A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 911
      removed outlier: 3.694A  pdb=" N   VAL A 907 " --> pdb=" O   ASN A 903 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   SER A 909 " --> pdb=" O   ARG A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 924
      removed outlier: 3.826A  pdb=" N   PHE A 916 " --> pdb=" O   GLN A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 924 through 966
      removed outlier: 3.563A  pdb=" N   ARG A 929 " --> pdb=" O   GLN A 925 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   GLY A 939 " --> pdb=" O   ALA A 935 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   TYR A 950 " --> pdb=" O   GLN A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 993
    Processing helix  chain 'A' and resid 998 through 1014
      removed outlier: 3.508A  pdb=" N   LYS A1014 " --> pdb=" O   MET A1010 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1084
    Processing helix  chain 'A' and resid 1105 through 1113
      removed outlier: 3.883A  pdb=" N   LEU A1109 " --> pdb=" O   ASN A1105 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ARG A1110 " --> pdb=" O   VAL A1106 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A1113 " --> pdb=" O   LEU A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1133
    Processing helix  chain 'A' and resid 1141 through 1152
    Processing helix  chain 'A' and resid 1154 through 1161
      removed outlier: 3.770A  pdb=" N   LEU A1161 " --> pdb=" O   PHE A1157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1174
      removed outlier: 3.896A  pdb=" N   GLY A1173 " --> pdb=" O   GLY A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1191
    Processing helix  chain 'A' and resid 1207 through 1222
      removed outlier: 3.945A  pdb=" N   LYS A1212 " --> pdb=" O   THR A1208 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A1213 " --> pdb=" O   GLU A1209 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ALA A1217 " --> pdb=" O   VAL A1213 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A1218 " --> pdb=" O   VAL A1214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1239
      removed outlier: 4.235A  pdb=" N   ASN A1239 " --> pdb=" O   SER A1235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1256 through 1263
    Processing helix  chain 'A' and resid 1265 through 1272
      removed outlier: 3.632A  pdb=" N   SER A1269 " --> pdb=" O   GLY A1265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 133
    Processing helix  chain 'B' and resid 191 through 195
      removed outlier: 3.704A  pdb=" N   ARG B 194 " --> pdb=" O   GLU B 191 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS B 195 " --> pdb=" O   TYR B 192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 191 through 195'
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'C' and resid 165 through 167
      No H-bonds generated for 'chain 'C' and resid 165 through 167'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 417
      removed outlier: 3.744A  pdb=" N   ARG A 395 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   MET A 450 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   VAL A 397 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   GLU A 448 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473
      removed outlier: 6.551A  pdb=" N   GLY A 471 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   ASP A 555 " --> pdb=" O   GLY A 471 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL A 473 " --> pdb=" O   ASP A 555 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   VAL A 423 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLY A 600 " --> pdb=" O   VAL A 607 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1060
      removed outlier: 5.226A  pdb=" N   LEU A1056 " --> pdb=" O   GLU A1039 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   VAL A1040 " --> pdb=" O   ALA A1091 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   ALA A1091 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1116
      removed outlier: 4.022A  pdb=" N   LEU A1198 " --> pdb=" O   GLY A1114 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A1116 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASP A1200 " --> pdb=" O   VAL A1116 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A1068 " --> pdb=" O   VAL A1229 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ALA A1067 " --> pdb=" O   VAL A1244 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   PHE A1246 " --> pdb=" O   ALA A1067 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   VAL A1069 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL A1245 " --> pdb=" O   LYS A1252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 23
    Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 53
      removed outlier: 5.166A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   LEU B  42 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 124
      removed outlier: 3.910A  pdb=" N   ASN B 143 " --> pdb=" O   THR B 120 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   TYR B 179 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161
      removed outlier: 4.520A  pdb=" N   TRP B 154 " --> pdb=" O   ARG B 161 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN B 151 " --> pdb=" O   THR B 203 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.794A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   PHE C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ILE C  34 " --> pdb=" O   PHE C  50 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU C  99 " --> pdb=" O   TYR C  33 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 129 through 133
      removed outlier: 4.127A  pdb=" N   GLY C 148 " --> pdb=" O   LEU C 133 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   CYS C 149 " --> pdb=" O   SER C 188 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 133
      removed outlier: 4.127A  pdb=" N   GLY C 148 " --> pdb=" O   LEU C 133 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   CYS C 149 " --> pdb=" O   SER C 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 163
      removed outlier: 3.654A  pdb=" N   THR C 160 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA C 207 " --> pdb=" O   THR C 160 " (cutoff:3.500A)

    715 hydrogen bonds defined for protein.
    2030 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2085
        1.30 -     1.44: 3518
        1.44 -     1.57: 7870
        1.57 -     1.70: 5
        1.70 -     1.83: 87
  Bond restraints: 13565
  Sorted by residual:
  bond pdb=" C7  NAG A1302 "
       pdb=" N2  NAG A1302 "
    ideal  model  delta    sigma   weight residual
    1.346  1.492 -0.146 2.00e-02 2.50e+03 5.33e+01
  bond pdb=" C7  NAG A1303 "
       pdb=" N2  NAG A1303 "
    ideal  model  delta    sigma   weight residual
    1.346  1.492 -0.146 2.00e-02 2.50e+03 5.31e+01
  bond pdb=" C7  NAG A1301 "
       pdb=" N2  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.346  1.482 -0.136 2.00e-02 2.50e+03 4.64e+01
  bond pdb=" C10 TA1 A1320 "
       pdb=" C18 TA1 A1320 "
    ideal  model  delta    sigma   weight residual
    1.611  1.490  0.121 2.00e-02 2.50e+03 3.66e+01
  bond pdb=" C1  NAG A1302 "
       pdb=" O5  NAG A1302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.521 -0.115 2.00e-02 2.50e+03 3.33e+01
  ... (remaining 13560 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.71: 18265
        4.71 -     9.42: 179
        9.42 -    14.13: 15
       14.13 -    18.84: 2
       18.84 -    23.55: 2
  Bond angle restraints: 18463
  Sorted by residual:
  angle pdb=" N   SER A  90 "
        pdb=" CA  SER A  90 "
        pdb=" C   SER A  90 "
      ideal   model   delta    sigma   weight residual
     111.28  121.42  -10.14 1.09e+00 8.42e-01 8.65e+01
  angle pdb=" N   GLU A  86 "
        pdb=" CA  GLU A  86 "
        pdb=" C   GLU A  86 "
      ideal   model   delta    sigma   weight residual
     111.28  120.68   -9.40 1.09e+00 8.42e-01 7.43e+01
  angle pdb=" O12 3PE A1322 "
        pdb=" P   3PE A1322 "
        pdb=" O14 3PE A1322 "
      ideal   model   delta    sigma   weight residual
     123.79  100.24   23.55 3.00e+00 1.11e-01 6.16e+01
  angle pdb=" O12 3PE A1321 "
        pdb=" P   3PE A1321 "
        pdb=" O14 3PE A1321 "
      ideal   model   delta    sigma   weight residual
     123.79  100.99   22.80 3.00e+00 1.11e-01 5.77e+01
  angle pdb=" C   SER B  94 "
        pdb=" N   GLN B  95 "
        pdb=" CA  GLN B  95 "
      ideal   model   delta    sigma   weight residual
     121.70  133.42  -11.72 1.80e+00 3.09e-01 4.24e+01
  ... (remaining 18458 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.31: 8611
       32.31 -    64.62: 317
       64.62 -    96.92: 26
       96.92 -   129.23: 3
      129.23 -   161.54: 1
  Dihedral angle restraints: 8958
    sinusoidal: 4273
      harmonic: 4685
  Sorted by residual:
  dihedral pdb=" CB  CYS B 220 "
           pdb=" SG  CYS B 220 "
           pdb=" SG  CYS C 137 "
           pdb=" CB  CYS C 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.43   87.43     1      1.00e+01 1.00e-02 9.17e+01
  dihedral pdb=" CA  LYS B  55 "
           pdb=" C   LYS B  55 "
           pdb=" N   VAL B  56 "
           pdb=" CA  VAL B  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.40  -43.60     0      5.00e+00 4.00e-02 7.61e+01
  dihedral pdb=" CA  PRO B 100 "
           pdb=" C   PRO B 100 "
           pdb=" N   PRO B 101 "
           pdb=" CA  PRO B 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.18   29.82     0      5.00e+00 4.00e-02 3.56e+01
  ... (remaining 8955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.329: 2121
       0.329 -    0.657: 26
       0.657 -    0.986: 1
       0.986 -    1.315: 2
       1.315 -    1.644: 2
  Chirality restraints: 2152
  Sorted by residual:
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A  91 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.76   -1.64 2.00e-01 2.50e+01 6.75e+01
  chirality pdb=" C1  NAG A1302 "
            pdb=" ND2 ASN A  94 "
            pdb=" C2  NAG A1302 "
            pdb=" O5  NAG A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.92   -1.48 2.00e-01 2.50e+01 5.45e+01
  chirality pdb=" C10 TA1 A1320 "
            pdb=" C02 TA1 A1320 "
            pdb=" C11 TA1 A1320 "
            pdb=" C18 TA1 A1320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    1.25    1.29 2.00e-01 2.50e+01 4.16e+01
  ... (remaining 2149 not shown)

  Planarity restraints: 2229
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C29 TA1 A1320 "    0.264 2.00e-02 2.50e+03   2.29e-01 6.57e+02
        pdb=" C30 TA1 A1320 "   -0.058 2.00e-02 2.50e+03
        pdb=" C31 TA1 A1320 "   -0.021 2.00e-02 2.50e+03
        pdb=" N01 TA1 A1320 "   -0.386 2.00e-02 2.50e+03
        pdb=" O14 TA1 A1320 "    0.202 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  94 "    0.017 2.00e-02 2.50e+03   1.04e-01 1.36e+02
        pdb=" CG  ASN A  94 "   -0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  94 "    0.077 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  94 "   -0.184 2.00e-02 2.50e+03
        pdb=" C1  NAG A1302 "    0.117 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  99 "   -0.037 2.00e-02 2.50e+03   6.22e-02 4.84e+01
        pdb=" CG  ASN A  99 "    0.016 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  99 "   -0.014 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  99 "    0.110 2.00e-02 2.50e+03
        pdb=" C1  NAG A1303 "   -0.074 2.00e-02 2.50e+03
  ... (remaining 2226 not shown)

  Histogram of nonbonded interaction distances:
        1.41 -     2.10: 3
        2.10 -     2.80: 3546
        2.80 -     3.50: 17424
        3.50 -     4.20: 29017
        4.20 -     4.90: 51313
  Nonbonded interactions: 101303
  Sorted by model distance:
  nonbonded pdb=" CD1 ILE A  92 "
            pdb=" CD  PRO B 100 "
     model   vdw
     1.406 3.860
  nonbonded pdb=" ND2 ASN A  84 "
            pdb=" O   THR A 740 "
     model   vdw
     1.623 3.120
  nonbonded pdb=" CD1 ILE A  92 "
            pdb=" CG  PRO B 100 "
     model   vdw
     1.999 3.860
  nonbonded pdb=" O   ILE A 700 "
            pdb=" CD1 ILE A 829 "
     model   vdw
     2.217 3.460
  nonbonded pdb=" OG1 THR A1203 "
            pdb=" OE1 GLU A1211 "
     model   vdw
     2.256 3.040
  ... (remaining 101298 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.47 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.090
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
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      :  0.010   0.468  13575  Z= 0.602
  Angle     :  1.358  41.778  18484  Z= 0.632
  Chirality :  0.103   1.644   2152
  Planarity :  0.008   0.229   2226
  Dihedral  : 16.115 161.541   5936
  Min Nonbonded Distance : 1.406

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.99 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  8.53 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.17), residues: 1620
  helix: -1.96 (0.14), residues: 774
  sheet: -1.77 (0.28), residues: 300
  loop : -2.64 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  98 
 TYR   0.029   0.003   TYR A 920 
 PHE   0.033   0.003   PHE C  50 
 TRP   0.075   0.003   TRP B 102 
 HIS   0.006   0.002   HIS B  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00937 (13565)
  covalent geometry    : angle       1.23560 (18463)
  SS BOND              : bond        0.00980 (    6)
  SS BOND              : angle       2.06412 (   12)
  hydrogen bonds       : bond        0.13940 (  703)
  hydrogen bonds       : angle       6.34489 ( 2030)
  Misc. bond           : bond        0.46850 (    1)
  link_NAG-ASN         : bond        0.14114 (    3)
  link_NAG-ASN         : angle      25.47653 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 175
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.4564 (OUTLIER) cc_final: 0.2434 (mtt90)
REVERT: A  155 ILE cc_start: 0.7631 (tt) cc_final: 0.7398 (tt)
REVERT: A  757 LEU cc_start: 0.8594 (tp) cc_final: 0.8373 (mt)
REVERT: B    4 MET cc_start: 0.8779 (mmm) cc_final: 0.8479 (mmm)
REVERT: B   99 ILE cc_start: 0.8898 (pt) cc_final: 0.8634 (pt)
REVERT: C  110 ASP cc_start: 0.8743 (p0) cc_final: 0.8516 (p0)
REVERT: C  131 TYR cc_start: 0.8500 (m-80) cc_final: 0.8209 (m-80)
REVERT: C  180 GLN cc_start: 0.7688 (pp30) cc_final: 0.7298 (pp30)
  outliers start: 10
  outliers final: 3
  residues processed: 184
  average time/residue: 0.1294
  time to fit residues: 34.1791
Evaluate side-chains
  121 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  148 ARG
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue 1242 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
A 387 ASN
A 438 GLN
A 508 ASN
** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 725 GLN
A 750 GLN
A 838 GLN
A 839 ASN
A1054 GLN
A1105 ASN
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 HIS
A1239 ASN
A1248 ASN
B 130 GLN
B 144 ASN
B 216 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.214449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.185500 restraints weight = 19957.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.185350 restraints weight = 38935.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.180476 restraints weight = 18861.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.180687 restraints weight = 21251.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.180981 restraints weight = 11992.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4186 r_free = 0.4186    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4186 r_free = 0.4186    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13575  Z= 0.152
  Angle     :  0.680  12.173  18484  Z= 0.340
  Chirality :  0.044   0.313   2152
  Planarity :  0.005   0.054   2226
  Dihedral  : 10.584 157.665   3041
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.14 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 11.95 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.19), residues: 1620
  helix: -0.15 (0.17), residues: 790
  sheet: -1.29 (0.29), residues: 297
  loop : -2.34 (0.23), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  95 
 TYR   0.017   0.002   TYR A 953 
 PHE   0.020   0.001   PHE B  92 
 TRP   0.021   0.001   TRP B 102 
 HIS   0.007   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (13565)
  covalent geometry    : angle       0.66766 (18463)
  SS BOND              : bond        0.00340 (    6)
  SS BOND              : angle       1.01223 (   12)
  hydrogen bonds       : bond        0.05448 (  703)
  hydrogen bonds       : angle       4.75996 ( 2030)
  Misc. bond           : bond        0.00012 (    1)
  link_NAG-ASN         : bond        0.00690 (    3)
  link_NAG-ASN         : angle       5.78594 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 MET cc_start: 0.4248 (mmm) cc_final: 0.3835 (mpp)
REVERT: A  953 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6811 (t80)
REVERT: A 1010 MET cc_start: 0.7047 (tmm) cc_final: 0.6716 (tmm)
REVERT: A 1193 GLN cc_start: 0.5953 (pp30) cc_final: 0.5143 (pm20)
REVERT: B   99 ILE cc_start: 0.8629 (pt) cc_final: 0.8423 (pt)
REVERT: C  183 LEU cc_start: 0.8487 (mp) cc_final: 0.8247 (mp)
  outliers start: 34
  outliers final: 10
  residues processed: 162
  average time/residue: 0.1145
  time to fit residues: 27.8536
Evaluate side-chains
  123 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  953 TYR
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 139 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 116 optimal weight:   30.0000
   chunk 94 optimal weight:   20.0000
   chunk 153 optimal weight:    0.0970
   chunk 102 optimal weight:    0.0870
   chunk 101 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
A 612 HIS
A 773 GLN
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 GLN
B 195 HIS
C  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.216692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.188903 restraints weight = 21013.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.188290 restraints weight = 41514.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.185129 restraints weight = 19616.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.185478 restraints weight = 21539.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.185468 restraints weight = 12942.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4259 r_free = 0.4259    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4259 r_free = 0.4259    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13575  Z= 0.123
  Angle     :  0.622   8.719  18484  Z= 0.311
  Chirality :  0.042   0.322   2152
  Planarity :  0.004   0.051   2226
  Dihedral  :  9.703 149.690   3034
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.80 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.20), residues: 1620
  helix:  0.68 (0.18), residues: 792
  sheet: -0.89 (0.30), residues: 297
  loop : -2.09 (0.24), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 798 
 TYR   0.016   0.001   TYR C 131 
 PHE   0.019   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A 232 
 HIS   0.003   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (13565)
  covalent geometry    : angle       0.60700 (18463)
  SS BOND              : bond        0.00258 (    6)
  SS BOND              : angle       2.95806 (   12)
  hydrogen bonds       : bond        0.04714 (  703)
  hydrogen bonds       : angle       4.38830 ( 2030)
  Misc. bond           : bond        0.00025 (    1)
  link_NAG-ASN         : bond        0.00615 (    3)
  link_NAG-ASN         : angle       5.12387 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.7511 (ttp) cc_final: 0.7236 (ttp)
REVERT: A  740 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8027 (m)
REVERT: A  948 MET cc_start: 0.7551 (tpp) cc_final: 0.7262 (tpp)
REVERT: A  953 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6617 (t80)
  outliers start: 33
  outliers final: 16
  residues processed: 144
  average time/residue: 0.1092
  time to fit residues: 23.6657
Evaluate side-chains
  123 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  953 TYR
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 133 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 61 optimal weight:    0.4980
   chunk 86 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   chunk 138 optimal weight:    5.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
A 537 GLN
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 GLN
B 130 GLN
C 102 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.210090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.184265 restraints weight = 25379.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.182092 restraints weight = 46175.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.178031 restraints weight = 22172.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.177768 restraints weight = 22579.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.178094 restraints weight = 12276.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4133 r_free = 0.4133    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4133 r_free = 0.4133    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  13575  Z= 0.199
  Angle     :  0.678   9.505  18484  Z= 0.342
  Chirality :  0.044   0.193   2152
  Planarity :  0.004   0.065   2226
  Dihedral  :  9.642 149.408   3034
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.40 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.20), residues: 1620
  helix:  0.79 (0.18), residues: 785
  sheet: -0.91 (0.30), residues: 304
  loop : -1.97 (0.24), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.017   0.002   TYR A 130 
 PHE   0.026   0.002   PHE B  92 
 TRP   0.026   0.002   TRP B 102 
 HIS   0.005   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (13565)
  covalent geometry    : angle       0.66669 (18463)
  SS BOND              : bond        0.00781 (    6)
  SS BOND              : angle       1.83858 (   12)
  hydrogen bonds       : bond        0.05381 (  703)
  hydrogen bonds       : angle       4.64465 ( 2030)
  Misc. bond           : bond        0.00026 (    1)
  link_NAG-ASN         : bond        0.00588 (    3)
  link_NAG-ASN         : angle       5.19747 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 105
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A   75 MET cc_start: 0.7793 (ttp) cc_final: 0.7446 (ttp)
REVERT: A   95 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.5313 (ptm160)
REVERT: A  724 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8168 (mp)
REVERT: A  948 MET cc_start: 0.7651 (tpp) cc_final: 0.7381 (tpp)
REVERT: A  953 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6657 (t80)
  outliers start: 47
  outliers final: 25
  residues processed: 146
  average time/residue: 0.1137
  time to fit residues: 24.7835
Evaluate side-chains
  125 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  797 LEU
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  953 TYR
Chi-restraints excluded: chain A residue  986 MET
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   chunk 116 optimal weight:    4.9990
   chunk 56 optimal weight:   50.0000
   chunk 63 optimal weight:    0.9980
   chunk 121 optimal weight:    0.6980
   chunk 101 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 518 HIS
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.212853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.182946 restraints weight = 17670.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.183202 restraints weight = 38577.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.179702 restraints weight = 19606.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.179274 restraints weight = 21433.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.179409 restraints weight = 15392.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13575  Z= 0.144
  Angle     :  0.629   9.152  18484  Z= 0.315
  Chirality :  0.042   0.204   2152
  Planarity :  0.004   0.055   2226
  Dihedral  :  9.326 144.674   3034
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.57 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.71 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.21), residues: 1620
  helix:  1.03 (0.18), residues: 786
  sheet: -0.74 (0.30), residues: 303
  loop : -1.87 (0.24), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.024   0.001   TYR C 131 
 PHE   0.024   0.001   PHE A 399 
 TRP   0.013   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (13565)
  covalent geometry    : angle       0.61951 (18463)
  SS BOND              : bond        0.00549 (    6)
  SS BOND              : angle       1.25331 (   12)
  hydrogen bonds       : bond        0.04857 (  703)
  hydrogen bonds       : angle       4.45371 ( 2030)
  Misc. bond           : bond        0.00041 (    1)
  link_NAG-ASN         : bond        0.00546 (    3)
  link_NAG-ASN         : angle       4.68960 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 110
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.7784 (ttp) cc_final: 0.7480 (ttp)
REVERT: A   95 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.5283 (ptm160)
REVERT: A  184 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6469 (mm-30)
REVERT: A  497 MET cc_start: 0.4106 (mmm) cc_final: 0.3765 (mpp)
REVERT: A  948 MET cc_start: 0.7647 (tpp) cc_final: 0.7380 (tpp)
REVERT: A  953 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6688 (t80)
REVERT: C   11 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7948 (tt)
  outliers start: 51
  outliers final: 36
  residues processed: 151
  average time/residue: 0.1069
  time to fit residues: 24.7059
Evaluate side-chains
  139 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 100
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  953 TYR
Chi-restraints excluded: chain A residue  986 MET
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain C residue  182 ASP
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 157 optimal weight:    0.0980
   chunk 82 optimal weight:    0.7980
   chunk 57 optimal weight:    0.2980
   chunk 1 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0970
   chunk 20 optimal weight:    6.9990
   chunk 117 optimal weight:    6.9990
   chunk 147 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 126 optimal weight:    0.4980
   chunk 159 optimal weight:    0.4980
   overall best weight:    0.2978

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

Flipped N/Q/H residues before XYZ refinement:
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.219482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.193473 restraints weight = 19118.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.191758 restraints weight = 39265.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.187562 restraints weight = 21171.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.188213 restraints weight = 22290.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.188197 restraints weight = 14610.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4250 r_free = 0.4250    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4250 r_free = 0.4250    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13575  Z= 0.113
  Angle     :  0.578   8.649  18484  Z= 0.290
  Chirality :  0.041   0.198   2152
  Planarity :  0.004   0.049   2226
  Dihedral  :  8.959 141.468   3034
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.90 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.21), residues: 1620
  helix:  1.42 (0.19), residues: 785
  sheet: -0.39 (0.32), residues: 292
  loop : -1.73 (0.24), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 161 
 TYR   0.018   0.001   TYR C 131 
 PHE   0.025   0.001   PHE A 399 
 TRP   0.012   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (13565)
  covalent geometry    : angle       0.57077 (18463)
  SS BOND              : bond        0.00377 (    6)
  SS BOND              : angle       1.04250 (   12)
  hydrogen bonds       : bond        0.04161 (  703)
  hydrogen bonds       : angle       4.11585 ( 2030)
  Misc. bond           : bond        0.00030 (    1)
  link_NAG-ASN         : bond        0.00766 (    3)
  link_NAG-ASN         : angle       4.10284 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.7478 (ttp) cc_final: 0.7266 (ttp)
REVERT: A   95 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.5511 (ptm160)
REVERT: A  443 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5849 (mp)
REVERT: A  884 LEU cc_start: 0.3542 (OUTLIER) cc_final: 0.3313 (tp)
REVERT: A  948 MET cc_start: 0.7617 (tpp) cc_final: 0.7270 (tpp)
REVERT: A  953 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6761 (t80)
REVERT: A 1010 MET cc_start: 0.6784 (tmm) cc_final: 0.6576 (tmm)
REVERT: B    5 THR cc_start: 0.8416 (m) cc_final: 0.8133 (p)
REVERT: C   11 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7874 (tt)
  outliers start: 39
  outliers final: 19
  residues processed: 145
  average time/residue: 0.1121
  time to fit residues: 24.4984
Evaluate side-chains
  124 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 TYR
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 136 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 153 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 108 optimal weight:    7.9990
   chunk 124 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.213838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.188764 restraints weight = 26626.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.187072 restraints weight = 45152.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.183742 restraints weight = 19263.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.184480 restraints weight = 14232.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.184662 restraints weight = 8999.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4208
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4208 r_free = 0.4208    target_work(ls_wunit_k1) = 0.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4208 r_free = 0.4208    target_work(ls_wunit_k1) = 0.179         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4208
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13575  Z= 0.142
  Angle     :  0.615   8.785  18484  Z= 0.308
  Chirality :  0.042   0.266   2152
  Planarity :  0.004   0.081   2226
  Dihedral  :  8.961 142.349   3034
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 19.75 %
    Favored  : 76.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.21), residues: 1620
  helix:  1.36 (0.19), residues: 787
  sheet: -0.47 (0.31), residues: 303
  loop : -1.61 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 467 
 TYR   0.016   0.001   TYR C 131 
 PHE   0.021   0.001   PHE A 399 
 TRP   0.016   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (13565)
  covalent geometry    : angle       0.60905 (18463)
  SS BOND              : bond        0.00599 (    6)
  SS BOND              : angle       0.97632 (   12)
  hydrogen bonds       : bond        0.04582 (  703)
  hydrogen bonds       : angle       4.26665 ( 2030)
  Misc. bond           : bond        0.00119 (    1)
  link_NAG-ASN         : bond        0.00679 (    3)
  link_NAG-ASN         : angle       3.74100 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 104
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.7584 (ttp) cc_final: 0.7374 (ttp)
REVERT: A   95 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.5613 (ptm160)
REVERT: A  884 LEU cc_start: 0.3622 (OUTLIER) cc_final: 0.3288 (tp)
REVERT: A  948 MET cc_start: 0.7660 (tpp) cc_final: 0.7306 (tpp)
REVERT: A  953 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6720 (t80)
REVERT: A 1010 MET cc_start: 0.6844 (tmm) cc_final: 0.6591 (tmm)
REVERT: C   11 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7943 (tt)
  outliers start: 46
  outliers final: 31
  residues processed: 142
  average time/residue: 0.1141
  time to fit residues: 24.5470
Evaluate side-chains
  136 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  953 TYR
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0040
   chunk 112 optimal weight:    0.9990
   chunk 130 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0470
   chunk 72 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 139 optimal weight:    3.9990
   overall best weight:    0.5092

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

Flipped N/Q/H residues before XYZ refinement:
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.216233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.191754 restraints weight = 27618.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.190734 restraints weight = 43839.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.187645 restraints weight = 19118.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.188552 restraints weight = 13041.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.188532 restraints weight = 8795.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4269 r_free = 0.4269    target_work(ls_wunit_k1) = 0.185         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4269 r_free = 0.4269    target_work(ls_wunit_k1) = 0.185         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13575  Z= 0.119
  Angle     :  0.601   8.991  18484  Z= 0.299
  Chirality :  0.041   0.258   2152
  Planarity :  0.004   0.047   2226
  Dihedral  :  8.757 140.158   3034
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.63 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.21), residues: 1620
  helix:  1.50 (0.19), residues: 787
  sheet: -0.30 (0.31), residues: 298
  loop : -1.51 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 467 
 TYR   0.016   0.001   TYR A 510 
 PHE   0.021   0.001   PHE A 994 
 TRP   0.010   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (13565)
  covalent geometry    : angle       0.59590 (18463)
  SS BOND              : bond        0.00438 (    6)
  SS BOND              : angle       0.81313 (   12)
  hydrogen bonds       : bond        0.04266 (  703)
  hydrogen bonds       : angle       4.17516 ( 2030)
  Misc. bond           : bond        0.00138 (    1)
  link_NAG-ASN         : bond        0.00663 (    3)
  link_NAG-ASN         : angle       3.59318 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 GLU cc_start: 0.5742 (tp30) cc_final: 0.5540 (pt0)
REVERT: A  497 MET cc_start: 0.3781 (mmm) cc_final: 0.3411 (mpp)
REVERT: A  884 LEU cc_start: 0.3605 (OUTLIER) cc_final: 0.3326 (tp)
REVERT: A  948 MET cc_start: 0.7672 (tpp) cc_final: 0.7321 (tpp)
REVERT: A 1010 MET cc_start: 0.6770 (tmm) cc_final: 0.6543 (tmm)
REVERT: C   11 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7931 (tt)
  outliers start: 37
  outliers final: 29
  residues processed: 136
  average time/residue: 0.1076
  time to fit residues: 22.3152
Evaluate side-chains
  133 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 155 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 113 optimal weight:   10.0000
   chunk 112 optimal weight:    0.5980
   chunk 142 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1232 HIS
B  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.209179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.181017 restraints weight = 26645.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.181426 restraints weight = 46354.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.180878 restraints weight = 17169.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.181710 restraints weight = 12692.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.181598 restraints weight = 8954.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4199 r_free = 0.4199    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4199 r_free = 0.4199    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13575  Z= 0.138
  Angle     :  0.628   9.857  18484  Z= 0.312
  Chirality :  0.042   0.225   2152
  Planarity :  0.004   0.049   2226
  Dihedral  :  8.631 140.064   3030
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.34 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.21), residues: 1620
  helix:  1.45 (0.19), residues: 788
  sheet: -0.38 (0.31), residues: 303
  loop : -1.44 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 217 
 TYR   0.021   0.001   TYR A 953 
 PHE   0.023   0.001   PHE A 994 
 TRP   0.013   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (13565)
  covalent geometry    : angle       0.62273 (18463)
  SS BOND              : bond        0.00566 (    6)
  SS BOND              : angle       0.95464 (   12)
  hydrogen bonds       : bond        0.04481 (  703)
  hydrogen bonds       : angle       4.25618 ( 2030)
  Misc. bond           : bond        0.00095 (    1)
  link_NAG-ASN         : bond        0.00597 (    3)
  link_NAG-ASN         : angle       3.46691 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 103
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 MET cc_start: 0.3795 (mmm) cc_final: 0.3477 (mpp)
REVERT: A  884 LEU cc_start: 0.3685 (OUTLIER) cc_final: 0.3363 (tp)
REVERT: A  948 MET cc_start: 0.7696 (tpp) cc_final: 0.7322 (tpp)
REVERT: A  974 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8564 (p)
REVERT: A 1010 MET cc_start: 0.6779 (tmm) cc_final: 0.6554 (tmm)
REVERT: C   11 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7939 (tt)
REVERT: C  182 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7117 (p0)
  outliers start: 46
  outliers final: 34
  residues processed: 138
  average time/residue: 0.1043
  time to fit residues: 22.5449
Evaluate side-chains
  139 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 101
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  974 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain C residue  182 ASP
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 134 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 160 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 145 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A1153 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.208554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.179941 restraints weight = 32666.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.180577 restraints weight = 51170.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.180138 restraints weight = 16119.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.181702 restraints weight = 10511.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.181247 restraints weight = 7719.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4175 r_free = 0.4175    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4175 r_free = 0.4175    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13575  Z= 0.139
  Angle     :  0.627   9.184  18484  Z= 0.312
  Chirality :  0.042   0.210   2152
  Planarity :  0.004   0.050   2226
  Dihedral  :  8.597 138.901   3030
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.77 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.21), residues: 1620
  helix:  1.46 (0.19), residues: 787
  sheet: -0.40 (0.31), residues: 303
  loop : -1.42 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 467 
 TYR   0.021   0.002   TYR A 953 
 PHE   0.024   0.001   PHE A 994 
 TRP   0.013   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (13565)
  covalent geometry    : angle       0.62249 (18463)
  SS BOND              : bond        0.00567 (    6)
  SS BOND              : angle       0.95823 (   12)
  hydrogen bonds       : bond        0.04532 (  703)
  hydrogen bonds       : angle       4.28357 ( 2030)
  Misc. bond           : bond        0.00099 (    1)
  link_NAG-ASN         : bond        0.00558 (    3)
  link_NAG-ASN         : angle       3.36731 (    9)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 100
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 MET cc_start: 0.3830 (mmm) cc_final: 0.3528 (mpp)
REVERT: A  878 MET cc_start: 0.7227 (ppp) cc_final: 0.6859 (ppp)
REVERT: A  884 LEU cc_start: 0.3728 (OUTLIER) cc_final: 0.3421 (tp)
REVERT: A  948 MET cc_start: 0.7787 (tpp) cc_final: 0.7370 (tpp)
REVERT: A 1129 GLU cc_start: 0.4498 (OUTLIER) cc_final: 0.3453 (mt-10)
REVERT: A 1192 ARG cc_start: 0.5768 (mmm160) cc_final: 0.5513 (mmm160)
REVERT: B    9 LEU cc_start: 0.7838 (mm) cc_final: 0.7610 (mm)
REVERT: C   11 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8032 (tt)
REVERT: C  182 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7118 (p0)
  outliers start: 41
  outliers final: 35
  residues processed: 132
  average time/residue: 0.0971
  time to fit residues: 20.2609
Evaluate side-chains
  136 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 97
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLU
Chi-restraints excluded: chain A residue   94 ASN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  303 PHE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1129 GLU
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  168 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  133 LEU
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  178 VAL
Chi-restraints excluded: chain C residue  182 ASP
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 147 optimal weight:    1.9990
   chunk 137 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 150 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A1153 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.207272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.175737 restraints weight = 21478.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.177527 restraints weight = 42581.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.176089 restraints weight = 17952.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.176780 restraints weight = 14724.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.176899 restraints weight = 10801.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13575  Z= 0.151
  Angle     :  0.638   9.424  18484  Z= 0.320
  Chirality :  0.042   0.201   2152
  Planarity :  0.004   0.070   2226
  Dihedral  :  8.612 138.420   3030
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.77 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.21), residues: 1620
  helix:  1.40 (0.19), residues: 786
  sheet: -0.44 (0.31), residues: 303
  loop : -1.41 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.000   ARG A 467 
 TYR   0.022   0.002   TYR A 953 
 PHE   0.025   0.002   PHE A 994 
 TRP   0.014   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (13565)
  covalent geometry    : angle       0.63398 (18463)
  SS BOND              : bond        0.00594 (    6)
  SS BOND              : angle       1.02918 (   12)
  hydrogen bonds       : bond        0.04655 (  703)
  hydrogen bonds       : angle       4.33340 ( 2030)
  Misc. bond           : bond        0.00139 (    1)
  link_NAG-ASN         : bond        0.00539 (    3)
  link_NAG-ASN         : angle       3.27544 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2161.87 seconds
wall clock time: 38 minutes 18.39 seconds (2298.39 seconds total)