Starting phenix.real_space_refine
on Wed Mar  4 15:07:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qex_4539/03_2026/6qex_4539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qex_4539/03_2026/6qex_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qex_4539/03_2026/6qex_4539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qex_4539/03_2026/6qex_4539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qex_4539/03_2026/6qex_4539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qex_4539/03_2026/6qex_4539.cif"
  }
  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-dev-5986/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: 3.50, per 1000 atoms: 0.26
  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: 1.43
  Conformation dependent library (CDL) restraints added in 578.4 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: 0.62
  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: 2.74

  Time building geometry restraints manager: 1.82 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:             5.150
  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:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.080
  Find NCS groups from input model:        0.070
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.180
-------------------------------------------------------------------------------
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  : 0.480 
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: 0.7632 (tt) cc_final: 0.7398 (tt)
REVERT: A  757 LEU cc_start: 0.8594 (tp) cc_final: 0.8372 (mt)
REVERT: A  862 LEU cc_start: 0.9164 (mt) cc_final: 0.8964 (mm)
REVERT: B    4 MET cc_start: 0.8779 (mmm) cc_final: 0.8480 (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: 34.2461
Evaluate side-chains
  122 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 118
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
A 438 GLN
A 508 ASN
** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 725 GLN
A 750 GLN
A 773 GLN
A 838 GLN
A 839 ASN
A1054 GLN
A1105 ASN
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 HIS
** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4498 r_free = 0.4498 target = 0.209179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.176316 restraints weight = 20170.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.178348 restraints weight = 41090.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.177327 restraints weight = 17585.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.177856 restraints weight = 14531.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.177986 restraints weight = 10924.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4177 r_free = 0.4177    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 = 0.4177 r_free = 0.4177    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13575  Z= 0.152
  Angle     :  0.677  10.309  18484  Z= 0.339
  Chirality :  0.044   0.310   2152
  Planarity :  0.005   0.055   2226
  Dihedral  : 10.515 157.486   3041
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.14 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.61 %
    Favored  : 84.91 %
  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: -1.64 (0.19), residues: 1620
  helix: -0.11 (0.18), residues: 790
  sheet: -1.27 (0.29), residues: 297
  loop : -2.34 (0.23), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  95 
 TYR   0.018   0.002   TYR A 953 
 PHE   0.020   0.001   PHE B  92 
 TRP   0.020   0.001   TRP B 102 
 HIS   0.007   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (13565)
  covalent geometry    : angle       0.66716 (18463)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       1.00112 (   12)
  hydrogen bonds       : bond        0.05356 (  703)
  hydrogen bonds       : angle       4.72945 ( 2030)
  Misc. bond           : bond        0.00029 (    1)
  link_NAG-ASN         : bond        0.00812 (    3)
  link_NAG-ASN         : angle       5.10965 (    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
  173 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 MET cc_start: 0.4234 (mmm) cc_final: 0.3879 (mpp)
REVERT: A  850 SER cc_start: 0.8252 (t) cc_final: 0.8039 (t)
REVERT: A  953 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6786 (t80)
REVERT: A 1193 GLN cc_start: 0.5859 (pp30) cc_final: 0.5478 (pt0)
REVERT: B   99 ILE cc_start: 0.8629 (pt) cc_final: 0.8415 (pt)
REVERT: C  183 LEU cc_start: 0.8496 (mp) cc_final: 0.8247 (mp)
  outliers start: 34
  outliers final: 11
  residues processed: 164
  average time/residue: 0.1157
  time to fit residues: 28.3612
Evaluate side-chains
  122 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
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  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 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:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 121 optimal weight:    0.2980
   chunk 53 optimal weight:    2.9990
   chunk 116 optimal weight:   30.0000
   chunk 94 optimal weight:    9.9990
   chunk 153 optimal weight:    0.8980
   chunk 102 optimal weight:    0.0570
   chunk 101 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
A 612 HIS
** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 HIS
C  62 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.211188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.178442 restraints weight = 21046.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.179897 restraints weight = 41209.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.177176 restraints weight = 17566.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.177064 restraints weight = 18868.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.177566 restraints weight = 10667.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4164 r_free = 0.4164    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4164 r_free = 0.4164    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13575  Z= 0.128
  Angle     :  0.628   8.754  18484  Z= 0.313
  Chirality :  0.042   0.233   2152
  Planarity :  0.004   0.049   2226
  Dihedral  :  9.747 150.047   3034
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.31 %
    Favored  : 82.00 %
  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: -0.76 (0.20), residues: 1620
  helix:  0.71 (0.18), residues: 786
  sheet: -0.88 (0.30), residues: 297
  loop : -2.06 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  24 
 TYR   0.019   0.001   TYR C 131 
 PHE   0.019   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A 232 
 HIS   0.005   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13565)
  covalent geometry    : angle       0.61444 (18463)
  SS BOND              : bond        0.00672 (    6)
  SS BOND              : angle       2.62509 (   12)
  hydrogen bonds       : bond        0.04803 (  703)
  hydrogen bonds       : angle       4.42305 ( 2030)
  Misc. bond           : bond        0.00019 (    1)
  link_NAG-ASN         : bond        0.00496 (    3)
  link_NAG-ASN         : angle       5.08872 (    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
  154 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8040 (m)
REVERT: A  850 SER cc_start: 0.8237 (t) cc_final: 0.8027 (t)
REVERT: A  948 MET cc_start: 0.7560 (tpp) cc_final: 0.7238 (tpp)
REVERT: A  953 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6632 (t80)
REVERT: B   99 ILE cc_start: 0.8533 (pt) cc_final: 0.8328 (pt)
  outliers start: 35
  outliers final: 21
  residues processed: 147
  average time/residue: 0.1085
  time to fit residues: 23.9926
Evaluate side-chains
  129 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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  133 VAL
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  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  168 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  117 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 133 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 93 optimal weight:    7.9990
   chunk 138 optimal weight:    0.0770
   overall best weight:    0.8142

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

Flipped N/Q/H residues before XYZ refinement:
A 537 GLN
** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.214289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.189129 restraints weight = 25270.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.186382 restraints weight = 45250.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.182694 restraints weight = 22404.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.182779 restraints weight = 22962.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.182948 restraints weight = 13288.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4193 r_free = 0.4193    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4193 r_free = 0.4193    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.2641

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= 0.140
  Angle     :  0.620   8.710  18484  Z= 0.310
  Chirality :  0.042   0.189   2152
  Planarity :  0.004   0.057   2226
  Dihedral  :  9.394 147.880   3034
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.84 %
    Favored  : 80.10 %
  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: -0.43 (0.21), residues: 1620
  helix:  1.00 (0.18), residues: 786
  sheet: -0.78 (0.30), residues: 302
  loop : -1.91 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.025   0.002   TYR C 131 
 PHE   0.021   0.001   PHE A 399 
 TRP   0.019   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       0.60853 (18463)
  SS BOND              : bond        0.00551 (    6)
  SS BOND              : angle       1.84357 (   12)
  hydrogen bonds       : bond        0.04795 (  703)
  hydrogen bonds       : angle       4.39661 ( 2030)
  Misc. bond           : bond        0.00014 (    1)
  link_NAG-ASN         : bond        0.00517 (    3)
  link_NAG-ASN         : angle       4.98759 (    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
  151 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 111
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.5533 (OUTLIER) cc_final: 0.5304 (ptm160)
REVERT: A  724 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8020 (mp)
REVERT: A  850 SER cc_start: 0.8220 (t) cc_final: 0.8003 (t)
REVERT: A  948 MET cc_start: 0.7609 (tpp) cc_final: 0.7298 (tpp)
REVERT: A  953 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6650 (t80)
  outliers start: 40
  outliers final: 26
  residues processed: 142
  average time/residue: 0.1059
  time to fit residues: 22.9502
Evaluate side-chains
  135 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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  121 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  204 PHE
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  413 LEU
Chi-restraints excluded: chain A residue  724 LEU
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  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   11 LEU
Chi-restraints excluded: chain C residue  103 PHE
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  189 SER
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:    0.8980
   chunk 98 optimal weight:    9.9990
   chunk 116 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9980
   chunk 121 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 65 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 518 HIS
** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4544 r_free = 0.4544 target = 0.213647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.185047 restraints weight = 17792.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.182552 restraints weight = 37722.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.178354 restraints weight = 22999.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.178593 restraints weight = 21990.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.178836 restraints weight = 14019.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4160 r_free = 0.4160    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4160 r_free = 0.4160    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.2902

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= 0.146
  Angle     :  0.628   8.903  18484  Z= 0.313
  Chirality :  0.042   0.200   2152
  Planarity :  0.004   0.055   2226
  Dihedral  :  9.231 144.449   3034
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.57 %
    Favored  : 78.57 %
  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: -0.24 (0.21), residues: 1620
  helix:  1.14 (0.18), residues: 786
  sheet: -0.67 (0.31), residues: 302
  loop : -1.79 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 217 
 TYR   0.015   0.002   TYR A 953 
 PHE   0.024   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        0.00321 (13565)
  covalent geometry    : angle       0.61891 (18463)
  SS BOND              : bond        0.00573 (    6)
  SS BOND              : angle       1.43838 (   12)
  hydrogen bonds       : bond        0.04763 (  703)
  hydrogen bonds       : angle       4.37611 ( 2030)
  Misc. bond           : bond        0.00027 (    1)
  link_NAG-ASN         : bond        0.00599 (    3)
  link_NAG-ASN         : angle       4.49380 (    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  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5205 (ptm160)
REVERT: A  184 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6415 (mm-30)
REVERT: A  497 MET cc_start: 0.4139 (mmm) cc_final: 0.3821 (mpp)
REVERT: A  724 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: A  850 SER cc_start: 0.8162 (t) cc_final: 0.7939 (t)
REVERT: A  948 MET cc_start: 0.7643 (tpp) cc_final: 0.7337 (tpp)
REVERT: A  953 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6728 (t80)
REVERT: A 1061 LYS cc_start: 0.5983 (tptp) cc_final: 0.5264 (ttpp)
  outliers start: 51
  outliers final: 34
  residues processed: 150
  average time/residue: 0.1099
  time to fit residues: 24.7635
Evaluate side-chains
  136 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
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  133 VAL
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  204 PHE
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  413 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  825 VAL
Chi-restraints excluded: chain A residue  864 ILE
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   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  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:    0.4980
   chunk 82 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 107 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 117 optimal weight:    8.9990
   chunk 147 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 126 optimal weight:    0.2980
   chunk 159 optimal weight:    0.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A1130 ASN
** 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 = 0.4506 r_free = 0.4506 target = 0.210064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.175554 restraints weight = 19176.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.177622 restraints weight = 39298.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.177222 restraints weight = 17049.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.177393 restraints weight = 14764.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.177591 restraints weight = 12605.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4169 r_free = 0.4169    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4169 r_free = 0.4169    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.3055

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= 0.131
  Angle     :  0.612   9.327  18484  Z= 0.306
  Chirality :  0.042   0.262   2152
  Planarity :  0.004   0.054   2226
  Dihedral  :  9.102 142.476   3034
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.39 %
    Favored  : 77.26 %
  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: -0.06 (0.21), residues: 1620
  helix:  1.26 (0.18), residues: 786
  sheet: -0.45 (0.31), residues: 295
  loop : -1.73 (0.25), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 161 
 TYR   0.014   0.001   TYR A 953 
 PHE   0.025   0.001   PHE A 399 
 TRP   0.014   0.001   TRP B 102 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (13565)
  covalent geometry    : angle       0.60454 (18463)
  SS BOND              : bond        0.00479 (    6)
  SS BOND              : angle       1.33860 (   12)
  hydrogen bonds       : bond        0.04606 (  703)
  hydrogen bonds       : angle       4.29684 ( 2030)
  Misc. bond           : bond        0.00056 (    1)
  link_NAG-ASN         : bond        0.00719 (    3)
  link_NAG-ASN         : angle       4.10297 (    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: 44
    poor density    : 110
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.5419 (ptm160)
REVERT: A  184 GLU cc_start: 0.6636 (mm-30) cc_final: 0.6410 (mm-30)
REVERT: A  497 MET cc_start: 0.4070 (mmm) cc_final: 0.3835 (mpp)
REVERT: A  850 SER cc_start: 0.8259 (t) cc_final: 0.8023 (t)
REVERT: A  948 MET cc_start: 0.7656 (tpp) cc_final: 0.7322 (tpp)
REVERT: A  953 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6684 (t80)
REVERT: A 1061 LYS cc_start: 0.5962 (tptp) cc_final: 0.5295 (ttpp)
  outliers start: 44
  outliers final: 33
  residues processed: 145
  average time/residue: 0.1055
  time to fit residues: 23.5391
Evaluate side-chains
  140 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 105
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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  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  345 VAL
Chi-restraints excluded: chain A residue  413 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  986 MET
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 153 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 124 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 824 GLN
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  95 GLN
C 102 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.209175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.182481 restraints weight = 26628.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.181099 restraints weight = 50236.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.177684 restraints weight = 20766.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.178535 restraints weight = 14405.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.178728 restraints weight = 9082.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4142 r_free = 0.4142    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4142 r_free = 0.4142    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  13575  Z= 0.205
  Angle     :  0.693  10.200  18484  Z= 0.348
  Chirality :  0.045   0.263   2152
  Planarity :  0.004   0.065   2226
  Dihedral  :  9.279 142.570   3034
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.19 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 19.97 %
    Favored  : 75.73 %
  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: -0.27 (0.21), residues: 1620
  helix:  1.03 (0.18), residues: 786
  sheet: -0.56 (0.31), residues: 302
  loop : -1.73 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 217 
 TYR   0.018   0.002   TYR A 277 
 PHE   0.028   0.002   PHE A 399 
 TRP   0.022   0.002   TRP B 102 
 HIS   0.006   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (13565)
  covalent geometry    : angle       0.68703 (18463)
  SS BOND              : bond        0.00711 (    6)
  SS BOND              : angle       1.29243 (   12)
  hydrogen bonds       : bond        0.05425 (  703)
  hydrogen bonds       : angle       4.61477 ( 2030)
  Misc. bond           : bond        0.00033 (    1)
  link_NAG-ASN         : bond        0.00799 (    3)
  link_NAG-ASN         : angle       4.05355 (    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
  163 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 106
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: A  497 MET cc_start: 0.3903 (mmm) cc_final: 0.3499 (mpp)
REVERT: A  724 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8082 (mp)
REVERT: A  850 SER cc_start: 0.8366 (t) cc_final: 0.8122 (t)
REVERT: A  948 MET cc_start: 0.7732 (tpp) cc_final: 0.7447 (tpp)
REVERT: A  953 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6657 (t80)
REVERT: B  142 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8521 (pp)
REVERT: C  182 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7153 (p0)
  outliers start: 57
  outliers final: 36
  residues processed: 154
  average time/residue: 0.0990
  time to fit residues: 23.7840
Evaluate side-chains
  138 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 98
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
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  125 VAL
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  337 SER
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  413 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  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 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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 824 GLN
** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.212278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.186771 restraints weight = 27650.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.184961 restraints weight = 48564.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.181528 restraints weight = 20629.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.182315 restraints weight = 14565.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.182510 restraints weight = 9151.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4181 r_free = 0.4181    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4181 r_free = 0.4181    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13575  Z= 0.146
  Angle     :  0.647   9.306  18484  Z= 0.322
  Chirality :  0.043   0.242   2152
  Planarity :  0.004   0.059   2226
  Dihedral  :  9.028 140.204   3034
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.77 %
    Favored  : 75.44 %
  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: -0.10 (0.21), residues: 1620
  helix:  1.19 (0.18), residues: 786
  sheet: -0.49 (0.31), residues: 302
  loop : -1.68 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 217 
 TYR   0.022   0.002   TYR A 510 
 PHE   0.028   0.001   PHE A 399 
 TRP   0.014   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (13565)
  covalent geometry    : angle       0.64125 (18463)
  SS BOND              : bond        0.00533 (    6)
  SS BOND              : angle       1.09967 (   12)
  hydrogen bonds       : bond        0.04920 (  703)
  hydrogen bonds       : angle       4.44163 ( 2030)
  Misc. bond           : bond        0.00064 (    1)
  link_NAG-ASN         : bond        0.00718 (    3)
  link_NAG-ASN         : angle       3.83651 (    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
  154 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 104
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.7384 (mmm) cc_final: 0.6916 (mmm)
REVERT: A  497 MET cc_start: 0.4011 (mmm) cc_final: 0.3748 (mpp)
REVERT: A  850 SER cc_start: 0.8303 (t) cc_final: 0.8052 (t)
REVERT: A  948 MET cc_start: 0.7711 (tpp) cc_final: 0.7426 (tpp)
REVERT: A  953 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6675 (t80)
REVERT: C   11 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7952 (tt)
REVERT: C  182 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7298 (p0)
  outliers start: 50
  outliers final: 41
  residues processed: 143
  average time/residue: 0.0991
  time to fit residues: 21.5846
Evaluate side-chains
  146 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 102
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
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  121 ILE
Chi-restraints excluded: chain A residue  125 VAL
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  337 SER
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  810 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 1060 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    4 MET
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 155 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 142 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.212392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.187066 restraints weight = 26417.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.185163 restraints weight = 46037.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.181816 restraints weight = 19698.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.182530 restraints weight = 14468.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.182670 restraints weight = 9029.171|
|-----------------------------------------------------------------------------|
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) = 0.177         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4186 r_free = 0.4186    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13575  Z= 0.147
  Angle     :  0.642   9.968  18484  Z= 0.319
  Chirality :  0.043   0.285   2152
  Planarity :  0.004   0.059   2226
  Dihedral  :  8.923 139.938   3034
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.70 %
    Favored  : 75.51 %
  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: -0.01 (0.21), residues: 1620
  helix:  1.25 (0.18), residues: 789
  sheet: -0.48 (0.31), residues: 302
  loop : -1.61 (0.25), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 467 
 TYR   0.015   0.002   TYR A 953 
 PHE   0.029   0.001   PHE A 399 
 TRP   0.014   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (13565)
  covalent geometry    : angle       0.63620 (18463)
  SS BOND              : bond        0.00549 (    6)
  SS BOND              : angle       1.20087 (   12)
  hydrogen bonds       : bond        0.04810 (  703)
  hydrogen bonds       : angle       4.40244 ( 2030)
  Misc. bond           : bond        0.00051 (    1)
  link_NAG-ASN         : bond        0.00686 (    3)
  link_NAG-ASN         : angle       3.61179 (    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
  151 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 101
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5433 (ptm160)
REVERT: A  850 SER cc_start: 0.8292 (t) cc_final: 0.8050 (t)
REVERT: A  948 MET cc_start: 0.7738 (tpp) cc_final: 0.7421 (tpp)
REVERT: A  953 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6704 (t80)
REVERT: A 1010 MET cc_start: 0.6829 (tmm) cc_final: 0.6592 (tmm)
REVERT: C   11 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7968 (tt)
REVERT: C  182 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7293 (p0)
  outliers start: 50
  outliers final: 42
  residues processed: 141
  average time/residue: 0.1033
  time to fit residues: 22.6156
Evaluate side-chains
  144 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 98
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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  121 ILE
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  297 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  345 VAL
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  810 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 1008 ILE
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1060 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    4 MET
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 134 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 160 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 145 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4536 r_free = 0.4536 target = 0.213091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.187647 restraints weight = 32270.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.188168 restraints weight = 52541.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.188999 restraints weight = 16134.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.189119 restraints weight = 10639.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.189553 restraints weight = 6460.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4279 r_free = 0.4279    target_work(ls_wunit_k1) = 0.186         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4279 r_free = 0.4279    target_work(ls_wunit_k1) = 0.186         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.3581

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= 0.138
  Angle     :  0.640   9.913  18484  Z= 0.318
  Chirality :  0.042   0.246   2152
  Planarity :  0.004   0.057   2226
  Dihedral  :  8.822 139.254   3034
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 21.14 %
    Favored  : 75.07 %
  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:  0.10 (0.21), residues: 1620
  helix:  1.34 (0.19), residues: 787
  sheet: -0.42 (0.31), residues: 301
  loop : -1.55 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 467 
 TYR   0.015   0.001   TYR A 953 
 PHE   0.029   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        0.00301 (13565)
  covalent geometry    : angle       0.63451 (18463)
  SS BOND              : bond        0.00514 (    6)
  SS BOND              : angle       1.10978 (   12)
  hydrogen bonds       : bond        0.04683 (  703)
  hydrogen bonds       : angle       4.38177 ( 2030)
  Misc. bond           : bond        0.00055 (    1)
  link_NAG-ASN         : bond        0.00659 (    3)
  link_NAG-ASN         : angle       3.57259 (    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
  148 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 98
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5641 (ptm160)
REVERT: A  850 SER cc_start: 0.8319 (t) cc_final: 0.8079 (t)
REVERT: A  948 MET cc_start: 0.7706 (tpp) cc_final: 0.7371 (tpp)
REVERT: A  953 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6639 (t80)
REVERT: A 1010 MET cc_start: 0.6712 (tmm) cc_final: 0.6497 (tmm)
REVERT: C   11 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7998 (tt)
REVERT: C  182 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7219 (p0)
  outliers start: 50
  outliers final: 43
  residues processed: 138
  average time/residue: 0.0968
  time to fit residues: 20.9592
Evaluate side-chains
  143 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 96
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
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  121 ILE
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  297 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  345 VAL
Chi-restraints excluded: chain A residue  413 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  810 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 1008 ILE
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1060 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    4 MET
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 147 optimal weight:    0.8980
   chunk 137 optimal weight:    4.9990
   chunk 128 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 150 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 120 optimal weight:    1.9990
   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 = 0.4549 r_free = 0.4549 target = 0.214632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.190987 restraints weight = 21502.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.189077 restraints weight = 42372.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.186449 restraints weight = 24205.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.186704 restraints weight = 23899.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.186501 restraints weight = 15188.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4249 r_free = 0.4249    target_work(ls_wunit_k1) = 0.182         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4249 r_free = 0.4249    target_work(ls_wunit_k1) = 0.182         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13575  Z= 0.143
  Angle     :  0.652   9.965  18484  Z= 0.326
  Chirality :  0.042   0.240   2152
  Planarity :  0.004   0.065   2226
  Dihedral  :  8.749 138.971   3034
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 21.28 %
    Favored  : 75.00 %
  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:  0.13 (0.21), residues: 1620
  helix:  1.36 (0.19), residues: 787
  sheet: -0.41 (0.31), residues: 301
  loop : -1.52 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 467 
 TYR   0.014   0.002   TYR A 953 
 PHE   0.029   0.001   PHE A 399 
 TRP   0.014   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (13565)
  covalent geometry    : angle       0.64713 (18463)
  SS BOND              : bond        0.00530 (    6)
  SS BOND              : angle       1.16381 (   12)
  hydrogen bonds       : bond        0.04701 (  703)
  hydrogen bonds       : angle       4.37483 ( 2030)
  Misc. bond           : bond        0.00052 (    1)
  link_NAG-ASN         : bond        0.00617 (    3)
  link_NAG-ASN         : angle       3.41546 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2148.36 seconds
wall clock time: 38 minutes 3.11 seconds (2283.11 seconds total)