Starting phenix.real_space_refine
on Thu Jul 31 00:43:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6fn1_4281/07_2025/6fn1_4281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6fn1_4281/07_2025/6fn1_4281.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6fn1_4281/07_2025/6fn1_4281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6fn1_4281/07_2025/6fn1_4281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6fn1_4281/07_2025/6fn1_4281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6fn1_4281/07_2025/6fn1_4281.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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 16 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
     S      50      5.16       5
     C    8174      2.51       5
     N    2128      2.21       5
     O    2383      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12739
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1182, 9186
          Classifications: {'peptide': 1182}
          Link IDs: {'CIS': 4, 'PTRANS': 27, 'TRANS': 1150}
          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: 1720
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 225, 1717
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211}
      Conformer: "B"
        Number of residues, atoms: 225, 1717
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211}
          bond proxies already assigned to first conformer: 1763
    Chain: "A"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 120
          Unusual residues: {'NAG': 3, 'ZQU': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 9.56, per 1000 atoms: 0.75
  Number of scatterers: 12739
  At special positions: 0
  Unit cell: (96.6, 93.24, 206.64, 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      50     16.00
     F       4      9.00
     O    2383      8.00
     N    2128      7.00
     C    8174      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 558 " - pdb=" SG  CYS A1203 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  93 " distance=2.05
    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=2.04
    Simple disulfide: pdb=" SG  CYS C 149 " - pdb=" SG ACYS C 204 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 149 " - pdb=" SG BCYS 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=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A  93 "
      " NAG A1303 " - " ASN A  98 "
  Time building additional restraints: 2.84
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3002

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 14 sheets defined
      50.2% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 43 through 62
      removed outlier: 3.847A  pdb=" N   ARG A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A  48 " --> pdb=" O   TRP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 88
      removed outlier: 3.839A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   MET A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 109
      removed outlier: 4.359A  pdb=" N   LEU A 106 " --> pdb=" O   PHE A 102 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLU A 108 " --> pdb=" O   MET A 104 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP A 109 " --> pdb=" O   ASN A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 156
      removed outlier: 3.655A  pdb=" N   TYR A 113 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TYR A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ILE A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 165
      removed outlier: 3.651A  pdb=" N   ASP A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 186
      removed outlier: 4.168A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY A 186 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 210
      removed outlier: 4.134A  pdb=" N   PHE A 193 " --> pdb=" O   ILE A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 237
      removed outlier: 3.622A  pdb=" N   THR A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ILE A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
      Proline residue:  A 222  - end of helix
      removed outlier: 4.030A  pdb=" N   SER A 237 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 259
    Processing helix  chain 'A' and resid 259 through 264
    Processing helix  chain 'A' and resid 268 through 321
      removed outlier: 4.096A  pdb=" N   GLU A 282 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA A 283 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ALA A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ALA A 310 " --> pdb=" O   TYR A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 347
      removed outlier: 3.845A  pdb=" N   GLY A 345 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 370
      removed outlier: 4.165A  pdb=" N   ILE A 351 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLU A 352 " --> pdb=" O   SER A 348 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   GLU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ASN A 370 " --> pdb=" O   LYS A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 440
      removed outlier: 3.962A  pdb=" N   THR A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   VAL A 436 " --> pdb=" O   LYS A 432 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLN A 440 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 460
      No H-bonds generated for 'chain 'A' and resid 458 through 460'
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 482 through 491
    Processing helix  chain 'A' and resid 495 through 506
    Processing helix  chain 'A' and resid 508 through 514
      removed outlier: 3.603A  pdb=" N   LYS A 514 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 546
    Processing helix  chain 'A' and resid 563 through 576
      removed outlier: 4.246A  pdb=" N   VAL A 567 " --> pdb=" O   GLU A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 618
      removed outlier: 3.827A  pdb=" N   LYS A 618 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 629
    Processing helix  chain 'A' and resid 695 through 703
      removed outlier: 3.776A  pdb=" N   ILE A 699 " --> pdb=" O   SER A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 738
      removed outlier: 3.623A  pdb=" N   PHE A 710 " --> pdb=" O   GLU A 706 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE A 719 " --> pdb=" O   PHE A 715 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN A 724 " --> pdb=" O   ASN A 720 " (cutoff:3.500A)
      Proline residue:  A 725  - end of helix
      removed outlier: 3.649A  pdb=" N   SER A 728 " --> pdb=" O   GLN A 724 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 798
      removed outlier: 3.756A  pdb=" N   THR A 768 " --> pdb=" O   ILE A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 799 through 804
      removed outlier: 3.721A  pdb=" N   PHE A 803 " --> pdb=" O   ASP A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 820
    Processing helix  chain 'A' and resid 824 through 853
      removed outlier: 3.818A  pdb=" N   THR A 828 " --> pdb=" O   VAL A 824 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   SER A 830 " --> pdb=" O   GLY A 826 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   ARG A 831 " --> pdb=" O   ALA A 827 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU A 832 " --> pdb=" O   THR A 828 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ALA A 833 " --> pdb=" O   GLY A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 879
      removed outlier: 3.588A  pdb=" N   THR A 857 " --> pdb=" O   GLY A 853 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 863 " --> pdb=" O   LEU A 859 " (cutoff:3.500A)
      Proline residue:  A 865  - end of helix
      removed outlier: 3.741A  pdb=" N   ALA A 868 " --> pdb=" O   VAL A 864 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 902
      removed outlier: 3.655A  pdb=" N   ALA A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 909
    Processing helix  chain 'A' and resid 911 through 965
      Proline residue:  A 926  - end of helix
      removed outlier: 3.896A  pdb=" N   HIS A 935 " --> pdb=" O   MET A 931 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLY A 938 " --> pdb=" O   ALA A 934 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE A 958 " --> pdb=" O   ALA A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 994
    Processing helix  chain 'A' and resid 997 through 1011
    Processing helix  chain 'A' and resid 1076 through 1083
      removed outlier: 4.060A  pdb=" N   GLN A1080 " --> pdb=" O   SER A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1103
      No H-bonds generated for 'chain 'A' and resid 1101 through 1103'
    Processing helix  chain 'A' and resid 1104 through 1111
    Processing helix  chain 'A' and resid 1125 through 1132
    Processing helix  chain 'A' and resid 1140 through 1151
      removed outlier: 3.560A  pdb=" N   ILE A1144 " --> pdb=" O   SER A1140 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL A1145 " --> pdb=" O   TYR A1141 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG A1146 " --> pdb=" O   GLU A1142 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA A1147 " --> pdb=" O   GLU A1143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1153 through 1158
    Processing helix  chain 'A' and resid 1176 through 1191
      removed outlier: 4.367A  pdb=" N   ARG A1191 " --> pdb=" O   ARG A1187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1209 through 1221
    Processing helix  chain 'A' and resid 1255 through 1262
    Processing helix  chain 'A' and resid 1264 through 1273
      removed outlier: 4.174A  pdb=" N   GLN A1273 " --> pdb=" O   MET A1269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 134
    Processing helix  chain 'B' and resid 190 through 194
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.526A  pdb=" N   SER C  91 " --> pdb=" O   PHE C  88 " (cutoff:3.500A)
    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 409 through 416
      removed outlier: 6.955A  pdb=" N   LYS A 410 " --> pdb=" O   HIS A 397 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   HIS A 397 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   LEU A 412 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE A 396 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ASP A 447 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 472
      removed outlier: 6.252A  pdb=" N   GLY A 470 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   ASP A 554 " --> pdb=" O   GLY A 470 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL A 472 " --> pdb=" O   ASP A 554 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU A 551 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   ILE A 584 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   LEU A 553 " --> pdb=" O   ILE A 584 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLU A 607 " --> pdb=" O   GLY A 599 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASP A 601 " --> pdb=" O   ILE A 605 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   ILE A 605 " --> pdb=" O   ASP A 601 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1059
      removed outlier: 6.728A  pdb=" N   GLN A1053 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A1040 " --> pdb=" O   GLN A1053 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   LEU A1055 " --> pdb=" O   GLY A1038 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   VAL A1039 " --> pdb=" O   ALA A1090 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   ALA A1090 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1113 through 1115
      removed outlier: 6.225A  pdb=" N   GLY A1113 " --> pdb=" O   LEU A1197 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ASP A1199 " --> pdb=" O   GLY A1113 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   VAL A1115 " --> pdb=" O   ASP A1199 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LEU A1196 " --> pdb=" O   ILE A1227 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   ILE A1229 " --> pdb=" O   LEU A1196 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LEU A1198 " --> pdb=" O   ILE A1229 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.712A  pdb=" N   SER B  68 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 54
      removed outlier: 5.196A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      removed outlier: 5.876A  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: 5.865A  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 160
      removed outlier: 6.295A  pdb=" N   HIS B 204 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   SER B 209 " --> pdb=" O   HIS B 204 " (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 59 through 60
      removed outlier: 4.926A  pdb=" N   TRP C  47 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   LYS C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   TYR C 111 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60
      removed outlier: 4.926A  pdb=" N   TRP C  47 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   LYS C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 133
    Processing sheet with id=AB4, first strand: chain 'C' and resid 129 through 133
    Processing sheet with id=AB5, first strand: chain 'C' and resid 160 through 163

    738 hydrogen bonds defined for protein.
    2107 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.95

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        1.16 -     1.31: 2067
        1.31 -     1.45: 3723
        1.45 -     1.59: 7139
        1.59 -     1.74: 0
        1.74 -     1.88: 85
  Bond restraints: 13014
  Sorted by residual:
  bond pdb=" C7  NAG A1303 "
       pdb=" N2  NAG A1303 "
    ideal  model  delta    sigma   weight residual
    1.346  1.480 -0.134 2.00e-02 2.50e+03 4.51e+01
  bond pdb=" C7  NAG A1302 "
       pdb=" N2  NAG A1302 "
    ideal  model  delta    sigma   weight residual
    1.346  1.480 -0.134 2.00e-02 2.50e+03 4.50e+01
  bond pdb=" C7  NAG A1301 "
       pdb=" N2  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.346  1.480 -0.134 2.00e-02 2.50e+03 4.49e+01
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.514 -0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" C1  NAG A1302 "
       pdb=" O5  NAG A1302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.514 -0.108 2.00e-02 2.50e+03 2.91e+01
  ... (remaining 13009 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.49: 17452
        4.49 -     8.99: 175
        8.99 -    13.48: 15
       13.48 -    17.97: 2
       17.97 -    22.47: 1
  Bond angle restraints: 17645
  Sorted by residual:
  angle pdb=" C   SER A 237 "
        pdb=" N   PHE A 238 "
        pdb=" CA  PHE A 238 "
      ideal   model   delta    sigma   weight residual
     121.70  135.87  -14.17 1.80e+00 3.09e-01 6.20e+01
  angle pdb=" C   ASN A 370 "
        pdb=" N   LYS A 371 "
        pdb=" CA  LYS A 371 "
      ideal   model   delta    sigma   weight residual
     121.70  133.65  -11.95 1.80e+00 3.09e-01 4.41e+01
  angle pdb=" CA  LEU A 723 "
        pdb=" CB  LEU A 723 "
        pdb=" CG  LEU A 723 "
      ideal   model   delta    sigma   weight residual
     116.30  138.77  -22.47 3.50e+00 8.16e-02 4.12e+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  132.11  -10.41 1.80e+00 3.09e-01 3.34e+01
  angle pdb=" N   VAL B  56 "
        pdb=" CA  VAL B  56 "
        pdb=" C   VAL B  56 "
      ideal   model   delta    sigma   weight residual
     109.34  120.19  -10.85 2.08e+00 2.31e-01 2.72e+01
  ... (remaining 17640 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 7267
       17.40 -    34.80: 448
       34.80 -    52.20: 77
       52.20 -    69.60: 15
       69.60 -    87.00: 5
  Dihedral angle restraints: 7812
    sinusoidal: 3126
      harmonic: 4686
  Sorted by residual:
  dihedral pdb=" CA  SER B   7 "
           pdb=" C   SER B   7 "
           pdb=" N   PRO B   8 "
           pdb=" CA  PRO B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  109.15   70.85     0      5.00e+00 4.00e-02 2.01e+02
  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 -133.84  -46.16     0      5.00e+00 4.00e-02 8.52e+01
  dihedral pdb=" CA  ASN A  93 "
           pdb=" C   ASN A  93 "
           pdb=" N   ARG A  94 "
           pdb=" CA  ARG A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.22  -44.78     0      5.00e+00 4.00e-02 8.02e+01
  ... (remaining 7809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.289: 2013
       0.289 -    0.578: 4
       0.578 -    0.867: 0
       0.867 -    1.156: 0
       1.156 -    1.445: 1
  Chirality restraints: 2018
  Sorted by residual:
  chirality pdb=" C1  NAG A1303 "
            pdb=" ND2 ASN A  98 "
            pdb=" C2  NAG A1303 "
            pdb=" O5  NAG A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.95   -1.45 2.00e-01 2.50e+01 5.22e+01
  chirality pdb=" CB  ILE C  20 "
            pdb=" CA  ILE C  20 "
            pdb=" CG1 ILE C  20 "
            pdb=" CG2 ILE C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.19    0.46 2.00e-01 2.50e+01 5.21e+00
  chirality pdb=" CB  ILE A  91 "
            pdb=" CA  ILE A  91 "
            pdb=" CG1 ILE A  91 "
            pdb=" CG2 ILE A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.91e+00
  ... (remaining 2015 not shown)

  Planarity restraints: 2227
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  98 "    0.164 2.00e-02 2.50e+03   2.82e-01 9.92e+02
        pdb=" CG  ASN A  98 "   -0.083 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  98 "    0.087 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  98 "   -0.497 2.00e-02 2.50e+03
        pdb=" C1  NAG A1303 "    0.329 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B   7 "    0.029 2.00e-02 2.50e+03   5.84e-02 3.42e+01
        pdb=" C   SER B   7 "   -0.101 2.00e-02 2.50e+03
        pdb=" O   SER B   7 "    0.037 2.00e-02 2.50e+03
        pdb=" N   PRO B   8 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B   7 "    0.083 5.00e-02 4.00e+02   1.26e-01 2.54e+01
        pdb=" N   PRO B   8 "   -0.218 5.00e-02 4.00e+02
        pdb=" CA  PRO B   8 "    0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO B   8 "    0.063 5.00e-02 4.00e+02
  ... (remaining 2224 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 284
        2.67 -     3.23: 12235
        3.23 -     3.79: 19656
        3.79 -     4.34: 25728
        4.34 -     4.90: 43223
  Nonbonded interactions: 101126
  Sorted by model distance:
  nonbonded pdb=" O   ASP A1162 "
            pdb=" OG1 THR A1166 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" OG  SER A1125 "
            pdb=" OE1 GLU A1128 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" OE2 GLU A 525 "
            pdb=" NH1 ARG A 526 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" O   LEU A 588 "
            pdb=" NH1 ARG A 592 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" NH1 ARG B  59 "
            pdb=" OD1 ASP B  65 "
     model   vdw
     2.228 3.120
  ... (remaining 101121 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.46 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.620
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     34.210
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.134  13024  Z= 0.395
  Angle     :  1.272  44.932  17667  Z= 0.638
  Chirality :  0.074   1.445   2018
  Planarity :  0.008   0.126   2225
  Dihedral  : 11.748  86.996   4786
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.36 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  6.51 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.97 (0.16), residues: 1621
  helix: -2.87 (0.13), residues: 764
  sheet: -1.63 (0.28), residues: 279
  loop : -2.48 (0.22), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.004   TRP C 112 
 HIS   0.028   0.003   HIS A1194 
 PHE   0.061   0.004   PHE A 958 
 TYR   0.063   0.004   TYR A 952 
 ARG   0.017   0.002   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02730 (    2)
  link_NAG-ASN         : angle      22.81709 (    6)
  hydrogen bonds       : bond        0.14280 (  710)
  hydrogen bonds       : angle       9.23018 ( 2107)
  SS BOND              : bond        0.01334 (    8)
  SS BOND              : angle       3.21515 (   16)
  covalent geometry    : bond        0.00912 (13014)
  covalent geometry    : angle       1.19748 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 222
  time to evaluate  : 1.493 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.7629 (t160) cc_final: 0.7392 (t0)
REVERT: A   94 ARG cc_start: 0.6522 (ptp90) cc_final: 0.5847 (mmm-85)
REVERT: A  395 ASN cc_start: 0.7940 (t0) cc_final: 0.7706 (t0)
REVERT: A  465 LEU cc_start: 0.7324 (tp) cc_final: 0.7110 (tp)
REVERT: A  507 ASN cc_start: 0.7674 (t0) cc_final: 0.7407 (t0)
REVERT: A  706 GLU cc_start: 0.7431 (pm20) cc_final: 0.7114 (pm20)
REVERT: A  842 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5590 (mm)
REVERT: A  869 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6712 (mp)
REVERT: A  886 LYS cc_start: 0.7175 (mttt) cc_final: 0.6847 (tptt)
REVERT: A  931 MET cc_start: 0.7897 (mmp) cc_final: 0.7313 (mmm)
REVERT: A 1118 GLU cc_start: 0.7633 (pp20) cc_final: 0.7102 (pm20)
REVERT: A 1211 LYS cc_start: 0.7280 (pptt) cc_final: 0.6933 (pttm)
REVERT: A 1218 ASP cc_start: 0.7453 (m-30) cc_final: 0.6989 (m-30)
REVERT: B  153 LYS cc_start: 0.7734 (tptt) cc_final: 0.7356 (tptp)
REVERT: C   67 LYS cc_start: 0.7953 (pttm) cc_final: 0.7472 (tmmt)
REVERT: C   83 PHE cc_start: 0.7259 (t80) cc_final: 0.7056 (t80)
REVERT: C   85 SER cc_start: 0.8280 (m) cc_final: 0.7867 (p)
REVERT: C  200 GLN cc_start: 0.7894 (mt0) cc_final: 0.7613 (mt0)
REVERT: C  216 ASP cc_start: 0.7644 (m-30) cc_final: 0.7429 (t70)
REVERT: C  219 ILE cc_start: 0.6801 (pp) cc_final: 0.6495 (mp)
  outliers start: 6
  outliers final: 1
  residues processed: 228
  average time/residue: 0.2909
  time to fit residues: 93.2762
Evaluate side-chains
  137 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 1.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  869 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 136 optimal weight:    8.9990
   chunk 122 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 126 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 147 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
A 105 ASN
A 142 GLN
A 152 HIS
A 420 GLN
A 569 GLN
A 586 HIS
** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 628 GLN
A 720 ASN
A 838 ASN
A 935 HIS
A 965 HIS
** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1063 GLN
** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 HIS
B  18 GLN
B 130 GLN
** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.149713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.119612 restraints weight = 27333.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.121448 restraints weight = 34006.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.123205 restraints weight = 17030.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13024  Z= 0.173
  Angle     :  0.758   9.946  17667  Z= 0.396
  Chirality :  0.046   0.232   2018
  Planarity :  0.006   0.105   2225
  Dihedral  :  7.118  72.333   1894
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.50 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 11.48 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.19), residues: 1621
  helix: -0.93 (0.17), residues: 785
  sheet: -1.20 (0.29), residues: 276
  loop : -2.12 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 112 
 HIS   0.006   0.001   HIS A1194 
 PHE   0.022   0.002   PHE C  50 
 TYR   0.019   0.002   TYR C  32 
 ARG   0.009   0.001   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00080 (    2)
  link_NAG-ASN         : angle       4.31123 (    6)
  hydrogen bonds       : bond        0.05281 (  710)
  hydrogen bonds       : angle       6.04469 ( 2107)
  SS BOND              : bond        0.00823 (    8)
  SS BOND              : angle       1.69375 (   16)
  covalent geometry    : bond        0.00379 (13014)
  covalent geometry    : angle       0.75240 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 158
  time to evaluate  : 1.134 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6924 (mp0)
REVERT: A   94 ARG cc_start: 0.6524 (ptp90) cc_final: 0.5902 (mmm-85)
REVERT: A  137 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7215 (mp)
REVERT: A  391 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6955 (tp)
REVERT: A  393 PHE cc_start: 0.8088 (m-10) cc_final: 0.7698 (m-10)
REVERT: A  523 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8151 (t)
REVERT: A  783 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8795 (tt)
REVERT: A  795 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7552 (mtm)
REVERT: A  869 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8332 (mp)
REVERT: A  886 LYS cc_start: 0.7250 (mttt) cc_final: 0.7035 (tptt)
REVERT: A  890 GLU cc_start: 0.7788 (pt0) cc_final: 0.7264 (tm-30)
REVERT: A  909 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7580 (pp)
REVERT: A  931 MET cc_start: 0.6893 (mmp) cc_final: 0.6656 (mmm)
REVERT: A  968 MET cc_start: 0.7864 (mtp) cc_final: 0.7594 (ttm)
REVERT: A 1251 LYS cc_start: 0.5621 (tptp) cc_final: 0.5347 (ttmt)
REVERT: B   24 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7385 (mtp85)
REVERT: B  196 ASN cc_start: 0.6363 (OUTLIER) cc_final: 0.6095 (t0)
REVERT: C   85 SER cc_start: 0.7849 (m) cc_final: 0.7610 (p)
REVERT: C  188 SER cc_start: 0.9178 (t) cc_final: 0.8887 (t)
  outliers start: 46
  outliers final: 19
  residues processed: 195
  average time/residue: 0.2339
  time to fit residues: 67.1843
Evaluate side-chains
  152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  420 GLN
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  795 MET
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  196 ASN
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue  190 VAL
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 5 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 119 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 151 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 118 optimal weight:    0.4980
   chunk 159 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS
A 611 HIS
** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.149912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.120404 restraints weight = 34361.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.122990 restraints weight = 44251.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.124825 restraints weight = 18787.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13024  Z= 0.158
  Angle     :  0.703  10.079  17667  Z= 0.366
  Chirality :  0.045   0.230   2018
  Planarity :  0.005   0.101   2225
  Dihedral  :  6.521  69.585   1894
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.56 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 12.35 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.20), residues: 1621
  helix: -0.13 (0.18), residues: 785
  sheet: -0.83 (0.31), residues: 277
  loop : -1.85 (0.24), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 112 
 HIS   0.004   0.001   HIS A 517 
 PHE   0.034   0.002   PHE A 769 
 TYR   0.017   0.002   TYR C  33 
 ARG   0.007   0.001   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00146 (    2)
  link_NAG-ASN         : angle       3.58067 (    6)
  hydrogen bonds       : bond        0.04735 (  710)
  hydrogen bonds       : angle       5.46323 ( 2107)
  SS BOND              : bond        0.00674 (    8)
  SS BOND              : angle       1.42633 (   16)
  covalent geometry    : bond        0.00346 (13014)
  covalent geometry    : angle       0.69884 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 140
  time to evaluate  : 1.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.6407 (ptp90) cc_final: 0.5976 (mmm-85)
REVERT: A  110 MET cc_start: 0.7536 (mmm) cc_final: 0.7263 (tpp)
REVERT: A  137 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7078 (mp)
REVERT: A  463 ARG cc_start: 0.6906 (ttm170) cc_final: 0.6521 (mtt-85)
REVERT: A  507 ASN cc_start: 0.8110 (t0) cc_final: 0.7873 (t0)
REVERT: A  783 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8789 (tt)
REVERT: A  890 GLU cc_start: 0.7771 (pt0) cc_final: 0.7355 (tm-30)
REVERT: A  909 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7629 (pp)
REVERT: A  931 MET cc_start: 0.6908 (mmp) cc_final: 0.6697 (mmm)
REVERT: A 1008 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8633 (mp)
REVERT: A 1211 LYS cc_start: 0.7982 (pptt) cc_final: 0.7540 (pttm)
REVERT: B   24 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7442 (mtt90)
REVERT: B   37 TYR cc_start: 0.7905 (m-80) cc_final: 0.6599 (m-80)
REVERT: B  129 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8074 (mt-10)
REVERT: B  196 ASN cc_start: 0.6420 (OUTLIER) cc_final: 0.6146 (t0)
REVERT: C   85 SER cc_start: 0.7617 (m) cc_final: 0.7338 (p)
REVERT: C  188 SER cc_start: 0.9124 (t) cc_final: 0.8813 (t)
  outliers start: 52
  outliers final: 27
  residues processed: 184
  average time/residue: 0.2604
  time to fit residues: 71.0737
Evaluate side-chains
  152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 1.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  908 SER
Chi-restraints excluded: chain A residue  909 LEU
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  196 ASN
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue  190 VAL
Chi-restraints excluded: chain C residue  202 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 106 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 128 optimal weight:    0.9980
   chunk 146 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 152 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1104 ASN
C 200 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.150933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.120587 restraints weight = 34503.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.122685 restraints weight = 42007.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.124643 restraints weight = 19002.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13024  Z= 0.150
  Angle     :  0.686  10.461  17667  Z= 0.352
  Chirality :  0.044   0.230   2018
  Planarity :  0.005   0.098   2225
  Dihedral  :  6.218  67.608   1892
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.08 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.20), residues: 1621
  helix:  0.29 (0.18), residues: 784
  sheet: -0.63 (0.32), residues: 278
  loop : -1.73 (0.25), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 935 
 PHE   0.030   0.002   PHE A 769 
 TYR   0.016   0.001   TYR C  32 
 ARG   0.004   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00170 (    2)
  link_NAG-ASN         : angle       3.26480 (    6)
  hydrogen bonds       : bond        0.04525 (  710)
  hydrogen bonds       : angle       5.21683 ( 2107)
  SS BOND              : bond        0.00627 (    8)
  SS BOND              : angle       1.30074 (   16)
  covalent geometry    : bond        0.00330 (13014)
  covalent geometry    : angle       0.68251 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 132
  time to evaluate  : 1.292 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.6354 (ptp90) cc_final: 0.5971 (mmm-85)
REVERT: A  110 MET cc_start: 0.7485 (mmm) cc_final: 0.7180 (tpt)
REVERT: A  137 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6954 (mp)
REVERT: A  507 ASN cc_start: 0.8098 (t0) cc_final: 0.7765 (t0)
REVERT: A  511 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6488 (p90)
REVERT: A  783 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8869 (tp)
REVERT: A  890 GLU cc_start: 0.7895 (pt0) cc_final: 0.7375 (tm-30)
REVERT: A  931 MET cc_start: 0.6902 (mmp) cc_final: 0.6655 (mmm)
REVERT: A 1008 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8590 (mp)
REVERT: A 1211 LYS cc_start: 0.7982 (pptt) cc_final: 0.7516 (pttm)
REVERT: B   37 TYR cc_start: 0.7833 (m-80) cc_final: 0.6505 (m-80)
REVERT: C   85 SER cc_start: 0.7522 (m) cc_final: 0.7207 (p)
REVERT: C  188 SER cc_start: 0.9143 (t) cc_final: 0.8810 (t)
  outliers start: 52
  outliers final: 28
  residues processed: 175
  average time/residue: 0.2626
  time to fit residues: 66.6187
Evaluate side-chains
  148 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  908 SER
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   51 ILE
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 134 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 122 optimal weight:    0.8980
   chunk 148 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 118 optimal weight:    0.4980
   chunk 49 optimal weight:   10.0000
   chunk 100 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 133 optimal weight:    0.0470
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1104 ASN
C 200 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.152106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.121987 restraints weight = 34400.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.124321 restraints weight = 41247.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.126300 restraints weight = 18332.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13024  Z= 0.135
  Angle     :  0.660   9.971  17667  Z= 0.341
  Chirality :  0.044   0.194   2018
  Planarity :  0.005   0.096   2225
  Dihedral  :  6.024  66.533   1892
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.18 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.21), residues: 1621
  helix:  0.50 (0.18), residues: 789
  sheet: -0.36 (0.32), residues: 274
  loop : -1.57 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B  98 
 PHE   0.023   0.001   PHE C  88 
 TYR   0.015   0.001   TYR C  32 
 ARG   0.004   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00237 (    2)
  link_NAG-ASN         : angle       2.96206 (    6)
  hydrogen bonds       : bond        0.04263 (  710)
  hydrogen bonds       : angle       5.01470 ( 2107)
  SS BOND              : bond        0.00582 (    8)
  SS BOND              : angle       1.46277 (   16)
  covalent geometry    : bond        0.00290 (13014)
  covalent geometry    : angle       0.65633 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 126
  time to evaluate  : 1.388 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.6303 (ptp90) cc_final: 0.5964 (mmm-85)
REVERT: A  110 MET cc_start: 0.7543 (mmm) cc_final: 0.7174 (tpt)
REVERT: A  137 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7179 (mp)
REVERT: A  309 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7705 (t80)
REVERT: A  507 ASN cc_start: 0.8080 (t0) cc_final: 0.7751 (t0)
REVERT: A  511 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6556 (p90)
REVERT: A  769 PHE cc_start: 0.7946 (p90) cc_final: 0.7667 (p90)
REVERT: A  890 GLU cc_start: 0.7755 (pt0) cc_final: 0.7135 (tm-30)
REVERT: A  931 MET cc_start: 0.6758 (mmp) cc_final: 0.6529 (mmm)
REVERT: A 1008 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8498 (mp)
REVERT: A 1269 MET cc_start: -0.0249 (OUTLIER) cc_final: -0.0817 (mpp)
REVERT: B   37 TYR cc_start: 0.7644 (m-80) cc_final: 0.6131 (m-80)
REVERT: B  102 TRP cc_start: 0.9289 (OUTLIER) cc_final: 0.8009 (m100)
REVERT: C   85 SER cc_start: 0.7351 (m) cc_final: 0.7048 (p)
REVERT: C  188 SER cc_start: 0.9119 (t) cc_final: 0.8800 (t)
  outliers start: 43
  outliers final: 25
  residues processed: 160
  average time/residue: 0.2337
  time to fit residues: 56.6663
Evaluate side-chains
  146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  908 SER
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1008 ILE
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1269 MET
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   81 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 141 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 99 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 122 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 96 optimal weight:   20.0000
   chunk 38 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   1 GLN
C 200 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.149590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119138 restraints weight = 29489.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.121932 restraints weight = 34035.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.123445 restraints weight = 15296.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13024  Z= 0.153
  Angle     :  0.680  10.067  17667  Z= 0.351
  Chirality :  0.044   0.199   2018
  Planarity :  0.005   0.094   2225
  Dihedral  :  5.978  65.816   1892
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.55 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.21), residues: 1621
  helix:  0.59 (0.18), residues: 790
  sheet: -0.28 (0.32), residues: 274
  loop : -1.53 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B  98 
 PHE   0.023   0.002   PHE C  50 
 TYR   0.014   0.001   TYR C  33 
 ARG   0.003   0.000   ARG B  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00117 (    2)
  link_NAG-ASN         : angle       2.87405 (    6)
  hydrogen bonds       : bond        0.04410 (  710)
  hydrogen bonds       : angle       4.96799 ( 2107)
  SS BOND              : bond        0.00671 (    8)
  SS BOND              : angle       1.46817 (   16)
  covalent geometry    : bond        0.00343 (13014)
  covalent geometry    : angle       0.67668 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 125
  time to evaluate  : 1.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7710 (mmm) cc_final: 0.7290 (tpt)
REVERT: A  137 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7119 (mp)
REVERT: A  309 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.7846 (t80)
REVERT: A  352 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7323 (mp0)
REVERT: A  507 ASN cc_start: 0.8094 (t0) cc_final: 0.7746 (t0)
REVERT: A  511 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6736 (p90)
REVERT: A  890 GLU cc_start: 0.7767 (pt0) cc_final: 0.7138 (tm-30)
REVERT: A  931 MET cc_start: 0.6874 (mmp) cc_final: 0.6655 (mmm)
REVERT: B  102 TRP cc_start: 0.9325 (OUTLIER) cc_final: 0.8061 (m100)
REVERT: C  188 SER cc_start: 0.9179 (t) cc_final: 0.8864 (t)
  outliers start: 44
  outliers final: 29
  residues processed: 157
  average time/residue: 0.2416
  time to fit residues: 56.8642
Evaluate side-chains
  145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 111
  time to evaluate  : 1.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  352 GLU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  908 SER
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  952 TYR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   81 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 65 optimal weight:    0.1980
   chunk 69 optimal weight:    2.9990
   chunk 144 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 154 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 150 optimal weight:    0.5980
   chunk 88 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.151070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.120676 restraints weight = 29250.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.122912 restraints weight = 35231.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.124981 restraints weight = 16200.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13024  Z= 0.134
  Angle     :  0.661  14.539  17667  Z= 0.341
  Chirality :  0.043   0.193   2018
  Planarity :  0.004   0.094   2225
  Dihedral  :  5.817  64.847   1892
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.50 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.21), residues: 1621
  helix:  0.73 (0.18), residues: 790
  sheet: -0.18 (0.33), residues: 274
  loop : -1.46 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 102 
 HIS   0.004   0.001   HIS B  98 
 PHE   0.016   0.001   PHE B  92 
 TYR   0.018   0.001   TYR A1132 
 ARG   0.003   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00279 (    2)
  link_NAG-ASN         : angle       2.73680 (    6)
  hydrogen bonds       : bond        0.04188 (  710)
  hydrogen bonds       : angle       4.83810 ( 2107)
  SS BOND              : bond        0.00602 (    8)
  SS BOND              : angle       1.28145 (   16)
  covalent geometry    : bond        0.00289 (13014)
  covalent geometry    : angle       0.65811 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 124
  time to evaluate  : 1.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 MET cc_start: 0.6226 (ppp) cc_final: 0.5906 (ppp)
REVERT: A  110 MET cc_start: 0.7610 (mmm) cc_final: 0.7189 (tpt)
REVERT: A  137 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7117 (mp)
REVERT: A  309 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.7879 (t80)
REVERT: A  507 ASN cc_start: 0.8077 (t0) cc_final: 0.7772 (t0)
REVERT: A  511 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6831 (p90)
REVERT: A  890 GLU cc_start: 0.7764 (pt0) cc_final: 0.7275 (tm-30)
REVERT: A  931 MET cc_start: 0.6835 (mmp) cc_final: 0.6613 (mmm)
REVERT: A 1029 MET cc_start: 0.5048 (tmm) cc_final: 0.4731 (tmm)
REVERT: A 1118 GLU cc_start: 0.7020 (pm20) cc_final: 0.6513 (pm20)
REVERT: B  102 TRP cc_start: 0.9272 (OUTLIER) cc_final: 0.7978 (m100)
REVERT: C  103 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8946 (p90)
REVERT: C  188 SER cc_start: 0.9138 (t) cc_final: 0.8821 (t)
  outliers start: 44
  outliers final: 32
  residues processed: 158
  average time/residue: 0.2540
  time to fit residues: 60.1198
Evaluate side-chains
  153 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 1.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  908 SER
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  952 TYR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  103 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 129 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0370
   chunk 100 optimal weight:    0.9990
   chunk 161 optimal weight:    4.9990
   chunk 143 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 152 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 109 optimal weight:    7.9990
   chunk 146 optimal weight:    1.9990
   overall best weight:    1.1264

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

Flipped N/Q/H residues before XYZ refinement:
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 208 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.149030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.118874 restraints weight = 22777.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.122565 restraints weight = 28580.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.122827 restraints weight = 13205.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13024  Z= 0.159
  Angle     :  0.678  10.360  17667  Z= 0.350
  Chirality :  0.044   0.201   2018
  Planarity :  0.004   0.093   2225
  Dihedral  :  5.839  64.224   1892
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.01 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.21), residues: 1621
  helix:  0.74 (0.18), residues: 789
  sheet: -0.14 (0.33), residues: 268
  loop : -1.48 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 102 
 HIS   0.004   0.001   HIS B  98 
 PHE   0.024   0.002   PHE C  50 
 TYR   0.018   0.001   TYR A1132 
 ARG   0.004   0.000   ARG B 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00089 (    2)
  link_NAG-ASN         : angle       2.57071 (    6)
  hydrogen bonds       : bond        0.04407 (  710)
  hydrogen bonds       : angle       4.88581 ( 2107)
  SS BOND              : bond        0.00645 (    8)
  SS BOND              : angle       1.42920 (   16)
  covalent geometry    : bond        0.00359 (13014)
  covalent geometry    : angle       0.67529 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 112
  time to evaluate  : 1.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7620 (mmm) cc_final: 0.7211 (tpt)
REVERT: A  137 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7074 (mp)
REVERT: A  309 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.7942 (t80)
REVERT: A  449 MET cc_start: 0.7647 (tmm) cc_final: 0.7352 (tmm)
REVERT: A  507 ASN cc_start: 0.8092 (t0) cc_final: 0.7789 (t0)
REVERT: A  511 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6988 (p90)
REVERT: A  890 GLU cc_start: 0.7758 (pt0) cc_final: 0.7296 (tm-30)
REVERT: A  931 MET cc_start: 0.6793 (mmp) cc_final: 0.6580 (mmm)
REVERT: A  968 MET cc_start: 0.7960 (ttm) cc_final: 0.7736 (ttt)
REVERT: A 1029 MET cc_start: 0.5022 (tmm) cc_final: 0.4763 (tmm)
REVERT: A 1067 LEU cc_start: 0.7475 (pp) cc_final: 0.7260 (pp)
REVERT: A 1118 GLU cc_start: 0.7053 (pm20) cc_final: 0.6513 (pm20)
REVERT: A 1211 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7829 (mmtm)
REVERT: B  102 TRP cc_start: 0.9337 (OUTLIER) cc_final: 0.8051 (m100)
REVERT: C  188 SER cc_start: 0.9191 (t) cc_final: 0.8887 (t)
  outliers start: 40
  outliers final: 32
  residues processed: 145
  average time/residue: 0.2520
  time to fit residues: 54.0626
Evaluate side-chains
  143 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 107
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  908 SER
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  952 TYR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue   98 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 161 optimal weight:    7.9990
   chunk 123 optimal weight:    0.5980
   chunk 130 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 119 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 102 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.150400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.120091 restraints weight = 27444.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.123687 restraints weight = 31473.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.124598 restraints weight = 13132.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13024  Z= 0.140
  Angle     :  0.660  13.711  17667  Z= 0.340
  Chirality :  0.043   0.198   2018
  Planarity :  0.004   0.093   2225
  Dihedral  :  5.728  63.294   1892
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.45 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.21), residues: 1621
  helix:  0.85 (0.18), residues: 790
  sheet: -0.12 (0.32), residues: 274
  loop : -1.42 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B  98 
 PHE   0.018   0.001   PHE C  50 
 TYR   0.017   0.001   TYR A1132 
 ARG   0.004   0.000   ARG B 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00164 (    2)
  link_NAG-ASN         : angle       2.41099 (    6)
  hydrogen bonds       : bond        0.04222 (  710)
  hydrogen bonds       : angle       4.79158 ( 2107)
  SS BOND              : bond        0.00596 (    8)
  SS BOND              : angle       1.30318 (   16)
  covalent geometry    : bond        0.00307 (13014)
  covalent geometry    : angle       0.65801 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 113
  time to evaluate  : 1.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7577 (mmm) cc_final: 0.7179 (tpt)
REVERT: A  137 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7093 (mp)
REVERT: A  309 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.7927 (t80)
REVERT: A  439 MET cc_start: 0.8484 (tpp) cc_final: 0.8266 (tpp)
REVERT: A  449 MET cc_start: 0.7600 (tmm) cc_final: 0.7247 (tmm)
REVERT: A  507 ASN cc_start: 0.8060 (t0) cc_final: 0.7770 (t0)
REVERT: A  511 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7043 (p90)
REVERT: A  890 GLU cc_start: 0.7749 (pt0) cc_final: 0.7313 (tm-30)
REVERT: A  931 MET cc_start: 0.6757 (mmp) cc_final: 0.6497 (mmm)
REVERT: A 1067 LEU cc_start: 0.7475 (pp) cc_final: 0.7250 (pp)
REVERT: A 1118 GLU cc_start: 0.7077 (pm20) cc_final: 0.6525 (pm20)
REVERT: A 1211 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7892 (mmtm)
REVERT: B  102 TRP cc_start: 0.9298 (OUTLIER) cc_final: 0.8011 (m100)
REVERT: C  188 SER cc_start: 0.9155 (t) cc_final: 0.8850 (t)
  outliers start: 39
  outliers final: 31
  residues processed: 145
  average time/residue: 0.2421
  time to fit residues: 51.7909
Evaluate side-chains
  146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  769 PHE
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  908 SER
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  952 TYR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue   98 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 154 optimal weight:    9.9990
   chunk 121 optimal weight:    1.9990
   chunk 134 optimal weight:    5.9990
   chunk 104 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1111 GLN
** B 204 HIS ** 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 = 0.3852 r_free = 0.3852 target = 0.145126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.114752 restraints weight = 26647.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.116634 restraints weight = 34688.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.118119 restraints weight = 18153.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  13024  Z= 0.259
  Angle     :  0.784  13.096  17667  Z= 0.408
  Chirality :  0.048   0.226   2018
  Planarity :  0.005   0.093   2225
  Dihedral  :  6.118  64.553   1892
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.99 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.89 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.21), residues: 1621
  helix:  0.49 (0.18), residues: 791
  sheet: -0.26 (0.32), residues: 268
  loop : -1.57 (0.25), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 102 
 HIS   0.006   0.001   HIS B  98 
 PHE   0.041   0.003   PHE C  50 
 TYR   0.023   0.002   TYR B  54 
 ARG   0.005   0.001   ARG A1167 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00070 (    2)
  link_NAG-ASN         : angle       2.67603 (    6)
  hydrogen bonds       : bond        0.05186 (  710)
  hydrogen bonds       : angle       5.19925 ( 2107)
  SS BOND              : bond        0.00814 (    8)
  SS BOND              : angle       1.74746 (   16)
  covalent geometry    : bond        0.00614 (13014)
  covalent geometry    : angle       0.78151 (17645)

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

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

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3242 Ramachandran restraints generated.
    1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7646 (mmm) cc_final: 0.7205 (tpt)
REVERT: A  449 MET cc_start: 0.7480 (tmm) cc_final: 0.7111 (tmm)
REVERT: A  507 ASN cc_start: 0.8158 (t0) cc_final: 0.7840 (t0)
REVERT: A  842 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7234 (mm)
REVERT: A  890 GLU cc_start: 0.7861 (pt0) cc_final: 0.7333 (tm-30)
REVERT: A 1067 LEU cc_start: 0.7553 (pp) cc_final: 0.7311 (pp)
REVERT: A 1118 GLU cc_start: 0.7225 (pm20) cc_final: 0.6676 (pm20)
REVERT: B  102 TRP cc_start: 0.9433 (OUTLIER) cc_final: 0.8134 (m100)
REVERT: C  188 SER cc_start: 0.9229 (t) cc_final: 0.8957 (t)
  outliers start: 33
  outliers final: 29
  residues processed: 142
  average time/residue: 0.2744
  time to fit residues: 56.6623
Evaluate side-chains
  142 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  768 THR
Chi-restraints excluded: chain A residue  769 PHE
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  908 SER
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue  996 ASP
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue  102 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue   98 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 160 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 107 optimal weight:    9.9990
   chunk 76 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0570
   chunk 85 optimal weight:    0.7980
   chunk 102 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 124 optimal weight:    0.2980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.150058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.119644 restraints weight = 35206.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.123787 restraints weight = 37976.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.124729 restraints weight = 13946.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13024  Z= 0.136
  Angle     :  0.674  11.190  17667  Z= 0.349
  Chirality :  0.043   0.196   2018
  Planarity :  0.005   0.093   2225
  Dihedral  :  5.804  64.017   1892
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.03 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.80 %
    Cis-general     : 0.32 %
    Twisted Proline : 1.96 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.21), residues: 1621
  helix:  0.73 (0.18), residues: 792
  sheet: -0.08 (0.33), residues: 258
  loop : -1.46 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 102 
 HIS   0.004   0.001   HIS B  98 
 PHE   0.015   0.001   PHE B  92 
 TYR   0.019   0.001   TYR A1132 
 ARG   0.007   0.000   ARG A 546 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    2)
  link_NAG-ASN         : angle       2.33074 (    6)
  hydrogen bonds       : bond        0.04304 (  710)
  hydrogen bonds       : angle       4.87992 ( 2107)
  SS BOND              : bond        0.00632 (    8)
  SS BOND              : angle       1.42806 (   16)
  covalent geometry    : bond        0.00295 (13014)
  covalent geometry    : angle       0.67155 (17645)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4540.80 seconds
wall clock time: 79 minutes 45.36 seconds (4785.36 seconds total)