Starting phenix.real_space_refine
on Wed Mar  4 08:16:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lcr_0873/03_2026/6lcr_0873.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lcr_0873/03_2026/6lcr_0873.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lcr_0873/03_2026/6lcr_0873.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lcr_0873/03_2026/6lcr_0873.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lcr_0873/03_2026/6lcr_0873.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lcr_0873/03_2026/6lcr_0873.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      1      5.21       5
     S      62      5.16       5
     C    7395      2.51       5
     N    1931      2.21       5
     O    2168      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11561
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 8280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1044, 8280
          Classifications: {'peptide': 1044}
          Link IDs: {'PTRANS': 35, 'TRANS': 1008}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3061
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 376, 3061
          Classifications: {'peptide': 376}
          Link IDs: {'PTRANS': 26, 'TRANS': 349}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 72
          Unusual residues: {' MG': 1, 'ACP': 1}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.61, per 1000 atoms: 0.23
  Number of scatterers: 11561
  At special positions: 0
  Unit cell: (143.48, 118.16, 128.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      62     16.00
     P       4     15.00
     Mg      1     11.99
     O    2168      8.00
     N    1931      7.00
     C    7395      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG B 508 " - " ASN B 241 "
      " NAG E   1 " - " ASN B 189 "
      " NAG F   1 " - " ASN B 314 "
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 703.0 milliseconds
  

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2676

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 10 sheets defined
      46.0% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 162 through 184
      removed outlier: 4.365A  pdb=" N   ILE A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 334
      No H-bonds generated for 'chain 'A' and resid 332 through 334'
    Processing helix  chain 'A' and resid 359 through 361
      No H-bonds generated for 'chain 'A' and resid 359 through 361'
    Processing helix  chain 'A' and resid 468 through 473
    Processing helix  chain 'A' and resid 483 through 488
    Processing helix  chain 'A' and resid 488 through 514
      removed outlier: 3.873A  pdb=" N   ILE A 512 " --> pdb=" O   ILE A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 525
      removed outlier: 4.168A  pdb=" N   TRP A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   PHE A 524 " --> pdb=" O   SER A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 548
      removed outlier: 3.935A  pdb=" N   PHE A 538 " --> pdb=" O   ALA A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 552
    Processing helix  chain 'A' and resid 553 through 573
      removed outlier: 3.582A  pdb=" N   TYR A 557 " --> pdb=" O   PRO A 553 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE A 558 " --> pdb=" O   ILE A 554 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE A 562 " --> pdb=" O   ILE A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 594
      removed outlier: 3.771A  pdb=" N   ILE A 593 " --> pdb=" O   SER A 590 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER A 594 " --> pdb=" O   TRP A 591 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 590 through 594'
    Processing helix  chain 'A' and resid 595 through 600
      removed outlier: 4.081A  pdb=" N   ILE A 600 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 642
    Processing helix  chain 'A' and resid 648 through 671
      removed outlier: 4.319A  pdb=" N   ARG A 655 " --> pdb=" O   ALA A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 696
      removed outlier: 3.911A  pdb=" N   GLY A 696 " --> pdb=" O   GLU A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 713
      removed outlier: 3.785A  pdb=" N   GLN A 704 " --> pdb=" O   PRO A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 748
      removed outlier: 4.189A  pdb=" N   LEU A 743 " --> pdb=" O   ASP A 739 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 744 " --> pdb=" O   GLU A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 751
      No H-bonds generated for 'chain 'A' and resid 749 through 751'
    Processing helix  chain 'A' and resid 806 through 811
      removed outlier: 3.703A  pdb=" N   ILE A 810 " --> pdb=" O   ALA A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 837
      removed outlier: 4.179A  pdb=" N   GLU A 825 " --> pdb=" O   ASP A 821 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN A 828 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 865
      removed outlier: 4.276A  pdb=" N   GLU A 859 " --> pdb=" O   GLU A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 869 through 878
      removed outlier: 4.123A  pdb=" N   GLU A 875 " --> pdb=" O   GLU A 871 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLU A 876 " --> pdb=" O   GLU A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 883
      removed outlier: 3.835A  pdb=" N   GLU A 882 " --> pdb=" O   ALA A 878 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ARG A 883 " --> pdb=" O   ASP A 879 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 878 through 883'
    Processing helix  chain 'A' and resid 900 through 911
      removed outlier: 3.978A  pdb=" N   ALA A 906 " --> pdb=" O   PRO A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 933
      removed outlier: 3.516A  pdb=" N   ALA A 926 " --> pdb=" O   LYS A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 972
      removed outlier: 3.625A  pdb=" N   TYR A 958 " --> pdb=" O   THR A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 986
    Processing helix  chain 'A' and resid 1003 through 1009
      removed outlier: 3.618A  pdb=" N   TRP A1007 " --> pdb=" O   PHE A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1024
      removed outlier: 3.601A  pdb=" N   CYS A1024 " --> pdb=" O   LEU A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1033 through 1047
      removed outlier: 4.152A  pdb=" N   ALA A1038 " --> pdb=" O   PRO A1034 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A1041 " --> pdb=" O   LYS A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1060
      No H-bonds generated for 'chain 'A' and resid 1058 through 1060'
    Processing helix  chain 'A' and resid 1061 through 1067
    Processing helix  chain 'A' and resid 1092 through 1094
      No H-bonds generated for 'chain 'A' and resid 1092 through 1094'
    Processing helix  chain 'A' and resid 1095 through 1100
    Processing helix  chain 'A' and resid 1102 through 1134
      removed outlier: 3.600A  pdb=" N   LEU A1111 " --> pdb=" O   SER A1107 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASN A1122 " --> pdb=" O   PHE A1118 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER A1128 " --> pdb=" O   ILE A1124 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TYR A1132 " --> pdb=" O   SER A1128 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS A1134 " --> pdb=" O   PHE A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1152
    Processing helix  chain 'A' and resid 1158 through 1167
    Processing helix  chain 'A' and resid 1174 through 1179
    Processing helix  chain 'A' and resid 1180 through 1182
      No H-bonds generated for 'chain 'A' and resid 1180 through 1182'
    Processing helix  chain 'A' and resid 1183 through 1188
    Processing helix  chain 'A' and resid 1193 through 1220
      removed outlier: 3.877A  pdb=" N   PHE A1197 " --> pdb=" O   THR A1193 " (cutoff:3.500A)
      Proline residue:  A1215  - end of helix
      removed outlier: 4.051A  pdb=" N   VAL A1219 " --> pdb=" O   PRO A1215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1236 through 1257
      Proline residue:  A1245  - end of helix
      removed outlier: 3.745A  pdb=" N   ASN A1251 " --> pdb=" O   VAL A1247 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN A1257 " --> pdb=" O   TYR A1253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1263 through 1285
      removed outlier: 3.851A  pdb=" N   ILE A1276 " --> pdb=" O   SER A1272 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   PHE A1277 " --> pdb=" O   ASP A1273 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA A1285 " --> pdb=" O   GLY A1281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1301
      removed outlier: 3.685A  pdb=" N   GLN A1301 " --> pdb=" O   PRO A1297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1303 through 1331
      Proline residue:  A1313  - end of helix
      Proline residue:  A1319  - end of helix
      removed outlier: 3.924A  pdb=" N   VAL A1323 " --> pdb=" O   PRO A1319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1333 through 1345
      removed outlier: 3.918A  pdb=" N   ILE A1337 " --> pdb=" O   TYR A1333 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG A1344 " --> pdb=" O   GLU A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1356
    Processing helix  chain 'B' and resid 50 through 55
    Processing helix  chain 'B' and resid 56 through 75
      removed outlier: 3.616A  pdb=" N   VAL B  75 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 89
      removed outlier: 3.612A  pdb=" N   ALA B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 171
      removed outlier: 4.263A  pdb=" N   ASN B 171 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 179
    Processing helix  chain 'B' and resid 185 through 190
    Processing helix  chain 'B' and resid 251 through 255
    Processing helix  chain 'B' and resid 269 through 273
    Processing helix  chain 'B' and resid 334 through 338
      removed outlier: 3.599A  pdb=" N   LYS B 338 " --> pdb=" O   THR B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 383
    Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 330
      removed outlier: 3.738A  pdb=" N   PHE A 339 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ALA A 356 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   VAL A 460 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 354 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 347
      removed outlier: 3.549A  pdb=" N   ASP A 346 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 943 through 945
      removed outlier: 3.910A  pdb=" N   ASP A1001 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ILE A 603 " --> pdb=" O   TRP A 916 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   THR A1052 " --> pdb=" O   VAL A1070 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   VAL A1072 " --> pdb=" O   THR A1052 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   SER A1054 " --> pdb=" O   VAL A1072 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ILE A1074 " --> pdb=" O   SER A1054 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLY A1056 " --> pdb=" O   ILE A1074 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE A1088 " --> pdb=" O   GLY A1071 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628
      removed outlier: 3.657A  pdb=" N   ALA A 621 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   MET A 616 " --> pdb=" O   ARG A 896 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   ARG A 896 " --> pdb=" O   MET A 616 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   PHE A 618 " --> pdb=" O   GLU A 894 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   GLU A 894 " --> pdb=" O   PHE A 618 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ILE A 843 " --> pdb=" O   LEU A 888 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ARG A 793 " --> pdb=" O   VAL A 775 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL A 775 " --> pdb=" O   ARG A 793 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 720 through 723
    Processing sheet with id=AA6, first strand: chain 'A' and resid 763 through 766
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1260 through 1262
    Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.733A  pdb=" N   ARG B 340 " --> pdb=" O   GLU B 160 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE B 153 " --> pdb=" O   LYS B 313 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LYS B 313 " --> pdb=" O   ILE B 153 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   PHE B 155 " --> pdb=" O   TYR B 311 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 96
      removed outlier: 3.518A  pdb=" N   THR B 221 " --> pdb=" O   GLU B 329 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 95 through 96

    502 hydrogen bonds defined for protein.
    1425 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: 1.68

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1898
        1.31 -     1.44: 3230
        1.44 -     1.56: 6586
        1.56 -     1.69: 9
        1.69 -     1.81: 100
  Bond restraints: 11823
  Sorted by residual:
  bond pdb=" O15 P5S A2003 "
       pdb=" P12 P5S A2003 "
    ideal  model  delta    sigma   weight residual
    1.493  1.600 -0.107 2.00e-02 2.50e+03 2.88e+01
  bond pdb=" C38 P5S A2003 "
       pdb=" O37 P5S A2003 "
    ideal  model  delta    sigma   weight residual
    1.345  1.451 -0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" O2B ACP A2002 "
       pdb=" PB  ACP A2002 "
    ideal  model  delta    sigma   weight residual
    1.507  1.610 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" C17 P5S A2003 "
       pdb=" O19 P5S A2003 "
    ideal  model  delta    sigma   weight residual
    1.351  1.449 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" O3A ACP A2002 "
       pdb=" PB  ACP A2002 "
    ideal  model  delta    sigma   weight residual
    1.698  1.610  0.088 2.00e-02 2.50e+03 1.96e+01
  ... (remaining 11818 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.11: 15778
        3.11 -     6.22: 231
        6.22 -     9.34: 29
        9.34 -    12.45: 9
       12.45 -    15.56: 5
  Bond angle restraints: 16052
  Sorted by residual:
  angle pdb=" C   GLN A 408 "
        pdb=" N   PRO A 409 "
        pdb=" CA  PRO A 409 "
      ideal   model   delta    sigma   weight residual
     119.84  127.83   -7.99 1.25e+00 6.40e-01 4.09e+01
  angle pdb=" C4  NAG D   2 "
        pdb=" C3  NAG D   2 "
        pdb=" O3  NAG D   2 "
      ideal   model   delta    sigma   weight residual
     112.02   96.46   15.56 3.00e+00 1.11e-01 2.69e+01
  angle pdb=" C4  NAG F   1 "
        pdb=" C5  NAG F   1 "
        pdb=" C6  NAG F   1 "
      ideal   model   delta    sigma   weight residual
     113.89   99.50   14.39 3.00e+00 1.11e-01 2.30e+01
  angle pdb=" C   ALA A 952 "
        pdb=" CA  ALA A 952 "
        pdb=" CB  ALA A 952 "
      ideal   model   delta    sigma   weight residual
     116.54  111.05    5.49 1.15e+00 7.56e-01 2.28e+01
  angle pdb=" N   PHE A 548 "
        pdb=" CA  PHE A 548 "
        pdb=" C   PHE A 548 "
      ideal   model   delta    sigma   weight residual
     112.97  108.13    4.84 1.06e+00 8.90e-01 2.08e+01
  ... (remaining 16047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.71: 6888
       30.71 -    61.42: 282
       61.42 -    92.13: 33
       92.13 -   122.84: 11
      122.84 -   153.55: 2
  Dihedral angle restraints: 7216
    sinusoidal: 3068
      harmonic: 4148
  Sorted by residual:
  dihedral pdb=" CA  SER A1233 "
           pdb=" C   SER A1233 "
           pdb=" N   GLU A1234 "
           pdb=" CA  GLU A1234 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.35   27.65     0      5.00e+00 4.00e-02 3.06e+01
  dihedral pdb=" CA  ASP A1231 "
           pdb=" C   ASP A1231 "
           pdb=" N   VAL A1232 "
           pdb=" CA  VAL A1232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.63   27.37     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  ASN A 990 "
           pdb=" C   ASN A 990 "
           pdb=" N   ALA A 991 "
           pdb=" CA  ALA A 991 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.90   26.10     0      5.00e+00 4.00e-02 2.72e+01
  ... (remaining 7213 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.223: 1801
       0.223 -    0.446: 3
       0.446 -    0.670: 3
       0.670 -    0.893: 1
       0.893 -    1.116: 2
  Chirality restraints: 1810
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.31   -1.09 2.00e-02 2.50e+03 2.98e+03
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.87    0.47 2.00e-02 2.50e+03 5.60e+02
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.79    0.39 2.00e-02 2.50e+03 3.72e+02
  ... (remaining 1807 not shown)

  Planarity restraints: 2039
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "    0.255 2.00e-02 2.50e+03   2.14e-01 5.70e+02
        pdb=" C7  NAG E   2 "   -0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "    0.173 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "   -0.359 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "    0.230 2.00e-02 2.50e+03   1.85e-01 4.29e+02
        pdb=" C7  NAG E   1 "   -0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "    0.169 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "   -0.289 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "    0.181 2.00e-02 2.50e+03   1.52e-01 2.87e+02
        pdb=" C7  NAG D   1 "   -0.049 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.131 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "   -0.250 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2036 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 116
        2.51 -     3.11: 9169
        3.11 -     3.71: 17852
        3.71 -     4.30: 26005
        4.30 -     4.90: 43443
  Nonbonded interactions: 96585
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 606 "
            pdb="MG    MG A2001 "
     model   vdw
     1.914 2.170
  nonbonded pdb=" O3  NAG E   1 "
            pdb=" O7  NAG E   1 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O3  NAG E   2 "
            pdb=" O7  NAG E   2 "
     model   vdw
     2.044 3.040
  nonbonded pdb=" O3  NAG F   1 "
            pdb=" O7  NAG F   1 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" OE1 GLU A1234 "
            pdb=" OG1 THR A1236 "
     model   vdw
     2.105 3.040
  ... (remaining 96580 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     11.650
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
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   0.194  11832  Z= 0.393
  Angle     :  1.072  24.958  16079  Z= 0.516
  Chirality :  0.070   1.116   1810
  Planarity :  0.009   0.214   2036
  Dihedral  : 17.258 153.553   4540
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 20.54
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 11.58 %
    Favored  : 88.21 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 10.33 %
    Favored  : 89.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.30 (0.19), residues: 1408
  helix: -2.74 (0.17), residues: 578
  sheet: -1.82 (0.37), residues: 174
  loop : -3.22 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A1260 
 TYR   0.025   0.002   TYR B 132 
 PHE   0.023   0.002   PHE A1017 
 TRP   0.038   0.002   TRP B 120 
 HIS   0.003   0.001   HIS A 717 

Details of bonding type rmsd
  covalent geometry    : bond        0.00872 (11823)
  covalent geometry    : angle       0.98647 (16052)
  hydrogen bonds       : bond        0.15897 (  484)
  hydrogen bonds       : angle       7.66913 ( 1425)
  link_BETA1-4         : bond        0.02944 (    6)
  link_BETA1-4         : angle       8.27416 (   18)
  link_NAG-ASN         : bond        0.11615 (    3)
  link_NAG-ASN         : angle      13.37580 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 151
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 GLN cc_start: 0.3650 (OUTLIER) cc_final: 0.0395 (pt0)
REVERT: A  683 MET cc_start: 0.1248 (mtt) cc_final: 0.1020 (mtt)
REVERT: A 1019 LEU cc_start: 0.7888 (mt) cc_final: 0.7641 (mp)
REVERT: B  188 ILE cc_start: 0.8628 (tp) cc_final: 0.8392 (tp)
  outliers start: 6
  outliers final: 4
  residues processed: 157
  average time/residue: 0.1335
  time to fit residues: 28.5381
Evaluate side-chains
  123 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 GLN
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue 1304 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0980
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 327 HIS
A 466 HIS
A 489 ASN
A 510 ASN
A 550 ASN
A 626 GLN
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 ASN
A 898 GLN
A 965 GLN
A 990 ASN
A1023 GLN
A1092 GLN
A1133 GLN
A1251 ASN
B  73 HIS
B 144 ASN
B 161 ASN
B 166 HIS
B 312 GLN
B 323 GLN
B 398 GLN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.190278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.142798 restraints weight = 13982.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 3.83
r_work: 0.3244 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11832  Z= 0.152
  Angle     :  0.746  12.644  16079  Z= 0.375
  Chirality :  0.048   0.330   1810
  Planarity :  0.005   0.057   2036
  Dihedral  : 11.678 146.169   1862
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.10 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.75 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.21), residues: 1408
  helix: -1.70 (0.19), residues: 610
  sheet: -1.25 (0.38), residues: 175
  loop : -2.68 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 944 
 TYR   0.021   0.002   TYR A1183 
 PHE   0.018   0.002   PHE A1197 
 TRP   0.022   0.001   TRP B 120 
 HIS   0.012   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (11823)
  covalent geometry    : angle       0.72847 (16052)
  hydrogen bonds       : bond        0.04594 (  484)
  hydrogen bonds       : angle       5.87243 ( 1425)
  link_BETA1-4         : bond        0.00750 (    6)
  link_BETA1-4         : angle       4.67426 (   18)
  link_NAG-ASN         : bond        0.00715 (    3)
  link_NAG-ASN         : angle       2.03158 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 GLN cc_start: 0.2676 (OUTLIER) cc_final: 0.2463 (mt0)
REVERT: A  639 MET cc_start: 0.5070 (mmp) cc_final: 0.4844 (ttm)
REVERT: A  944 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7638 (ttt180)
REVERT: A  975 MET cc_start: 0.7017 (tmm) cc_final: 0.6781 (tmm)
REVERT: A 1183 TYR cc_start: 0.8768 (t80) cc_final: 0.8346 (t80)
REVERT: B   78 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8750 (tt)
REVERT: B   94 PHE cc_start: 0.8514 (m-80) cc_final: 0.8254 (m-10)
REVERT: B  142 ARG cc_start: 0.7583 (mtm180) cc_final: 0.7247 (mtm180)
REVERT: B  161 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8543 (t0)
  outliers start: 26
  outliers final: 15
  residues processed: 165
  average time/residue: 0.1148
  time to fit residues: 26.8357
Evaluate side-chains
  141 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 GLN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1274 VAL
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  161 ASN
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  336 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 115 optimal weight:    0.6980
   chunk 103 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 133 optimal weight:    0.8980
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 636 GLN
** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 828 GLN
** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1117 ASN
A1257 ASN
B  99 GLN
B 161 ASN
B 323 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.188400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.145983 restraints weight = 14070.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.83
r_work: 0.3246 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11832  Z= 0.175
  Angle     :  0.707   9.841  16079  Z= 0.357
  Chirality :  0.047   0.319   1810
  Planarity :  0.005   0.060   2036
  Dihedral  : 10.398 132.839   1860
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.46 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.30 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.21), residues: 1408
  helix: -1.16 (0.20), residues: 586
  sheet: -0.98 (0.39), residues: 176
  loop : -2.48 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 787 
 TYR   0.019   0.002   TYR B 375 
 PHE   0.017   0.002   PHE A1197 
 TRP   0.021   0.001   TRP B 120 
 HIS   0.018   0.001   HIS A 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (11823)
  covalent geometry    : angle       0.69256 (16052)
  hydrogen bonds       : bond        0.04567 (  484)
  hydrogen bonds       : angle       5.62598 ( 1425)
  link_BETA1-4         : bond        0.00552 (    6)
  link_BETA1-4         : angle       4.07247 (   18)
  link_NAG-ASN         : bond        0.00369 (    3)
  link_NAG-ASN         : angle       2.28047 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 GLN cc_start: 0.2782 (OUTLIER) cc_final: 0.1941 (pt0)
REVERT: A  466 HIS cc_start: 0.5004 (OUTLIER) cc_final: 0.4792 (t70)
REVERT: A 1019 LEU cc_start: 0.7962 (mt) cc_final: 0.7651 (mt)
REVERT: A 1183 TYR cc_start: 0.8731 (t80) cc_final: 0.7991 (t80)
REVERT: B   78 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8744 (tt)
REVERT: B   94 PHE cc_start: 0.8482 (m-80) cc_final: 0.8271 (m-10)
REVERT: B  142 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7221 (mtm180)
REVERT: B  161 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8574 (t0)
REVERT: B  188 ILE cc_start: 0.8495 (tp) cc_final: 0.8290 (tp)
  outliers start: 39
  outliers final: 23
  residues processed: 155
  average time/residue: 0.1129
  time to fit residues: 24.8057
Evaluate side-chains
  143 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 GLN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  466 HIS
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  811 TYR
Chi-restraints excluded: chain A residue  932 SER
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue 1001 ASP
Chi-restraints excluded: chain A residue 1030 CYS
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1274 VAL
Chi-restraints excluded: chain A residue 1304 THR
Chi-restraints excluded: chain A residue 1308 CYS
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  161 ASN
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  336 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 408 GLN
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.189076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145482 restraints weight = 14134.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.95
r_work: 0.3239 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11832  Z= 0.178
  Angle     :  0.692   9.165  16079  Z= 0.351
  Chirality :  0.046   0.294   1810
  Planarity :  0.005   0.060   2036
  Dihedral  :  9.574 120.593   1860
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.32 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 18.52 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.22), residues: 1408
  helix: -0.88 (0.21), residues: 588
  sheet: -0.86 (0.39), residues: 176
  loop : -2.40 (0.23), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 787 
 TYR   0.020   0.002   TYR B 375 
 PHE   0.022   0.002   PHE A 833 
 TRP   0.014   0.001   TRP B 120 
 HIS   0.003   0.001   HIS A 989 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (11823)
  covalent geometry    : angle       0.67804 (16052)
  hydrogen bonds       : bond        0.04463 (  484)
  hydrogen bonds       : angle       5.49354 ( 1425)
  link_BETA1-4         : bond        0.00453 (    6)
  link_BETA1-4         : angle       3.95746 (   18)
  link_NAG-ASN         : bond        0.00365 (    3)
  link_NAG-ASN         : angle       2.32786 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 126
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 GLN cc_start: 0.2024 (OUTLIER) cc_final: 0.1400 (pt0)
REVERT: A  653 VAL cc_start: 0.7043 (OUTLIER) cc_final: 0.6823 (p)
REVERT: A 1019 LEU cc_start: 0.8044 (mt) cc_final: 0.7711 (mt)
REVERT: A 1183 TYR cc_start: 0.8727 (t80) cc_final: 0.7979 (t80)
REVERT: A 1265 MET cc_start: 0.8400 (tpp) cc_final: 0.8089 (tpt)
REVERT: B   78 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8742 (tt)
REVERT: B   94 PHE cc_start: 0.8499 (m-80) cc_final: 0.8219 (m-10)
REVERT: B  142 ARG cc_start: 0.7657 (mtm180) cc_final: 0.7257 (mtm180)
  outliers start: 55
  outliers final: 35
  residues processed: 170
  average time/residue: 0.0995
  time to fit residues: 24.7292
Evaluate side-chains
  155 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 117
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  408 GLN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  811 TYR
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  932 SER
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue  988 ASP
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1001 ASP
Chi-restraints excluded: chain A residue 1030 CYS
Chi-restraints excluded: chain A residue 1050 VAL
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1173 ASP
Chi-restraints excluded: chain A residue 1219 VAL
Chi-restraints excluded: chain A residue 1274 VAL
Chi-restraints excluded: chain A residue 1304 THR
Chi-restraints excluded: chain A residue 1308 CYS
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  319 MET
Chi-restraints excluded: chain B residue  336 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 132 optimal weight:    0.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.196142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.156736 restraints weight = 13986.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 2.74
r_work: 0.3328 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11832  Z= 0.157
  Angle     :  0.663   8.708  16079  Z= 0.337
  Chirality :  0.045   0.255   1810
  Planarity :  0.005   0.060   2036
  Dihedral  :  8.956 111.128   1859
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.10 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 18.69 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.22), residues: 1408
  helix: -0.64 (0.21), residues: 589
  sheet: -1.07 (0.38), residues: 187
  loop : -2.25 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1260 
 TYR   0.021   0.002   TYR B 375 
 PHE   0.022   0.002   PHE A 833 
 TRP   0.015   0.001   TRP B 120 
 HIS   0.004   0.001   HIS A 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (11823)
  covalent geometry    : angle       0.64996 (16052)
  hydrogen bonds       : bond        0.04252 (  484)
  hydrogen bonds       : angle       5.31838 ( 1425)
  link_BETA1-4         : bond        0.00440 (    6)
  link_BETA1-4         : angle       3.68574 (   18)
  link_NAG-ASN         : bond        0.00501 (    3)
  link_NAG-ASN         : angle       2.33050 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 129
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  329 ASP cc_start: 0.6775 (m-30) cc_final: 0.6553 (m-30)
REVERT: A  408 GLN cc_start: 0.2332 (OUTLIER) cc_final: 0.1657 (pt0)
REVERT: A  828 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6683 (pp30)
REVERT: A  832 MET cc_start: 0.6548 (mmp) cc_final: 0.6126 (mmt)
REVERT: A 1051 MET cc_start: 0.7718 (mmm) cc_final: 0.7449 (mmt)
REVERT: A 1183 TYR cc_start: 0.8766 (t80) cc_final: 0.7989 (t80)
REVERT: A 1265 MET cc_start: 0.8392 (tpp) cc_final: 0.8091 (tpt)
REVERT: B   78 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8730 (tt)
REVERT: B   91 LYS cc_start: 0.8855 (tptp) cc_final: 0.7991 (mmtm)
REVERT: B   94 PHE cc_start: 0.8483 (m-80) cc_final: 0.8066 (m-10)
REVERT: B  142 ARG cc_start: 0.7578 (mtm180) cc_final: 0.7165 (mtm180)
REVERT: B  161 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8545 (t0)
  outliers start: 62
  outliers final: 40
  residues processed: 181
  average time/residue: 0.0978
  time to fit residues: 26.3287
Evaluate side-chains
  168 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 124
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  408 GLN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  739 ASP
Chi-restraints excluded: chain A residue  811 TYR
Chi-restraints excluded: chain A residue  828 GLN
Chi-restraints excluded: chain A residue  919 THR
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  932 SER
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue  988 ASP
Chi-restraints excluded: chain A residue  989 HIS
Chi-restraints excluded: chain A residue  998 LEU
Chi-restraints excluded: chain A residue 1001 ASP
Chi-restraints excluded: chain A residue 1030 CYS
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1050 VAL
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1219 VAL
Chi-restraints excluded: chain A residue 1274 VAL
Chi-restraints excluded: chain A residue 1308 CYS
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  161 ASN
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  346 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 128 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 81 optimal weight:    0.1980
   chunk 50 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 124 optimal weight:    0.1980
   chunk 38 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 120 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 717 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 = 0.4261 r_free = 0.4261 target = 0.199034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.154075 restraints weight = 13951.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 3.15
r_work: 0.3339 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11832  Z= 0.133
  Angle     :  0.655   8.500  16079  Z= 0.331
  Chirality :  0.045   0.247   1810
  Planarity :  0.005   0.060   2036
  Dihedral  :  8.648 107.880   1859
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.75 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 20.41 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.22), residues: 1408
  helix: -0.46 (0.22), residues: 588
  sheet: -1.03 (0.38), residues: 189
  loop : -2.15 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 870 
 TYR   0.020   0.001   TYR B 375 
 PHE   0.031   0.002   PHE A 833 
 TRP   0.014   0.001   TRP A1279 
 HIS   0.004   0.001   HIS A 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11823)
  covalent geometry    : angle       0.64185 (16052)
  hydrogen bonds       : bond        0.04117 (  484)
  hydrogen bonds       : angle       5.23573 ( 1425)
  link_BETA1-4         : bond        0.00363 (    6)
  link_BETA1-4         : angle       3.55945 (   18)
  link_NAG-ASN         : bond        0.00420 (    3)
  link_NAG-ASN         : angle       2.31702 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 133
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A  329 ASP cc_start: 0.6491 (m-30) cc_final: 0.6239 (m-30)
REVERT: A  597 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8415 (t)
REVERT: A  731 MET cc_start: 0.4620 (ttm) cc_final: 0.4304 (ttm)
REVERT: A  828 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6604 (pp30)
REVERT: A  832 MET cc_start: 0.6572 (mmp) cc_final: 0.6090 (mmt)
REVERT: A 1067 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7647 (mm-30)
REVERT: A 1183 TYR cc_start: 0.8753 (t80) cc_final: 0.7951 (t80)
REVERT: A 1265 MET cc_start: 0.8401 (tpp) cc_final: 0.8106 (tpt)
REVERT: B   94 PHE cc_start: 0.8439 (m-80) cc_final: 0.7984 (m-10)
REVERT: B  142 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7153 (mtm180)
  outliers start: 50
  outliers final: 40
  residues processed: 173
  average time/residue: 0.0983
  time to fit residues: 25.5912
Evaluate side-chains
  169 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 127
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  408 GLN
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  739 ASP
Chi-restraints excluded: chain A residue  828 GLN
Chi-restraints excluded: chain A residue  919 THR
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  932 SER
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue  988 ASP
Chi-restraints excluded: chain A residue  989 HIS
Chi-restraints excluded: chain A residue 1001 ASP
Chi-restraints excluded: chain A residue 1030 CYS
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1050 VAL
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain A residue 1304 THR
Chi-restraints excluded: chain A residue 1308 CYS
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  327 GLU
Chi-restraints excluded: chain B residue  329 GLU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  346 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0020
   chunk 49 optimal weight:    7.9990
   chunk 90 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0470
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.3086

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 717 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 = 0.4293 r_free = 0.4293 target = 0.201849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.161353 restraints weight = 13839.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 2.60
r_work: 0.3431 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11832  Z= 0.112
  Angle     :  0.623   7.814  16079  Z= 0.314
  Chirality :  0.043   0.193   1810
  Planarity :  0.005   0.060   2036
  Dihedral  :  7.987 100.135   1859
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.39 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.07 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.22), residues: 1408
  helix: -0.06 (0.22), residues: 589
  sheet: -0.86 (0.38), residues: 190
  loop : -2.09 (0.24), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1080 
 TYR   0.022   0.001   TYR B 375 
 PHE   0.030   0.001   PHE A 833 
 TRP   0.016   0.001   TRP A1279 
 HIS   0.004   0.001   HIS A 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (11823)
  covalent geometry    : angle       0.61033 (16052)
  hydrogen bonds       : bond        0.03768 (  484)
  hydrogen bonds       : angle       4.99105 ( 1425)
  link_BETA1-4         : bond        0.00393 (    6)
  link_BETA1-4         : angle       3.38449 (   18)
  link_NAG-ASN         : bond        0.00416 (    3)
  link_NAG-ASN         : angle       2.24161 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 140
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  329 ASP cc_start: 0.6524 (m-30) cc_final: 0.6293 (m-30)
REVERT: A  597 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8313 (t)
REVERT: A  731 MET cc_start: 0.4339 (ttm) cc_final: 0.4091 (ttm)
REVERT: A  828 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7288 (mm-40)
REVERT: A 1067 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7564 (mm-30)
REVERT: A 1078 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7642 (mt-10)
REVERT: A 1135 TYR cc_start: 0.8831 (m-80) cc_final: 0.8479 (m-80)
REVERT: A 1183 TYR cc_start: 0.8690 (t80) cc_final: 0.7908 (t80)
REVERT: A 1265 MET cc_start: 0.8333 (tpp) cc_final: 0.8049 (tpt)
REVERT: A 1351 ASP cc_start: 0.5432 (m-30) cc_final: 0.5068 (m-30)
REVERT: B   94 PHE cc_start: 0.8444 (m-80) cc_final: 0.7992 (m-10)
REVERT: B  142 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7142 (mtm180)
  outliers start: 47
  outliers final: 34
  residues processed: 181
  average time/residue: 0.0991
  time to fit residues: 26.2758
Evaluate side-chains
  167 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  828 GLN
Chi-restraints excluded: chain A residue  919 THR
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  932 SER
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  988 ASP
Chi-restraints excluded: chain A residue  989 HIS
Chi-restraints excluded: chain A residue 1001 ASP
Chi-restraints excluded: chain A residue 1030 CYS
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1050 VAL
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain A residue 1274 VAL
Chi-restraints excluded: chain A residue 1286 THR
Chi-restraints excluded: chain A residue 1304 THR
Chi-restraints excluded: chain A residue 1308 CYS
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  319 MET
Chi-restraints excluded: chain B residue  346 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 114 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0030
   chunk 90 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 130 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 717 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 = 0.4273 r_free = 0.4273 target = 0.199741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.153929 restraints weight = 13883.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 3.90
r_work: 0.3377 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11832  Z= 0.134
  Angle     :  0.644  10.563  16079  Z= 0.322
  Chirality :  0.044   0.206   1810
  Planarity :  0.005   0.060   2036
  Dihedral  :  7.809  99.112   1856
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.96 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 21.31 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.22), residues: 1408
  helix: -0.01 (0.22), residues: 592
  sheet: -0.85 (0.39), residues: 184
  loop : -2.04 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1260 
 TYR   0.021   0.001   TYR B 375 
 PHE   0.029   0.002   PHE A 833 
 TRP   0.012   0.001   TRP A1279 
 HIS   0.004   0.001   HIS A 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (11823)
  covalent geometry    : angle       0.63228 (16052)
  hydrogen bonds       : bond        0.03855 (  484)
  hydrogen bonds       : angle       4.98653 ( 1425)
  link_BETA1-4         : bond        0.00356 (    6)
  link_BETA1-4         : angle       3.35276 (   18)
  link_NAG-ASN         : bond        0.00312 (    3)
  link_NAG-ASN         : angle       2.17172 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 126
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A  329 ASP cc_start: 0.5948 (m-30) cc_final: 0.5675 (m-30)
REVERT: A  597 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8409 (t)
REVERT: A 1067 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7643 (mm-30)
REVERT: A 1135 TYR cc_start: 0.8906 (m-80) cc_final: 0.8507 (m-80)
REVERT: A 1183 TYR cc_start: 0.8747 (t80) cc_final: 0.7912 (t80)
REVERT: A 1265 MET cc_start: 0.8356 (tpp) cc_final: 0.8026 (tpt)
REVERT: A 1351 ASP cc_start: 0.5370 (m-30) cc_final: 0.4991 (m-30)
REVERT: B   94 PHE cc_start: 0.8379 (m-80) cc_final: 0.7885 (m-10)
REVERT: B  142 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7087 (mtm180)
  outliers start: 51
  outliers final: 38
  residues processed: 169
  average time/residue: 0.1010
  time to fit residues: 25.0585
Evaluate side-chains
  162 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  739 ASP
Chi-restraints excluded: chain A residue  893 ILE
Chi-restraints excluded: chain A residue  919 THR
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  932 SER
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue  988 ASP
Chi-restraints excluded: chain A residue  989 HIS
Chi-restraints excluded: chain A residue 1030 CYS
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1050 VAL
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1128 SER
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain A residue 1219 VAL
Chi-restraints excluded: chain A residue 1274 VAL
Chi-restraints excluded: chain A residue 1304 THR
Chi-restraints excluded: chain A residue 1308 CYS
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  346 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 127 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 133 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 124 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 549 GLN
A 702 GLN
A 708 HIS
** A 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 782 ASN
A1092 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.195177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.154948 restraints weight = 13845.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.74
r_work: 0.3306 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11832  Z= 0.212
  Angle     :  0.714  10.379  16079  Z= 0.357
  Chirality :  0.047   0.235   1810
  Planarity :  0.005   0.061   2036
  Dihedral  :  8.104 102.573   1856
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.03 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.05 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.22), residues: 1408
  helix: -0.24 (0.22), residues: 593
  sheet: -0.91 (0.39), residues: 184
  loop : -2.07 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1094 
 TYR   0.021   0.002   TYR B 157 
 PHE   0.034   0.002   PHE A 833 
 TRP   0.014   0.002   TRP B 120 
 HIS   0.005   0.001   HIS A 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (11823)
  covalent geometry    : angle       0.70347 (16052)
  hydrogen bonds       : bond        0.04381 (  484)
  hydrogen bonds       : angle       5.14055 ( 1425)
  link_BETA1-4         : bond        0.00398 (    6)
  link_BETA1-4         : angle       3.48241 (   18)
  link_NAG-ASN         : bond        0.00239 (    3)
  link_NAG-ASN         : angle       2.24656 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 121
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  329 ASP cc_start: 0.6485 (m-30) cc_final: 0.6222 (m-30)
REVERT: A  597 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8503 (t)
REVERT: A  731 MET cc_start: 0.4162 (ttm) cc_final: 0.3758 (ttm)
REVERT: A 1067 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7682 (mm-30)
REVERT: A 1096 LEU cc_start: 0.8864 (mm) cc_final: 0.8621 (mm)
REVERT: A 1183 TYR cc_start: 0.8786 (t80) cc_final: 0.8012 (t80)
REVERT: A 1351 ASP cc_start: 0.5445 (m-30) cc_final: 0.5231 (m-30)
  outliers start: 48
  outliers final: 40
  residues processed: 164
  average time/residue: 0.0975
  time to fit residues: 23.9437
Evaluate side-chains
  159 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 118
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  739 ASP
Chi-restraints excluded: chain A residue  919 THR
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  932 SER
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue  988 ASP
Chi-restraints excluded: chain A residue  989 HIS
Chi-restraints excluded: chain A residue 1030 CYS
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1050 VAL
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1128 SER
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain A residue 1219 VAL
Chi-restraints excluded: chain A residue 1274 VAL
Chi-restraints excluded: chain A residue 1304 THR
Chi-restraints excluded: chain A residue 1308 CYS
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  327 GLU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  346 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 137 optimal weight:    0.8980
   chunk 46 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 128 optimal weight:    0.0020
   chunk 139 optimal weight:    0.6980
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 717 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.197785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.151740 restraints weight = 13898.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 4.26
r_work: 0.3318 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11832  Z= 0.163
  Angle     :  0.685  10.323  16079  Z= 0.342
  Chirality :  0.045   0.226   1810
  Planarity :  0.005   0.060   2036
  Dihedral  :  8.027 100.712   1856
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.24 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.38 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.22), residues: 1408
  helix: -0.18 (0.22), residues: 590
  sheet: -0.88 (0.39), residues: 187
  loop : -2.02 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1094 
 TYR   0.021   0.002   TYR B 375 
 PHE   0.034   0.002   PHE A 833 
 TRP   0.011   0.001   TRP A 542 
 HIS   0.005   0.001   HIS A 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (11823)
  covalent geometry    : angle       0.67373 (16052)
  hydrogen bonds       : bond        0.04170 (  484)
  hydrogen bonds       : angle       5.08973 ( 1425)
  link_BETA1-4         : bond        0.00363 (    6)
  link_BETA1-4         : angle       3.40935 (   18)
  link_NAG-ASN         : bond        0.00289 (    3)
  link_NAG-ASN         : angle       2.21207 (    9)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 124
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A  329 ASP cc_start: 0.5997 (m-30) cc_final: 0.5721 (m-30)
REVERT: A  597 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8414 (t)
REVERT: A  731 MET cc_start: 0.4760 (ttm) cc_final: 0.4367 (ttm)
REVERT: A 1067 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7676 (mm-30)
REVERT: A 1078 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7685 (mt-10)
REVERT: A 1183 TYR cc_start: 0.8783 (t80) cc_final: 0.7960 (t80)
REVERT: A 1201 MET cc_start: 0.8214 (mtt) cc_final: 0.8003 (mtt)
REVERT: A 1351 ASP cc_start: 0.5457 (m-30) cc_final: 0.5065 (m-30)
REVERT: B   94 PHE cc_start: 0.8263 (m-10) cc_final: 0.7001 (m-10)
  outliers start: 45
  outliers final: 41
  residues processed: 162
  average time/residue: 0.0906
  time to fit residues: 22.1277
Evaluate side-chains
  162 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  454 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  739 ASP
Chi-restraints excluded: chain A residue  919 THR
Chi-restraints excluded: chain A residue  923 VAL
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  932 SER
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  976 THR
Chi-restraints excluded: chain A residue  988 ASP
Chi-restraints excluded: chain A residue  989 HIS
Chi-restraints excluded: chain A residue 1030 CYS
Chi-restraints excluded: chain A residue 1033 SER
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1050 VAL
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1128 SER
Chi-restraints excluded: chain A residue 1150 LEU
Chi-restraints excluded: chain A residue 1208 SER
Chi-restraints excluded: chain A residue 1219 VAL
Chi-restraints excluded: chain A residue 1274 VAL
Chi-restraints excluded: chain A residue 1304 THR
Chi-restraints excluded: chain A residue 1308 CYS
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  327 GLU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  346 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 73 optimal weight:    0.4980
   chunk 61 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 102 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 127 optimal weight:    1.9990
   chunk 47 optimal weight:   30.0000
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 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 = 0.4257 r_free = 0.4257 target = 0.197929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.160334 restraints weight = 13935.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 2.73
r_work: 0.3351 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11832  Z= 0.145
  Angle     :  0.670  10.157  16079  Z= 0.335
  Chirality :  0.045   0.218   1810
  Planarity :  0.005   0.060   2036
  Dihedral  :  7.917  98.958   1855
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.32 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 22.54 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.22), residues: 1408
  helix: -0.11 (0.22), residues: 593
  sheet: -0.86 (0.39), residues: 187
  loop : -2.02 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1094 
 TYR   0.021   0.001   TYR B 375 
 PHE   0.033   0.002   PHE A 833 
 TRP   0.012   0.001   TRP A1279 
 HIS   0.004   0.001   HIS A 829 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (11823)
  covalent geometry    : angle       0.65950 (16052)
  hydrogen bonds       : bond        0.04038 (  484)
  hydrogen bonds       : angle       5.02852 ( 1425)
  link_BETA1-4         : bond        0.00337 (    6)
  link_BETA1-4         : angle       3.32653 (   18)
  link_NAG-ASN         : bond        0.00313 (    3)
  link_NAG-ASN         : angle       2.21793 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2666.75 seconds
wall clock time: 46 minutes 25.76 seconds (2785.76 seconds total)