Starting phenix.real_space_refine
on Sun May 11 10:31:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f1r_50135/05_2025/9f1r_50135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f1r_50135/05_2025/9f1r_50135.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f1r_50135/05_2025/9f1r_50135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f1r_50135/05_2025/9f1r_50135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f1r_50135/05_2025/9f1r_50135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f1r_50135/05_2025/9f1r_50135.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5092      2.51       5
     N    1292      2.21       5
     O    1430      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7870
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4333
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 12, 'TRANS': 534}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3425
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 413, 3414
          Classifications: {'peptide': 413}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 404}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 413, 3414
          Classifications: {'peptide': 413}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 404}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 3471
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUL': 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: "D"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 60
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      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: 7.46, per 1000 atoms: 0.95
  Number of scatterers: 7870
  At special positions: 0
  Unit cell: (94.9, 146.25, 82.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1430      8.00
     N    1292      7.00
     C    5092      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 141 " - pdb=" SG  CYS A 526 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-6
      " NAG C   1 " - " FUL C   3 "
       ~> Even though FUL is a beta isomer, an alpha linkage is required...
      " BMA D   3 " - " MAN D   4 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    BETA1-6
      " NAG D   1 " - " FUC D   5 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 701 " - " ASN A 441 "
      " NAG C   1 " - " ASN A 491 "
      " NAG D   1 " - " ASN A 516 "
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1786

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      41.5% alpha, 25.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 92 through 103
    Processing helix  chain 'A' and resid 105 through 131
      removed outlier: 4.238A  pdb=" N   ALA A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 168
      removed outlier: 3.681A  pdb=" N   LEU A 156 " --> pdb=" O   MET A 152 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU A 168 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 174 through 194
      removed outlier: 3.548A  pdb=" N   PHE A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 213
    Processing helix  chain 'A' and resid 215 through 225
      removed outlier: 3.554A  pdb=" N   GLU A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 232 through 258
      removed outlier: 3.849A  pdb=" N   ILE A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   PHE A 242 " --> pdb=" O   TRP A 238 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TRP A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER A 256 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 283
    Processing helix  chain 'A' and resid 284 through 294
    Processing helix  chain 'A' and resid 300 through 308
    Processing helix  chain 'A' and resid 309 through 329
    Processing helix  chain 'A' and resid 371 through 381
    Processing helix  chain 'A' and resid 387 through 426
      removed outlier: 3.676A  pdb=" N   TYR A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   VAL A 409 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      Proline residue:  A 412  - end of helix
      removed outlier: 3.844A  pdb=" N   LYS A 426 " --> pdb=" O   GLU A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 507
      No H-bonds generated for 'chain 'A' and resid 505 through 507'
    Processing helix  chain 'A' and resid 538 through 548
    Processing helix  chain 'A' and resid 548 through 558
      removed outlier: 4.308A  pdb=" N   GLY A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE A 554 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ILE A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   SER A 556 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 581
    Processing helix  chain 'A' and resid 582 through 586
    Processing helix  chain 'A' and resid 588 through 603
    Processing helix  chain 'A' and resid 604 through 617
      removed outlier: 3.681A  pdb=" N   LEU A 617 " --> pdb=" O   ILE A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 648
      removed outlier: 3.963A  pdb=" N   ALA A 646 " --> pdb=" O   ASN A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 671
      removed outlier: 3.510A  pdb=" N   ILE A 657 " --> pdb=" O   LYS A 653 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 929 through 933
    Processing helix  chain 'B' and resid 954 through 958
    Processing helix  chain 'B' and resid 1080 through 1093
      removed outlier: 4.205A  pdb=" N   ASN B1093 " --> pdb=" O   ASP B1089 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1266 through 1271
      removed outlier: 3.551A  pdb=" N   ILE B1271 " --> pdb=" O   TYR B1267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1272 through 1274
      No H-bonds generated for 'chain 'B' and resid 1272 through 1274'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 431
      removed outlier: 6.404A  pdb=" N   LYS A 428 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   GLN A 450 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   PHE A 430 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET A 444 " --> pdb=" O   TYR A 463 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 465 " --> pdb=" O   MET A 444 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 467 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ILE A 448 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   PHE A 469 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   GLN A 450 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 428 through 431
      removed outlier: 6.404A  pdb=" N   LYS A 428 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   GLN A 450 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   PHE A 430 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET A 444 " --> pdb=" O   TYR A 463 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 465 " --> pdb=" O   MET A 444 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 467 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ILE A 448 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   PHE A 469 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   GLN A 450 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   TYR A 488 " --> pdb=" O   LYS A 465 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   VAL A 467 " --> pdb=" O   TYR A 488 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   LYS A 490 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   PHE A 469 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   PHE A 489 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 434 through 436
      removed outlier: 5.773A  pdb=" N   VAL A 435 " --> pdb=" O   VAL A 455 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU A 454 " --> pdb=" O   ASP A 475 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 439 through 440
      removed outlier: 6.281A  pdb=" N   PHE A 459 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE A 499 " --> pdb=" O   THR A 518 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   SER A 517 " --> pdb=" O   MET B1144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 495
    Processing sheet with id=AA6, first strand: chain 'B' and resid 888 through 890
      removed outlier: 4.239A  pdb=" N   PHE B1072 " --> pdb=" O   LEU B 881 " (cutoff:3.500A)
      removed outlier: 9.865A  pdb=" N   TYR B 883 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 11.807A  pdb=" N   LYS B1070 " --> pdb=" O   TYR B 883 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 888 through 890
      removed outlier: 4.239A  pdb=" N   PHE B1072 " --> pdb=" O   LEU B 881 " (cutoff:3.500A)
      removed outlier: 9.865A  pdb=" N   TYR B 883 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 11.807A  pdb=" N   LYS B1070 " --> pdb=" O   TYR B 883 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   PHE B1072 " --> pdb=" O   SER B 944 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   SER B 944 " --> pdb=" O   PHE B1072 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   LEU B1074 " --> pdb=" O   SER B 942 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   SER B 942 " --> pdb=" O   LEU B1074 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   ILE B1031 " --> pdb=" O   LEU B1035 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   LEU B1035 " --> pdb=" O   ILE B1031 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 897 through 900
    Processing sheet with id=AA9, first strand: chain 'B' and resid 897 through 900
      removed outlier: 9.905A  pdb=" N   ASN B1052 " --> pdb=" O   GLU B 969 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   GLU B 969 " --> pdb=" O   ASN B1052 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   MET B1054 " --> pdb=" O   CYS B 967 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   CYS B 967 " --> pdb=" O   MET B1054 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   LYS B1056 " --> pdb=" O   ILE B 965 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ILE B 965 " --> pdb=" O   LYS B1056 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   THR B 963 " --> pdb=" O   LEU B 978 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   LEU B 978 " --> pdb=" O   THR B 963 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1112 through 1115
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1122 through 1126
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1159 through 1164
      removed outlier: 4.050A  pdb=" N   LYS B1159 " --> pdb=" O   VAL B1185 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   ILE B1182 " --> pdb=" O   LEU B1193 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 1159 through 1164
      removed outlier: 4.050A  pdb=" N   LYS B1159 " --> pdb=" O   VAL B1185 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP B1178 " --> pdb=" O   MET B1223 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   MET B1237 " --> pdb=" O   ILE B1250 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1116 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.96

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2447
        1.34 -     1.46: 2076
        1.46 -     1.58: 3444
        1.58 -     1.70: 0
        1.70 -     1.82: 93
  Bond restraints: 8060
  Sorted by residual:
  bond pdb=" C1  FUL C   3 "
       pdb=" O5  FUL C   3 "
    ideal  model  delta    sigma   weight residual
    1.392  1.428 -0.036 2.00e-02 2.50e+03 3.27e+00
  bond pdb=" N   ASN A 491 "
       pdb=" CA  ASN A 491 "
    ideal  model  delta    sigma   weight residual
    1.462  1.490 -0.028 1.54e-02 4.22e+03 3.23e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.39e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" C1  FUL C   3 "
       pdb=" C2  FUL C   3 "
    ideal  model  delta    sigma   weight residual
    1.534  1.505  0.029 2.00e-02 2.50e+03 2.13e+00
  ... (remaining 8055 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 10729
        2.13 -     4.26: 136
        4.26 -     6.39: 23
        6.39 -     8.52: 1
        8.52 -    10.65: 4
  Bond angle restraints: 10893
  Sorted by residual:
  angle pdb=" CB  MET A 267 "
        pdb=" CG  MET A 267 "
        pdb=" SD  MET A 267 "
      ideal   model   delta    sigma   weight residual
     112.70  122.12   -9.42 3.00e+00 1.11e-01 9.87e+00
  angle pdb=" CA  LEU B1278 "
        pdb=" CB  LEU B1278 "
        pdb=" CG  LEU B1278 "
      ideal   model   delta    sigma   weight residual
     116.30  126.95  -10.65 3.50e+00 8.16e-02 9.26e+00
  angle pdb=" CA  LEU A 583 "
        pdb=" CB  LEU A 583 "
        pdb=" CG  LEU A 583 "
      ideal   model   delta    sigma   weight residual
     116.30  126.75  -10.45 3.50e+00 8.16e-02 8.92e+00
  angle pdb=" CA  ASN A 491 "
        pdb=" C   ASN A 491 "
        pdb=" O   ASN A 491 "
      ideal   model   delta    sigma   weight residual
     121.08  117.54    3.54 1.25e+00 6.40e-01 8.01e+00
  angle pdb=" CA  LEU A 540 "
        pdb=" CB  LEU A 540 "
        pdb=" CG  LEU A 540 "
      ideal   model   delta    sigma   weight residual
     116.30  126.06   -9.76 3.50e+00 8.16e-02 7.77e+00
  ... (remaining 10888 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.07: 4353
       24.07 -    48.13: 394
       48.13 -    72.20: 62
       72.20 -    96.26: 11
       96.26 -   120.32: 5
  Dihedral angle restraints: 4825
    sinusoidal: 2032
      harmonic: 2793
  Sorted by residual:
  dihedral pdb=" CB  CYS A 141 "
           pdb=" SG  CYS A 141 "
           pdb=" SG  CYS A 526 "
           pdb=" CB  CYS A 526 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.39   81.39     1      1.00e+01 1.00e-02 8.16e+01
  dihedral pdb=" C2  FUC D   5 "
           pdb=" C1  FUC D   5 "
           pdb=" O5  FUC D   5 "
           pdb=" C5  FUC D   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.68  -62.64  120.32     1      3.00e+01 1.11e-03 1.61e+01
  dihedral pdb=" O4  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  177.92  110.79     1      3.00e+01 1.11e-03 1.45e+01
  ... (remaining 4822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1186
       0.118 -    0.235: 16
       0.235 -    0.353: 1
       0.353 -    0.471: 0
       0.471 -    0.589: 1
  Chirality restraints: 1204
  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   -2.26   -0.14 2.00e-02 2.50e+03 4.72e+01
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 441 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.81   -0.59 2.00e-01 2.50e+01 8.66e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.53    0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 1201 not shown)

  Planarity restraints: 1361
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.183 2.00e-02 2.50e+03   1.52e-01 2.87e+02
        pdb=" C7  NAG C   1 "    0.049 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "   -0.133 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.247 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "    0.044 2.00e-02 2.50e+03   3.67e-02 1.68e+01
        pdb=" C7  NAG C   2 "   -0.015 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.035 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "   -0.057 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 273 "   -0.021 2.00e-02 2.50e+03   2.71e-02 1.28e+01
        pdb=" CG  PHE A 273 "    0.062 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 273 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 273 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 273 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 273 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 273 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1358 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 83
        2.61 -     3.18: 6954
        3.18 -     3.75: 12107
        3.75 -     4.33: 16634
        4.33 -     4.90: 27735
  Nonbonded interactions: 63513
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 222 "
            pdb=" O   PRO A 298 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" OG  SER A 181 "
            pdb=" O   GLY A 211 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   SER A 603 "
            pdb=" OG  SER A 603 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   SER A 190 "
            pdb=" OG  SER A 193 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OE2 GLU A 137 "
            pdb=" OH  TYR A 198 "
     model   vdw
     2.228 3.040
  ... (remaining 63508 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     24.400
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
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      :  0.004   0.049   8070  Z= 0.174
  Angle     :  0.673  14.770  10922  Z= 0.334
  Chirality :  0.046   0.589   1204
  Planarity :  0.005   0.152   1358
  Dihedral  : 17.911 120.325   3036
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 27.28 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.27), residues: 952
  helix:  0.60 (0.28), residues: 368
  sheet: -0.10 (0.44), residues: 130
  loop : -1.16 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 985 
 HIS   0.003   0.001   HIS B1064 
 PHE   0.062   0.002   PHE A 273 
 TYR   0.021   0.001   TYR B1117 
 ARG   0.005   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01025 (    3)
  link_NAG-ASN         : angle       6.01584 (    9)
  link_ALPHA1-6        : bond        0.02705 (    2)
  link_ALPHA1-6        : angle       2.96634 (    6)
  link_BETA1-4         : bond        0.02888 (    3)
  link_BETA1-4         : angle       2.97735 (    9)
  hydrogen bonds       : bond        0.15109 (  383)
  hydrogen bonds       : angle       6.48409 ( 1116)
  link_BETA1-6         : bond        0.00117 (    1)
  link_BETA1-6         : angle       1.76097 (    3)
  SS BOND              : bond        0.00355 (    1)
  SS BOND              : angle       1.49664 (    2)
  covalent geometry    : bond        0.00361 ( 8060)
  covalent geometry    : angle       0.64135 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.823 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 113
  average time/residue: 0.1456
  time to fit residues: 24.5795
Evaluate side-chains
  105 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 447 GLN
A 522 GLN
** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 913 GLN
B 935 ASN
B1026 ASN
B1115 ASN
B1270 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.152591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.128152 restraints weight = 33994.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.132607 restraints weight = 22889.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.136965 restraints weight = 11296.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3762 r_free = 0.3762    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3762 r_free = 0.3762    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.0775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8070  Z= 0.156
  Angle     :  0.614  13.424  10922  Z= 0.312
  Chirality :  0.045   0.522   1204
  Planarity :  0.003   0.036   1358
  Dihedral  :  9.526 102.393   1224
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 24.56 %
    Favored  : 72.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.27), residues: 952
  helix:  1.03 (0.27), residues: 366
  sheet: -0.16 (0.43), residues: 130
  loop : -0.99 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 255 
 HIS   0.004   0.001   HIS A 235 
 PHE   0.020   0.001   PHE B1284 
 TYR   0.016   0.001   TYR B1030 
 ARG   0.004   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00764 (    3)
  link_NAG-ASN         : angle       5.27358 (    9)
  link_ALPHA1-6        : bond        0.00815 (    2)
  link_ALPHA1-6        : angle       1.51198 (    6)
  link_BETA1-4         : bond        0.00484 (    3)
  link_BETA1-4         : angle       2.03620 (    9)
  hydrogen bonds       : bond        0.05134 (  383)
  hydrogen bonds       : angle       5.01866 ( 1116)
  link_BETA1-6         : bond        0.00759 (    1)
  link_BETA1-6         : angle       2.17536 (    3)
  SS BOND              : bond        0.00388 (    1)
  SS BOND              : angle       1.16262 (    2)
  covalent geometry    : bond        0.00345 ( 8060)
  covalent geometry    : angle       0.59051 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  615 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8485 (p)
  outliers start: 29
  outliers final: 20
  residues processed: 126
  average time/residue: 0.1499
  time to fit residues: 28.1421
Evaluate side-chains
  124 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 449 HIS
** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.151137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.127176 restraints weight = 20406.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.130876 restraints weight = 10951.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133322 restraints weight = 8079.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3740 r_free = 0.3740    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3740 r_free = 0.3740    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8070  Z= 0.180
  Angle     :  0.615  13.232  10922  Z= 0.312
  Chirality :  0.046   0.498   1204
  Planarity :  0.003   0.028   1358
  Dihedral  :  8.593  96.096   1222
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 24.08 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.27), residues: 952
  helix:  1.09 (0.27), residues: 366
  sheet: -0.20 (0.43), residues: 130
  loop : -0.94 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 255 
 HIS   0.005   0.001   HIS A 235 
 PHE   0.018   0.002   PHE B1284 
 TYR   0.015   0.001   TYR B1030 
 ARG   0.003   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00826 (    3)
  link_NAG-ASN         : angle       5.20327 (    9)
  link_ALPHA1-6        : bond        0.00728 (    2)
  link_ALPHA1-6        : angle       1.41576 (    6)
  link_BETA1-4         : bond        0.00466 (    3)
  link_BETA1-4         : angle       1.93242 (    9)
  hydrogen bonds       : bond        0.04877 (  383)
  hydrogen bonds       : angle       4.92390 ( 1116)
  link_BETA1-6         : bond        0.00367 (    1)
  link_BETA1-6         : angle       2.48574 (    3)
  SS BOND              : bond        0.00366 (    1)
  SS BOND              : angle       0.90686 (    2)
  covalent geometry    : bond        0.00412 ( 8060)
  covalent geometry    : angle       0.59185 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 106
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8260 (t80)
REVERT: A  615 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8556 (p)
  outliers start: 40
  outliers final: 28
  residues processed: 133
  average time/residue: 0.1625
  time to fit residues: 31.9647
Evaluate side-chains
  131 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain B residue 1044 LEU
Chi-restraints excluded: chain B residue 1174 VAL
Chi-restraints excluded: chain B residue 1196 ASN
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.154031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.129441 restraints weight = 28420.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.135140 restraints weight = 17580.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.136921 restraints weight = 9941.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3756 r_free = 0.3756    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3756 r_free = 0.3756    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8070  Z= 0.142
  Angle     :  0.593  12.595  10922  Z= 0.296
  Chirality :  0.045   0.484   1204
  Planarity :  0.003   0.027   1358
  Dihedral  :  7.717  87.691   1222
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 25.50 %
    Favored  : 69.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.28), residues: 952
  helix:  1.12 (0.28), residues: 368
  sheet: -0.08 (0.43), residues: 130
  loop : -0.91 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 235 
 PHE   0.017   0.001   PHE A 188 
 TYR   0.017   0.001   TYR B1117 
 ARG   0.003   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00800 (    3)
  link_NAG-ASN         : angle       4.97894 (    9)
  link_ALPHA1-6        : bond        0.00931 (    2)
  link_ALPHA1-6        : angle       1.31788 (    6)
  link_BETA1-4         : bond        0.00439 (    3)
  link_BETA1-4         : angle       1.77922 (    9)
  hydrogen bonds       : bond        0.04414 (  383)
  hydrogen bonds       : angle       4.76946 ( 1116)
  link_BETA1-6         : bond        0.00914 (    1)
  link_BETA1-6         : angle       2.63501 (    3)
  SS BOND              : bond        0.00292 (    1)
  SS BOND              : angle       0.94418 (    2)
  covalent geometry    : bond        0.00314 ( 8060)
  covalent geometry    : angle       0.57182 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 108
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8505 (ttp) cc_final: 0.8287 (ttm)
REVERT: A  152 MET cc_start: 0.7950 (mmp) cc_final: 0.7669 (mmt)
REVERT: A  249 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8219 (t80)
REVERT: A  372 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7210 (ptmm)
REVERT: A  615 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8464 (p)
  outliers start: 38
  outliers final: 29
  residues processed: 134
  average time/residue: 0.1623
  time to fit residues: 31.8379
Evaluate side-chains
  134 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  581 PHE
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain B residue  990 THR
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain B residue 1174 VAL
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0980
   chunk 20 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   overall best weight:    1.1382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.150178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.125930 restraints weight = 33233.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.130858 restraints weight = 21146.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.132903 restraints weight = 10990.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3736 r_free = 0.3736    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8070  Z= 0.163
  Angle     :  0.605  12.363  10922  Z= 0.301
  Chirality :  0.045   0.470   1204
  Planarity :  0.003   0.027   1358
  Dihedral  :  7.298  80.971   1222
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 24.20 %
    Favored  : 70.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.27), residues: 952
  helix:  1.13 (0.28), residues: 367
  sheet: -0.11 (0.43), residues: 130
  loop : -0.95 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 235 
 PHE   0.016   0.001   PHE A 188 
 TYR   0.017   0.001   TYR B1117 
 ARG   0.002   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00793 (    3)
  link_NAG-ASN         : angle       4.89421 (    9)
  link_ALPHA1-6        : bond        0.00899 (    2)
  link_ALPHA1-6        : angle       1.27260 (    6)
  link_BETA1-4         : bond        0.00393 (    3)
  link_BETA1-4         : angle       1.65001 (    9)
  hydrogen bonds       : bond        0.04443 (  383)
  hydrogen bonds       : angle       4.77971 ( 1116)
  link_BETA1-6         : bond        0.00947 (    1)
  link_BETA1-6         : angle       2.87792 (    3)
  SS BOND              : bond        0.00304 (    1)
  SS BOND              : angle       0.93958 (    2)
  covalent geometry    : bond        0.00370 ( 8060)
  covalent geometry    : angle       0.58423 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 106
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8195 (t80)
REVERT: A  372 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7211 (ptmm)
REVERT: A  568 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6905 (ttm)
REVERT: A  615 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8484 (p)
REVERT: A  651 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7335 (pt)
  outliers start: 44
  outliers final: 33
  residues processed: 137
  average time/residue: 0.1659
  time to fit residues: 33.3974
Evaluate side-chains
  141 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 103
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  581 PHE
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain B residue  990 THR
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain B residue 1044 LEU
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1174 VAL
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 79 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 74 optimal weight:    0.1980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.155839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.131283 restraints weight = 26477.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.136240 restraints weight = 16750.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.137457 restraints weight = 11090.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8070  Z= 0.121
  Angle     :  0.579  11.939  10922  Z= 0.290
  Chirality :  0.044   0.460   1204
  Planarity :  0.003   0.027   1358
  Dihedral  :  6.511  63.275   1222
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 25.62 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.28), residues: 952
  helix:  1.27 (0.28), residues: 367
  sheet:  0.02 (0.44), residues: 130
  loop : -0.83 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 274 
 PHE   0.018   0.001   PHE A 203 
 TYR   0.018   0.001   TYR B1117 
 ARG   0.003   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00793 (    3)
  link_NAG-ASN         : angle       4.72832 (    9)
  link_ALPHA1-6        : bond        0.00988 (    2)
  link_ALPHA1-6        : angle       1.23279 (    6)
  link_BETA1-4         : bond        0.00478 (    3)
  link_BETA1-4         : angle       1.47233 (    9)
  hydrogen bonds       : bond        0.04012 (  383)
  hydrogen bonds       : angle       4.66621 ( 1116)
  link_BETA1-6         : bond        0.01515 (    1)
  link_BETA1-6         : angle       2.66059 (    3)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.44365 (    2)
  covalent geometry    : bond        0.00258 ( 8060)
  covalent geometry    : angle       0.55975 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8126 (t80)
REVERT: A  372 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7237 (ptmm)
REVERT: A  568 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6748 (ttm)
REVERT: B 1196 ASN cc_start: 0.5914 (OUTLIER) cc_final: 0.5532 (m-40)
  outliers start: 34
  outliers final: 24
  residues processed: 135
  average time/residue: 0.1576
  time to fit residues: 31.0042
Evaluate side-chains
  133 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  581 PHE
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue 1044 LEU
Chi-restraints excluded: chain B residue 1196 ASN
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0470
   overall best weight:    0.7080

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.154096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.129353 restraints weight = 31722.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.134968 restraints weight = 20120.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.136301 restraints weight = 11418.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8070  Z= 0.135
  Angle     :  0.609  11.781  10922  Z= 0.302
  Chirality :  0.044   0.450   1204
  Planarity :  0.003   0.029   1358
  Dihedral  :  6.069  55.257   1222
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 24.91 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.28), residues: 952
  helix:  1.29 (0.28), residues: 362
  sheet:  0.07 (0.44), residues: 130
  loop : -0.81 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.013   0.001   PHE A 188 
 TYR   0.018   0.001   TYR B1117 
 ARG   0.002   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00781 (    3)
  link_NAG-ASN         : angle       4.65630 (    9)
  link_ALPHA1-6        : bond        0.00999 (    2)
  link_ALPHA1-6        : angle       1.25042 (    6)
  link_BETA1-4         : bond        0.00492 (    3)
  link_BETA1-4         : angle       1.39917 (    9)
  hydrogen bonds       : bond        0.04036 (  383)
  hydrogen bonds       : angle       4.66501 ( 1116)
  link_BETA1-6         : bond        0.01467 (    1)
  link_BETA1-6         : angle       2.36539 (    3)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       0.96122 (    2)
  covalent geometry    : bond        0.00298 ( 8060)
  covalent geometry    : angle       0.59175 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8152 (t80)
REVERT: A  372 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7268 (ptmm)
REVERT: A  568 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6798 (ttm)
REVERT: A  615 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8390 (p)
REVERT: B 1196 ASN cc_start: 0.6056 (OUTLIER) cc_final: 0.5733 (m-40)
  outliers start: 40
  outliers final: 29
  residues processed: 133
  average time/residue: 0.1575
  time to fit residues: 30.6468
Evaluate side-chains
  137 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  311 ASP
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  581 PHE
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain B residue  990 THR
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue 1044 LEU
Chi-restraints excluded: chain B residue 1174 VAL
Chi-restraints excluded: chain B residue 1196 ASN
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.152244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.127842 restraints weight = 31815.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.132640 restraints weight = 20473.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.135798 restraints weight = 11253.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3770 r_free = 0.3770    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3770 r_free = 0.3770    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8070  Z= 0.137
  Angle     :  0.591  11.581  10922  Z= 0.293
  Chirality :  0.044   0.442   1204
  Planarity :  0.003   0.029   1358
  Dihedral  :  5.743  55.355   1222
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 24.44 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.28), residues: 952
  helix:  1.28 (0.28), residues: 367
  sheet: -0.01 (0.44), residues: 133
  loop : -0.82 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 255 
 HIS   0.002   0.000   HIS A 235 
 PHE   0.018   0.001   PHE A 203 
 TYR   0.019   0.001   TYR B1117 
 ARG   0.002   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00755 (    3)
  link_NAG-ASN         : angle       4.58478 (    9)
  link_ALPHA1-6        : bond        0.00929 (    2)
  link_ALPHA1-6        : angle       1.26282 (    6)
  link_BETA1-4         : bond        0.00454 (    3)
  link_BETA1-4         : angle       1.29586 (    9)
  hydrogen bonds       : bond        0.04031 (  383)
  hydrogen bonds       : angle       4.63594 ( 1116)
  link_BETA1-6         : bond        0.01588 (    1)
  link_BETA1-6         : angle       2.10546 (    3)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.35324 (    2)
  covalent geometry    : bond        0.00305 ( 8060)
  covalent geometry    : angle       0.57383 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8174 (t80)
REVERT: A  372 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7223 (ptmm)
REVERT: A  568 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6841 (ttm)
REVERT: A  615 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8510 (p)
REVERT: B 1255 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.6412 (m-80)
  outliers start: 39
  outliers final: 30
  residues processed: 132
  average time/residue: 0.1493
  time to fit residues: 29.2548
Evaluate side-chains
  141 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  311 ASP
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  581 PHE
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain B residue  990 THR
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue 1044 LEU
Chi-restraints excluded: chain B residue 1174 VAL
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 68 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 87 optimal weight:    0.2980
   chunk 20 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0370
   chunk 37 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.4860

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.155240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.130385 restraints weight = 19241.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.136105 restraints weight = 11268.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.138872 restraints weight = 6710.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3808 r_free = 0.3808    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3808 r_free = 0.3808    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8070  Z= 0.119
  Angle     :  0.589  11.324  10922  Z= 0.294
  Chirality :  0.043   0.437   1204
  Planarity :  0.003   0.028   1358
  Dihedral  :  5.462  55.622   1222
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 24.79 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.28), residues: 952
  helix:  1.31 (0.28), residues: 367
  sheet:  0.04 (0.44), residues: 133
  loop : -0.80 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 255 
 HIS   0.003   0.000   HIS A 272 
 PHE   0.014   0.001   PHE A 398 
 TYR   0.018   0.001   TYR B1117 
 ARG   0.002   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00773 (    3)
  link_NAG-ASN         : angle       4.49016 (    9)
  link_ALPHA1-6        : bond        0.00931 (    2)
  link_ALPHA1-6        : angle       1.24813 (    6)
  link_BETA1-4         : bond        0.00494 (    3)
  link_BETA1-4         : angle       1.22501 (    9)
  hydrogen bonds       : bond        0.03816 (  383)
  hydrogen bonds       : angle       4.58705 ( 1116)
  link_BETA1-6         : bond        0.01668 (    1)
  link_BETA1-6         : angle       1.73191 (    3)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.45266 (    2)
  covalent geometry    : bond        0.00255 ( 8060)
  covalent geometry    : angle       0.57279 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8106 (t80)
REVERT: A  372 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7224 (ptmm)
REVERT: A  532 GLN cc_start: 0.8178 (mt0) cc_final: 0.7766 (mp10)
REVERT: A  568 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6740 (ttm)
REVERT: B 1255 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.6338 (m-80)
  outliers start: 34
  outliers final: 28
  residues processed: 129
  average time/residue: 0.1588
  time to fit residues: 30.3563
Evaluate side-chains
  136 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  581 PHE
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue 1044 LEU
Chi-restraints excluded: chain B residue 1174 VAL
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 22 optimal weight:    0.1980
   chunk 5 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 92 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.155280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.132150 restraints weight = 19566.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.135552 restraints weight = 12392.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.136851 restraints weight = 7942.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8070  Z= 0.124
  Angle     :  0.592  11.147  10922  Z= 0.293
  Chirality :  0.043   0.428   1204
  Planarity :  0.003   0.028   1358
  Dihedral  :  5.248  55.437   1222
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 24.91 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.28), residues: 952
  helix:  1.30 (0.28), residues: 367
  sheet:  0.05 (0.44), residues: 133
  loop : -0.79 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 255 
 HIS   0.003   0.000   HIS A 507 
 PHE   0.025   0.001   PHE A 112 
 TYR   0.019   0.001   TYR B1117 
 ARG   0.002   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00761 (    3)
  link_NAG-ASN         : angle       4.41787 (    9)
  link_ALPHA1-6        : bond        0.00908 (    2)
  link_ALPHA1-6        : angle       1.26809 (    6)
  link_BETA1-4         : bond        0.00493 (    3)
  link_BETA1-4         : angle       1.21162 (    9)
  hydrogen bonds       : bond        0.03823 (  383)
  hydrogen bonds       : angle       4.58744 ( 1116)
  link_BETA1-6         : bond        0.01397 (    1)
  link_BETA1-6         : angle       1.47391 (    3)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.89929 (    2)
  covalent geometry    : bond        0.00270 ( 8060)
  covalent geometry    : angle       0.57613 (10893)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 0.859 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8076 (t80)
REVERT: A  372 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7266 (ptmm)
REVERT: A  568 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6876 (ttm)
REVERT: B 1255 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6388 (m-80)
  outliers start: 35
  outliers final: 30
  residues processed: 133
  average time/residue: 0.1500
  time to fit residues: 29.6409
Evaluate side-chains
  140 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  196 GLN
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  309 LYS
Chi-restraints excluded: chain A residue  311 ASP
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  581 PHE
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain B residue  994 LYS
Chi-restraints excluded: chain B residue 1044 LEU
Chi-restraints excluded: chain B residue 1174 VAL
Chi-restraints excluded: chain B residue 1255 PHE
Chi-restraints excluded: chain B residue 1278 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 2 optimal weight:    0.3980
   chunk 72 optimal weight:    5.9990
   chunk 73 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0980
   overall best weight:    0.4518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.156447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.131829 restraints weight = 31410.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.137547 restraints weight = 19902.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.139336 restraints weight = 10821.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3802 r_free = 0.3802    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3802 r_free = 0.3802    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8070  Z= 0.113
  Angle     :  0.579  10.909  10922  Z= 0.285
  Chirality :  0.043   0.422   1204
  Planarity :  0.002   0.029   1358
  Dihedral  :  5.155  55.382   1222
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 25.03 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.28), residues: 952
  helix:  1.32 (0.28), residues: 368
  sheet:  0.09 (0.44), residues: 135
  loop : -0.76 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 255 
 HIS   0.003   0.000   HIS A 274 
 PHE   0.021   0.001   PHE A 112 
 TYR   0.018   0.001   TYR B1117 
 ARG   0.002   0.000   ARG A 174 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00767 (    3)
  link_NAG-ASN         : angle       4.32369 (    9)
  link_ALPHA1-6        : bond        0.00821 (    2)
  link_ALPHA1-6        : angle       1.26040 (    6)
  link_BETA1-4         : bond        0.00486 (    3)
  link_BETA1-4         : angle       1.17317 (    9)
  hydrogen bonds       : bond        0.03664 (  383)
  hydrogen bonds       : angle       4.55620 ( 1116)
  link_BETA1-6         : bond        0.01232 (    1)
  link_BETA1-6         : angle       1.33970 (    3)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.69999 (    2)
  covalent geometry    : bond        0.00242 ( 8060)
  covalent geometry    : angle       0.56380 (10893)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3099.00 seconds
wall clock time: 54 minutes 55.65 seconds (3295.65 seconds total)