Starting phenix.real_space_refine
on Fri Aug 22 21:04:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f1r_50135/08_2025/9f1r_50135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f1r_50135/08_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_50135/08_2025/9f1r_50135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f1r_50135/08_2025/9f1r_50135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f1r_50135/08_2025/9f1r_50135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f1r_50135/08_2025/9f1r_50135.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.30, per 1000 atoms: 0.29
  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: 0.68
  Conformation dependent library (CDL) restraints added in 332.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.26
  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: 1.37

  Time building geometry restraints manager: 0.85 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:             7.380
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.640
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.500
-------------------------------------------------------------------------------
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 : 12.62
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.000   ARG A 174 
 TYR   0.021   0.001   TYR B1117 
 PHE   0.062   0.002   PHE A 273 
 TRP   0.011   0.001   TRP B 985 
 HIS   0.003   0.001   HIS B1064 

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

*********************** 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  : 0.292 
Fit side-chains
REVERT: A  139 ASP cc_start: 0.7862 (t70) cc_final: 0.7512 (p0)
REVERT: A  142 LEU cc_start: 0.8812 (mt) cc_final: 0.8001 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 113
  average time/residue: 0.0625
  time to fit residues: 10.7288
Evaluate side-chains
  106 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3993 r_free = 0.3993 target = 0.153154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.128473 restraints weight = 26394.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.132582 restraints weight = 15756.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.134320 restraints weight = 11259.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135661 restraints weight = 7804.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.139111 restraints weight = 6664.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3800
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3800 r_free = 0.3800    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 = 0.3800 r_free = 0.3800    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3800
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.0731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8070  Z= 0.146
  Angle     :  0.605  13.594  10922  Z= 0.308
  Chirality :  0.045   0.512   1204
  Planarity :  0.003   0.032   1358
  Dihedral  :  9.674 103.593   1224
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 24.91 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.27), residues: 952
  helix:  1.06 (0.27), residues: 366
  sheet: -0.11 (0.43), residues: 130
  loop : -0.98 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 174 
 TYR   0.016   0.001   TYR B1030 
 PHE   0.019   0.001   PHE B1284 
 TRP   0.019   0.001   TRP A 255 
 HIS   0.004   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8060)
  covalent geometry    : angle       0.58100 (10893)
  SS BOND              : bond        0.00320 (    1)
  SS BOND              : angle       1.14912 (    2)
  hydrogen bonds       : bond        0.05245 (  383)
  hydrogen bonds       : angle       5.02796 ( 1116)
  link_ALPHA1-6        : bond        0.00865 (    2)
  link_ALPHA1-6        : angle       1.53115 (    6)
  link_BETA1-4         : bond        0.00499 (    3)
  link_BETA1-4         : angle       2.00999 (    9)
  link_BETA1-6         : bond        0.00698 (    1)
  link_BETA1-6         : angle       2.06114 (    3)
  link_NAG-ASN         : bond        0.00833 (    3)
  link_NAG-ASN         : angle       5.33583 (    9)

*********************** 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
  133 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  615 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8424 (p)
  outliers start: 27
  outliers final: 18
  residues processed: 122
  average time/residue: 0.0546
  time to fit residues: 10.2532
Evaluate side-chains
  123 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0470
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7080

-------------------------------------------------------------------------------
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 = 0.4006 r_free = 0.4006 target = 0.154198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.129211 restraints weight = 30645.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135001 restraints weight = 18530.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.136620 restraints weight = 10571.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137789 restraints weight = 7396.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.142239 restraints weight = 6259.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1028

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= 0.129
  Angle     :  0.579  13.030  10922  Z= 0.292
  Chirality :  0.044   0.488   1204
  Planarity :  0.003   0.026   1358
  Dihedral  :  8.283  93.608   1222
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 23.96 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.28), residues: 952
  helix:  1.27 (0.28), residues: 362
  sheet: -0.04 (0.44), residues: 130
  loop : -0.80 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 174 
 TYR   0.015   0.001   TYR B1117 
 PHE   0.015   0.001   PHE B1284 
 TRP   0.031   0.001   TRP A 255 
 HIS   0.005   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8060)
  covalent geometry    : angle       0.55598 (10893)
  SS BOND              : bond        0.00077 (    1)
  SS BOND              : angle       0.28942 (    2)
  hydrogen bonds       : bond        0.04475 (  383)
  hydrogen bonds       : angle       4.79280 ( 1116)
  link_ALPHA1-6        : bond        0.00881 (    2)
  link_ALPHA1-6        : angle       1.37608 (    6)
  link_BETA1-4         : bond        0.00434 (    3)
  link_BETA1-4         : angle       1.93598 (    9)
  link_BETA1-6         : bond        0.00720 (    1)
  link_BETA1-6         : angle       2.38134 (    3)
  link_NAG-ASN         : bond        0.00829 (    3)
  link_NAG-ASN         : angle       5.10217 (    9)

*********************** 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
  148 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 112
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8224 (t80)
REVERT: A  592 MET cc_start: 0.7790 (tpp) cc_final: 0.7387 (tpt)
  outliers start: 36
  outliers final: 23
  residues processed: 136
  average time/residue: 0.0543
  time to fit residues: 10.9986
Evaluate side-chains
  129 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  639 ILE
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 1231 ILE
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 24 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   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 449 HIS
A 553 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.153339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.129575 restraints weight = 21813.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.133895 restraints weight = 11874.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.135321 restraints weight = 8467.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.136334 restraints weight = 6506.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.137053 restraints weight = 5829.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3778 r_free = 0.3778    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 = 0.3778 r_free = 0.3778    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1227

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= 0.143
  Angle     :  0.607  12.528  10922  Z= 0.300
  Chirality :  0.045   0.476   1204
  Planarity :  0.003   0.026   1358
  Dihedral  :  7.618  86.743   1222
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 23.96 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.28), residues: 952
  helix:  1.12 (0.27), residues: 368
  sheet:  0.00 (0.44), residues: 130
  loop : -0.85 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 174 
 TYR   0.017   0.001   TYR B1117 
 PHE   0.017   0.001   PHE A 188 
 TRP   0.029   0.001   TRP A 255 
 HIS   0.004   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8060)
  covalent geometry    : angle       0.58566 (10893)
  SS BOND              : bond        0.00265 (    1)
  SS BOND              : angle       0.70724 (    2)
  hydrogen bonds       : bond        0.04359 (  383)
  hydrogen bonds       : angle       4.74022 ( 1116)
  link_ALPHA1-6        : bond        0.00905 (    2)
  link_ALPHA1-6        : angle       1.29191 (    6)
  link_BETA1-4         : bond        0.00461 (    3)
  link_BETA1-4         : angle       1.78272 (    9)
  link_BETA1-6         : bond        0.00942 (    1)
  link_BETA1-6         : angle       2.72113 (    3)
  link_NAG-ASN         : bond        0.00814 (    3)
  link_NAG-ASN         : angle       4.94009 (    9)

*********************** 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
  149 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 110
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8147 (t80)
REVERT: A  372 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7238 (ptmm)
REVERT: A  592 MET cc_start: 0.7972 (tpp) cc_final: 0.7612 (tpt)
REVERT: A  615 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8453 (p)
  outliers start: 39
  outliers final: 28
  residues processed: 138
  average time/residue: 0.0566
  time to fit residues: 11.6999
Evaluate side-chains
  138 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  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  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  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 1231 ILE
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 4 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 553 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.149846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.125053 restraints weight = 25506.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.131019 restraints weight = 15960.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.132355 restraints weight = 9004.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.133315 restraints weight = 6837.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.134505 restraints weight = 5920.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    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 = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   8070  Z= 0.241
  Angle     :  0.667  12.517  10922  Z= 0.337
  Chirality :  0.047   0.470   1204
  Planarity :  0.003   0.029   1358
  Dihedral  :  7.530  83.348   1222
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 24.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.27), residues: 952
  helix:  0.99 (0.28), residues: 365
  sheet: -0.26 (0.43), residues: 128
  loop : -1.01 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1192 
 TYR   0.018   0.002   TYR B 962 
 PHE   0.020   0.002   PHE B1284 
 TRP   0.032   0.002   TRP A 255 
 HIS   0.003   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 8060)
  covalent geometry    : angle       0.64795 (10893)
  SS BOND              : bond        0.00335 (    1)
  SS BOND              : angle       0.80847 (    2)
  hydrogen bonds       : bond        0.04991 (  383)
  hydrogen bonds       : angle       4.96585 ( 1116)
  link_ALPHA1-6        : bond        0.00925 (    2)
  link_ALPHA1-6        : angle       1.41629 (    6)
  link_BETA1-4         : bond        0.00403 (    3)
  link_BETA1-4         : angle       1.65098 (    9)
  link_BETA1-6         : bond        0.00673 (    1)
  link_BETA1-6         : angle       3.16382 (    3)
  link_NAG-ASN         : bond        0.00758 (    3)
  link_NAG-ASN         : angle       4.96954 (    9)

*********************** 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
  146 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 103
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8240 (t80)
REVERT: A  372 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7255 (ptmm)
REVERT: A  553 ASN cc_start: 0.9419 (OUTLIER) cc_final: 0.9178 (t0)
REVERT: A  568 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7014 (ttm)
REVERT: A  615 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8556 (p)
  outliers start: 43
  outliers final: 34
  residues processed: 134
  average time/residue: 0.0613
  time to fit residues: 12.2417
Evaluate side-chains
  140 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 101
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  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  553 ASN
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  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 A residue  672 LEU
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 1196 ASN
Chi-restraints excluded: chain B residue 1231 ILE
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 53 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0170
   chunk 16 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.154583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130646 restraints weight = 25392.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.135723 restraints weight = 14977.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.136640 restraints weight = 9767.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.137874 restraints weight = 7273.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.138576 restraints weight = 6343.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    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 = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8070  Z= 0.123
  Angle     :  0.589  11.978  10922  Z= 0.294
  Chirality :  0.044   0.467   1204
  Planarity :  0.003   0.026   1358
  Dihedral  :  6.895  71.340   1222
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 25.27 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.28), residues: 952
  helix:  1.18 (0.28), residues: 366
  sheet: -0.08 (0.44), residues: 130
  loop : -0.88 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 174 
 TYR   0.019   0.001   TYR B1117 
 PHE   0.016   0.001   PHE A 188 
 TRP   0.031   0.001   TRP A 255 
 HIS   0.003   0.000   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8060)
  covalent geometry    : angle       0.56984 (10893)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.42886 (    2)
  hydrogen bonds       : bond        0.04281 (  383)
  hydrogen bonds       : angle       4.73033 ( 1116)
  link_ALPHA1-6        : bond        0.00925 (    2)
  link_ALPHA1-6        : angle       1.27981 (    6)
  link_BETA1-4         : bond        0.00463 (    3)
  link_BETA1-4         : angle       1.47860 (    9)
  link_BETA1-6         : bond        0.01422 (    1)
  link_BETA1-6         : angle       2.69633 (    3)
  link_NAG-ASN         : bond        0.00771 (    3)
  link_NAG-ASN         : angle       4.75693 (    9)

*********************** 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
  149 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 111
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8157 (t80)
REVERT: A  372 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7221 (ptmm)
REVERT: A  528 MET cc_start: 0.6391 (ttm) cc_final: 0.6002 (mtm)
REVERT: A  615 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8425 (p)
  outliers start: 38
  outliers final: 30
  residues processed: 138
  average time/residue: 0.0592
  time to fit residues: 12.1163
Evaluate side-chains
  138 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  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  291 MET
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  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 1231 ILE
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 56 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3996 r_free = 0.3996 target = 0.153618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.128937 restraints weight = 17631.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133012 restraints weight = 10231.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.135864 restraints weight = 7140.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.137785 restraints weight = 5574.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.139103 restraints weight = 4679.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1480

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= 0.132
  Angle     :  0.608  11.865  10922  Z= 0.301
  Chirality :  0.044   0.455   1204
  Planarity :  0.003   0.027   1358
  Dihedral  :  6.398  57.508   1222
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 25.03 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.28), residues: 952
  helix:  1.25 (0.28), residues: 362
  sheet:  0.00 (0.44), residues: 130
  loop : -0.86 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.018   0.001   TYR B1117 
 PHE   0.015   0.001   PHE A 188 
 TRP   0.030   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8060)
  covalent geometry    : angle       0.59008 (10893)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       0.51204 (    2)
  hydrogen bonds       : bond        0.04114 (  383)
  hydrogen bonds       : angle       4.68992 ( 1116)
  link_ALPHA1-6        : bond        0.00981 (    2)
  link_ALPHA1-6        : angle       1.27960 (    6)
  link_BETA1-4         : bond        0.00421 (    3)
  link_BETA1-4         : angle       1.40986 (    9)
  link_BETA1-6         : bond        0.01558 (    1)
  link_BETA1-6         : angle       2.61275 (    3)
  link_NAG-ASN         : bond        0.00766 (    3)
  link_NAG-ASN         : angle       4.69224 (    9)

*********************** 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: 39
    poor density    : 109
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8089 (t80)
REVERT: A  372 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7235 (ptmm)
REVERT: A  568 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6784 (ttm)
REVERT: A  615 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8365 (p)
  outliers start: 39
  outliers final: 31
  residues processed: 136
  average time/residue: 0.0594
  time to fit residues: 12.2198
Evaluate side-chains
  139 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
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  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  994 LYS
Chi-restraints excluded: chain B residue 1044 LEU
Chi-restraints excluded: chain B residue 1174 VAL
Chi-restraints excluded: chain B residue 1231 ILE
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 46 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0570
   chunk 78 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.152479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.127767 restraints weight = 28486.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.133247 restraints weight = 18034.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.134252 restraints weight = 10993.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.135775 restraints weight = 7672.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.140035 restraints weight = 6469.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1611

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= 0.130
  Angle     :  0.597  11.617  10922  Z= 0.296
  Chirality :  0.044   0.445   1204
  Planarity :  0.003   0.027   1358
  Dihedral  :  5.859  55.446   1222
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 25.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.28), residues: 952
  helix:  1.27 (0.28), residues: 363
  sheet:  0.05 (0.45), residues: 130
  loop : -0.86 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.017   0.001   TYR B1117 
 PHE   0.019   0.001   PHE A 203 
 TRP   0.030   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8060)
  covalent geometry    : angle       0.57983 (10893)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.34963 (    2)
  hydrogen bonds       : bond        0.03990 (  383)
  hydrogen bonds       : angle       4.62921 ( 1116)
  link_ALPHA1-6        : bond        0.00946 (    2)
  link_ALPHA1-6        : angle       1.26355 (    6)
  link_BETA1-4         : bond        0.00471 (    3)
  link_BETA1-4         : angle       1.29903 (    9)
  link_BETA1-6         : bond        0.01684 (    1)
  link_BETA1-6         : angle       2.19891 (    3)
  link_NAG-ASN         : bond        0.00768 (    3)
  link_NAG-ASN         : angle       4.59947 (    9)

*********************** 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
  147 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 109
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8123 (t80)
REVERT: A  372 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7222 (ptmm)
REVERT: A  568 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6743 (ttm)
REVERT: A  615 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8342 (p)
  outliers start: 38
  outliers final: 29
  residues processed: 135
  average time/residue: 0.0628
  time to fit residues: 12.6335
Evaluate side-chains
  140 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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  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  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 1231 ILE
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 59 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3996 r_free = 0.3996 target = 0.154391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.129470 restraints weight = 27385.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.134532 restraints weight = 17834.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.135980 restraints weight = 11347.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.137104 restraints weight = 7908.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.139939 restraints weight = 6780.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    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 = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8070  Z= 0.146
  Angle     :  0.600  11.464  10922  Z= 0.298
  Chirality :  0.044   0.439   1204
  Planarity :  0.003   0.029   1358
  Dihedral  :  5.634  55.264   1222
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 24.91 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.28), residues: 952
  helix:  1.23 (0.28), residues: 363
  sheet:  0.02 (0.44), residues: 130
  loop : -0.91 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1179 
 TYR   0.019   0.001   TYR B1117 
 PHE   0.013   0.001   PHE A 188 
 TRP   0.031   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8060)
  covalent geometry    : angle       0.58375 (10893)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.92587 (    2)
  hydrogen bonds       : bond        0.04083 (  383)
  hydrogen bonds       : angle       4.66599 ( 1116)
  link_ALPHA1-6        : bond        0.00934 (    2)
  link_ALPHA1-6        : angle       1.28791 (    6)
  link_BETA1-4         : bond        0.00426 (    3)
  link_BETA1-4         : angle       1.24579 (    9)
  link_BETA1-6         : bond        0.01376 (    1)
  link_BETA1-6         : angle       1.90068 (    3)
  link_NAG-ASN         : bond        0.00754 (    3)
  link_NAG-ASN         : angle       4.54676 (    9)

*********************** 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
  144 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8127 (t80)
REVERT: A  372 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7247 (ptmm)
REVERT: A  568 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6847 (ttm)
REVERT: A  615 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8318 (p)
REVERT: B 1255 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.6360 (m-80)
  outliers start: 37
  outliers final: 30
  residues processed: 133
  average time/residue: 0.0621
  time to fit residues: 12.1989
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  : 0.177 
-------------------------------------------------------------------------------
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  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  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 1231 ILE
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 59 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 43 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4006 r_free = 0.4006 target = 0.155215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.129868 restraints weight = 27051.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.135026 restraints weight = 16984.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.137209 restraints weight = 10358.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.138170 restraints weight = 7290.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.142216 restraints weight = 6259.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3828 r_free = 0.3828    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3828 r_free = 0.3828    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1735

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= 0.132
  Angle     :  0.594  11.264  10922  Z= 0.296
  Chirality :  0.043   0.434   1204
  Planarity :  0.003   0.029   1358
  Dihedral  :  5.436  55.464   1222
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 24.56 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.28), residues: 952
  helix:  1.23 (0.28), residues: 364
  sheet:  0.05 (0.45), residues: 130
  loop : -0.89 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.019   0.001   TYR B1117 
 PHE   0.019   0.001   PHE A 203 
 TRP   0.030   0.001   TRP A 255 
 HIS   0.002   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8060)
  covalent geometry    : angle       0.57795 (10893)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.76830 (    2)
  hydrogen bonds       : bond        0.03965 (  383)
  hydrogen bonds       : angle       4.65170 ( 1116)
  link_ALPHA1-6        : bond        0.00887 (    2)
  link_ALPHA1-6        : angle       1.27591 (    6)
  link_BETA1-4         : bond        0.00474 (    3)
  link_BETA1-4         : angle       1.20863 (    9)
  link_BETA1-6         : bond        0.01386 (    1)
  link_BETA1-6         : angle       1.62536 (    3)
  link_NAG-ASN         : bond        0.00754 (    3)
  link_NAG-ASN         : angle       4.48459 (    9)

********************** 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
  150 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 111
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8112 (t80)
REVERT: A  372 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7234 (ptmm)
REVERT: A  568 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6811 (ttm)
REVERT: A  615 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8383 (p)
REVERT: B 1255 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.6282 (m-80)
  outliers start: 39
  outliers final: 31
  residues processed: 137
  average time/residue: 0.0658
  time to fit residues: 13.2551
Evaluate side-chains
  145 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  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  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 1231 ILE
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 72 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0870
   chunk 45 optimal weight:    4.9990
   chunk 43 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.8560

-------------------------------------------------------------------------------
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 = 0.3996 r_free = 0.3996 target = 0.153468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.128762 restraints weight = 26692.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.133278 restraints weight = 16161.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.134506 restraints weight = 11436.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135903 restraints weight = 7945.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.140688 restraints weight = 6591.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3821 r_free = 0.3821    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3821 r_free = 0.3821    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1757

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= 0.140
  Angle     :  0.602  11.126  10922  Z= 0.299
  Chirality :  0.044   0.427   1204
  Planarity :  0.003   0.028   1358
  Dihedral  :  5.336  55.268   1222
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.28), residues: 952
  helix:  1.26 (0.28), residues: 363
  sheet: -0.05 (0.44), residues: 133
  loop : -0.91 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1179 
 TYR   0.019   0.001   TYR B1117 
 PHE   0.013   0.001   PHE A 188 
 TRP   0.030   0.001   TRP A 255 
 HIS   0.002   0.000   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8060)
  covalent geometry    : angle       0.58692 (10893)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.91912 (    2)
  hydrogen bonds       : bond        0.04023 (  383)
  hydrogen bonds       : angle       4.63550 ( 1116)
  link_ALPHA1-6        : bond        0.00801 (    2)
  link_ALPHA1-6        : angle       1.27754 (    6)
  link_BETA1-4         : bond        0.00468 (    3)
  link_BETA1-4         : angle       1.19946 (    9)
  link_BETA1-6         : bond        0.01277 (    1)
  link_BETA1-6         : angle       1.50114 (    3)
  link_NAG-ASN         : bond        0.00736 (    3)
  link_NAG-ASN         : angle       4.43076 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1416.50 seconds
wall clock time: 25 minutes 13.27 seconds (1513.27 seconds total)