Starting phenix.real_space_refine
on Wed Mar  4 09:59:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cm3_30400/03_2026/7cm3_30400.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cm3_30400/03_2026/7cm3_30400.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cm3_30400/03_2026/7cm3_30400.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cm3_30400/03_2026/7cm3_30400.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cm3_30400/03_2026/7cm3_30400.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cm3_30400/03_2026/7cm3_30400.cif"
  }
  resolution = 3.1
  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=   0.012 sd=   0.096
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: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      96      5.16       5
     C    8194      2.51       5
     N    1956      2.21       5
     O    2162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12418
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 10442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1278, 10442
          Classifications: {'peptide': 1278}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 1232}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 1483
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1483
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 8, 'TRANS': 173}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 412
          Unusual residues: {'NAG': 1, 'PC1': 10}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 143
          Unresolved non-hydrogen angles: 152
          Unresolved non-hydrogen dihedrals: 140
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PC1:plan-1': 2}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.91, per 1000 atoms: 0.23
  Number of scatterers: 12418
  At special positions: 0
  Unit cell: (160.876, 108.7, 111.961, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      96     16.00
     P      10     15.00
     O    2162      8.00
     N    1956      7.00
     C    8194      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 207 " - pdb=" SG  CYS A 239 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 229 " - pdb=" SG  CYS A 245 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1046 " - pdb=" SG  CYS A1057 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1405 " - pdb=" SG  CYS A1417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 226 " - pdb=" SG  CYS B 313 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 246 " - pdb=" SG  CYS B 261 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 304 " - pdb=" SG  CYS B 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 324 " - pdb=" SG  CYS B 377 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 330 " - pdb=" SG  CYS B 376 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 334 " - pdb=" SG  CYS B 361 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A1801 " - " ASN A 216 "
      " NAG B 501 " - " ASN B 217 "
      " NAG C   1 " - " ASN A1064 "
      " NAG D   1 " - " ASN A 210 "
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 550.6 milliseconds
  

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2784

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 5 sheets defined
      71.9% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 55
      removed outlier: 3.969A  pdb=" N   LEU A  41 " --> pdb=" O   TRP A  37 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ALA A  46 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE A  47 " --> pdb=" O   ARG A  43 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 64
    Processing helix  chain 'A' and resid 65 through 92
      removed outlier: 4.171A  pdb=" N   TYR A  69 " --> pdb=" O   PRO A  65 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   PHE A  72 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET A  90 " --> pdb=" O   MET A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 129
    Processing helix  chain 'A' and resid 137 through 144
      removed outlier: 3.770A  pdb=" N   GLY A 140 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 148
      removed outlier: 3.669A  pdb=" N   LEU A 148 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 145 through 148'
    Processing helix  chain 'A' and resid 149 through 155
      removed outlier: 3.603A  pdb=" N   ALA A 153 " --> pdb=" O   ILE A 149 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   PHE A 154 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 200
      removed outlier: 3.562A  pdb=" N   GLN A 177 " --> pdb=" O   ARG A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.603A  pdb=" N   LEU A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 259
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 281 through 293
    Processing helix  chain 'A' and resid 294 through 310
      removed outlier: 3.834A  pdb=" N   SER A 298 " --> pdb=" O   PRO A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 336
      removed outlier: 3.794A  pdb=" N   VAL A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 317 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   TRP A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 375
      No H-bonds generated for 'chain 'A' and resid 373 through 375'
    Processing helix  chain 'A' and resid 376 through 381
      removed outlier: 3.884A  pdb=" N   MET A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 403
    Processing helix  chain 'A' and resid 419 through 441
    Processing helix  chain 'A' and resid 441 through 446
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 3.501A  pdb=" N   THR A 462 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 480
      removed outlier: 3.957A  pdb=" N   GLN A 478 " --> pdb=" O   PHE A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 488
      removed outlier: 3.577A  pdb=" N   LYS A 487 " --> pdb=" O   ARG A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 501
      removed outlier: 3.590A  pdb=" N   GLU A 493 " --> pdb=" O   SER A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 529
      removed outlier: 4.228A  pdb=" N   LEU A 506 " --> pdb=" O   PRO A 502 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER A 508 " --> pdb=" O   LYS A 504 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A 509 " --> pdb=" O   LYS A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 552
    Processing helix  chain 'A' and resid 555 through 568
      removed outlier: 3.658A  pdb=" N   GLY A 568 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 589
    Processing helix  chain 'A' and resid 589 through 603
    Processing helix  chain 'A' and resid 605 through 617
      removed outlier: 3.525A  pdb=" N   SER A 617 " --> pdb=" O   GLN A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 855
    Processing helix  chain 'A' and resid 873 through 883
    Processing helix  chain 'A' and resid 886 through 904
    Processing helix  chain 'A' and resid 911 through 914
    Processing helix  chain 'A' and resid 915 through 941
      removed outlier: 4.893A  pdb=" N   ALA A 921 " --> pdb=" O   THR A 917 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLU A 922 " --> pdb=" O   LEU A 918 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A 926 " --> pdb=" O   GLU A 922 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE A 931 " --> pdb=" O   ILE A 927 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 972
    Processing helix  chain 'A' and resid 980 through 989
    Processing helix  chain 'A' and resid 990 through 993
      Proline residue:  A 993  - end of helix
      No H-bonds generated for 'chain 'A' and resid 990 through 993'
    Processing helix  chain 'A' and resid 994 through 1000
      removed outlier: 3.934A  pdb=" N   LYS A 998 " --> pdb=" O   LEU A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1000 through 1012
    Processing helix  chain 'A' and resid 1013 through 1040
    Processing helix  chain 'A' and resid 1053 through 1057
    Processing helix  chain 'A' and resid 1100 through 1113
      removed outlier: 3.686A  pdb=" N   SER A1113 " --> pdb=" O   PHE A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1116 through 1128
    Processing helix  chain 'A' and resid 1132 through 1145
      removed outlier: 3.980A  pdb=" N   ILE A1136 " --> pdb=" O   HIS A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1163
      removed outlier: 4.083A  pdb=" N   PHE A1151 " --> pdb=" O   GLY A1147 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL A1152 " --> pdb=" O   LEU A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1168
    Processing helix  chain 'A' and resid 1169 through 1185
    Processing helix  chain 'A' and resid 1197 through 1209
      removed outlier: 3.740A  pdb=" N   ALA A1201 " --> pdb=" O   ASP A1197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1209 through 1225
      removed outlier: 3.978A  pdb=" N   ARG A1214 " --> pdb=" O   PRO A1210 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A1221 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1226 through 1228
      No H-bonds generated for 'chain 'A' and resid 1226 through 1228'
    Processing helix  chain 'A' and resid 1237 through 1263
      removed outlier: 3.579A  pdb=" N   LEU A1241 " --> pdb=" O   VAL A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1269
    Processing helix  chain 'A' and resid 1271 through 1295
    Processing helix  chain 'A' and resid 1296 through 1312
    Processing helix  chain 'A' and resid 1313 through 1317
    Processing helix  chain 'A' and resid 1318 through 1335
    Processing helix  chain 'A' and resid 1335 through 1358
    Processing helix  chain 'A' and resid 1374 through 1388
    Processing helix  chain 'A' and resid 1390 through 1399
    Processing helix  chain 'A' and resid 1419 through 1436
      removed outlier: 3.611A  pdb=" N   CYS A1428 " --> pdb=" O   LEU A1424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1438 through 1454
      removed outlier: 4.189A  pdb=" N   LEU A1442 " --> pdb=" O   MET A1438 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL A1443 " --> pdb=" O   LEU A1439 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   SER A1451 " --> pdb=" O   VAL A1447 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU A1452 " --> pdb=" O   GLU A1448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1463 through 1478
      removed outlier: 3.681A  pdb=" N   VAL A1477 " --> pdb=" O   ILE A1473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1487 through 1494
      removed outlier: 4.207A  pdb=" N   LYS A1491 " --> pdb=" O   THR A1487 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   PHE A1492 " --> pdb=" O   PHE A1488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1498 through 1502
      removed outlier: 4.396A  pdb=" N   LEU A1501 " --> pdb=" O   ARG A1498 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU A1502 " --> pdb=" O   GLY A1499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1498 through 1502'
    Processing helix  chain 'A' and resid 1508 through 1523
      removed outlier: 3.532A  pdb=" N   MET A1519 " --> pdb=" O   MET A1515 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   HIS A1523 " --> pdb=" O   MET A1519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1530 through 1540
    Processing helix  chain 'A' and resid 1543 through 1548
    Processing helix  chain 'A' and resid 1549 through 1577
      removed outlier: 3.985A  pdb=" N   LEU A1554 " --> pdb=" O   LEU A1550 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA A1555 " --> pdb=" O   GLU A1551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1590 through 1602
    Processing helix  chain 'B' and resid 230 through 237
    Processing helix  chain 'B' and resid 262 through 288
      removed outlier: 4.213A  pdb=" N   GLU B 266 " --> pdb=" O   ARG B 262 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU B 281 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 317
    Processing helix  chain 'B' and resid 331 through 341
      removed outlier: 4.000A  pdb=" N   LEU B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 209
      removed outlier: 4.023A  pdb=" N   HIS A 206 " --> pdb=" O   MET A 246 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   MET A 246 " --> pdb=" O   HIS A 206 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1045 through 1046
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1060 through 1064
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1484 through 1486
    Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 329

    720 hydrogen bonds defined for protein.
    2109 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: 1.40

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1861
        1.28 -     1.41: 3408
        1.41 -     1.55: 7233
        1.55 -     1.69: 67
        1.69 -     1.82: 150
  Bond restraints: 12719
  Sorted by residual:
  bond pdb=" C   LEU A  78 "
       pdb=" N   MET A  79 "
    ideal  model  delta    sigma   weight residual
    1.335  1.245  0.090 1.30e-02 5.92e+03 4.83e+01
  bond pdb=" C38 PC1 A1808 "
       pdb=" C39 PC1 A1808 "
    ideal  model  delta    sigma   weight residual
    1.523  1.433  0.090 2.00e-02 2.50e+03 2.01e+01
  bond pdb=" N   GLU B 373 "
       pdb=" CA  GLU B 373 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 7.40e-03 1.83e+04 1.68e+01
  bond pdb=" N   VAL A 458 "
       pdb=" CA  VAL A 458 "
    ideal  model  delta    sigma   weight residual
    1.459  1.510 -0.051 1.30e-02 5.92e+03 1.54e+01
  bond pdb=" C   ARG A 992 "
       pdb=" O   ARG A 992 "
    ideal  model  delta    sigma   weight residual
    1.243  1.204  0.039 9.90e-03 1.02e+04 1.52e+01
  ... (remaining 12714 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 14775
        2.62 -     5.24: 2285
        5.24 -     7.85: 105
        7.85 -    10.47: 9
       10.47 -    13.09: 6
  Bond angle restraints: 17180
  Sorted by residual:
  angle pdb=" N   GLN A 414 "
        pdb=" CA  GLN A 414 "
        pdb=" C   GLN A 414 "
      ideal   model   delta    sigma   weight residual
     112.93   99.84   13.09 1.33e+00 5.65e-01 9.69e+01
  angle pdb=" N   ASP B 372 "
        pdb=" CA  ASP B 372 "
        pdb=" C   ASP B 372 "
      ideal   model   delta    sigma   weight residual
     111.28  103.22    8.06 1.09e+00 8.42e-01 5.47e+01
  angle pdb=" N   TYR A 419 "
        pdb=" CA  TYR A 419 "
        pdb=" C   TYR A 419 "
      ideal   model   delta    sigma   weight residual
     113.55  105.76    7.79 1.26e+00 6.30e-01 3.82e+01
  angle pdb=" CA  ASP A 247 "
        pdb=" CB  ASP A 247 "
        pdb=" CG  ASP A 247 "
      ideal   model   delta    sigma   weight residual
     112.60  118.21   -5.61 1.00e+00 1.00e+00 3.15e+01
  angle pdb=" N   PRO A  65 "
        pdb=" CA  PRO A  65 "
        pdb=" C   PRO A  65 "
      ideal   model   delta    sigma   weight residual
     110.70  117.39   -6.69 1.22e+00 6.72e-01 3.00e+01
  ... (remaining 17175 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.60: 7008
       19.60 -    39.21: 508
       39.21 -    58.81: 143
       58.81 -    78.41: 38
       78.41 -    98.02: 9
  Dihedral angle restraints: 7706
    sinusoidal: 3412
      harmonic: 4294
  Sorted by residual:
  dihedral pdb=" CB  CYS A1046 "
           pdb=" SG  CYS A1046 "
           pdb=" SG  CYS A1057 "
           pdb=" CB  CYS A1057 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.69   69.69     1      1.00e+01 1.00e-02 6.27e+01
  dihedral pdb=" CA  CYS A 229 "
           pdb=" C   CYS A 229 "
           pdb=" N   SER A 230 "
           pdb=" CA  SER A 230 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.67   26.33     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CB  CYS B 324 "
           pdb=" SG  CYS B 324 "
           pdb=" SG  CYS B 377 "
           pdb=" CB  CYS B 377 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.75   39.75     1      1.00e+01 1.00e-02 2.22e+01
  ... (remaining 7703 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.182: 1809
       0.182 -    0.365: 104
       0.365 -    0.547: 0
       0.547 -    0.729: 1
       0.729 -    0.911: 1
  Chirality restraints: 1915
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 210 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.49   -0.91 2.00e-01 2.50e+01 2.08e+01
  chirality pdb=" C1  BMA D   3 "
            pdb=" O4  NAG D   2 "
            pdb=" C2  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.33   -0.07 2.00e-02 2.50e+03 1.30e+01
  chirality pdb=" C1  NAG B 501 "
            pdb=" ND2 ASN B 217 "
            pdb=" C2  NAG B 501 "
            pdb=" O5  NAG B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.95    0.55 2.00e-01 2.50e+01 7.69e+00
  ... (remaining 1912 not shown)

  Planarity restraints: 2082
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.359 2.00e-02 2.50e+03   2.95e-01 1.09e+03
        pdb=" C7  NAG D   1 "    0.101 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.216 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.500 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.277 2.00e-02 2.50e+03   2.30e-01 6.61e+02
        pdb=" C7  NAG D   2 "    0.075 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.186 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.384 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 217 "   -0.081 2.00e-02 2.50e+03   1.16e-01 1.69e+02
        pdb=" CG  ASN B 217 "    0.035 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 217 "   -0.029 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 217 "    0.205 2.00e-02 2.50e+03
        pdb=" C1  NAG B 501 "   -0.130 2.00e-02 2.50e+03
  ... (remaining 2079 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 334
        2.74 -     3.28: 12331
        3.28 -     3.82: 18812
        3.82 -     4.36: 25064
        4.36 -     4.90: 40190
  Nonbonded interactions: 96731
  Sorted by model distance:
  nonbonded pdb=" O3  NAG D   1 "
            pdb=" O7  NAG D   1 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" CE  MET A 545 "
            pdb=" O22 PC1 A1805 "
     model   vdw
     2.224 3.460
  nonbonded pdb=" NH1 ARG A 542 "
            pdb=" O14 PC1 A1805 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" O   ASN A1072 "
            pdb=" ND2 ASN A1072 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" NH1 ARG A1273 "
            pdb=" C13 PC1 A1804 "
     model   vdw
     2.295 3.540
  ... (remaining 96726 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  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:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     11.660
  Find NCS groups from input model:        0.050
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
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      :  0.015   0.090  12736  Z= 0.891
  Angle     :  1.796  27.187  17221  Z= 1.188
  Chirality :  0.098   0.911   1915
  Planarity :  0.014   0.295   2078
  Dihedral  : 15.850  98.016   4892
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.85 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  4.69 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.21), residues: 1444
  helix: -0.05 (0.15), residues: 934
  sheet:  None (None), residues: 0
  loop : -1.56 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1481 
 TYR   0.081   0.009   TYR A 274 
 PHE   0.066   0.009   PHE A 997 
 TRP   0.061   0.011   TRP B 311 
 HIS   0.013   0.003   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.01471 (12719)
  covalent geometry    : angle       1.77018 (17180)
  SS BOND              : bond        0.00709 (   10)
  SS BOND              : angle       1.83607 (   20)
  hydrogen bonds       : bond        0.18640 (  720)
  hydrogen bonds       : angle       6.70007 ( 2109)
  link_BETA1-4         : bond        0.01978 (    3)
  link_BETA1-4         : angle       3.50139 (    9)
  link_NAG-ASN         : bond        0.03478 (    4)
  link_NAG-ASN         : angle      11.41754 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 329
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 8
  residues processed: 348
  average time/residue: 0.1247
  time to fit residues: 60.7345
Evaluate side-chains
  203 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 195
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain B residue  216 TRP
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  218 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  56 ASN
A 279 GLN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 ASN
A 451 HIS
A 569 HIS
A1072 ASN
A1270 GLN
A1460 GLN
A1589 GLN
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 291 GLN
B 371 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.150830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.117318 restraints weight = 18613.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.48
r_work: 0.3374 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12736  Z= 0.161
  Angle     :  0.692  12.329  17221  Z= 0.352
  Chirality :  0.044   0.394   1915
  Planarity :  0.005   0.043   2078
  Dihedral  : 13.459  70.244   2088
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.22 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  :  9.69 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.22), residues: 1444
  helix:  1.17 (0.16), residues: 952
  sheet:  None (None), residues: 0
  loop : -1.29 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 155 
 TYR   0.013   0.001   TYR A1426 
 PHE   0.020   0.002   PHE A1530 
 TRP   0.026   0.002   TRP A 107 
 HIS   0.005   0.001   HIS A1514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (12719)
  covalent geometry    : angle       0.66962 (17180)
  SS BOND              : bond        0.00596 (   10)
  SS BOND              : angle       1.17837 (   20)
  hydrogen bonds       : bond        0.06099 (  720)
  hydrogen bonds       : angle       4.64286 ( 2109)
  link_BETA1-4         : bond        0.00989 (    3)
  link_BETA1-4         : angle       1.90628 (    9)
  link_NAG-ASN         : bond        0.00540 (    4)
  link_NAG-ASN         : angle       6.28787 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 225
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 MET cc_start: 0.8776 (ppp) cc_final: 0.8339 (ppp)
REVERT: A  388 MET cc_start: 0.6865 (ppp) cc_final: 0.6597 (ppp)
REVERT: A  554 GLU cc_start: 0.8120 (tp30) cc_final: 0.7903 (tp30)
REVERT: A  892 MET cc_start: 0.7906 (mmt) cc_final: 0.7675 (mmt)
REVERT: A  972 MET cc_start: 0.8217 (mmt) cc_final: 0.7991 (mmt)
REVERT: A 1476 MET cc_start: 0.8091 (ptp) cc_final: 0.7419 (ppp)
REVERT: A 1506 ASP cc_start: 0.8897 (t0) cc_final: 0.8473 (t0)
REVERT: A 1515 MET cc_start: 0.9259 (mmm) cc_final: 0.8924 (mmp)
REVERT: A 1536 MET cc_start: 0.8790 (ttp) cc_final: 0.8449 (ttp)
REVERT: A 1602 GLN cc_start: 0.6557 (mt0) cc_final: 0.6034 (mt0)
REVERT: B  262 ARG cc_start: 0.7861 (tmm-80) cc_final: 0.7615 (tmm-80)
REVERT: B  340 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8540 (mtt180)
REVERT: B  349 ASP cc_start: 0.8612 (t70) cc_final: 0.8367 (t70)
  outliers start: 39
  outliers final: 26
  residues processed: 248
  average time/residue: 0.1085
  time to fit residues: 39.1588
Evaluate side-chains
  212 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 186
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1072 ASN
Chi-restraints excluded: chain A residue 1184 ILE
Chi-restraints excluded: chain A residue 1209 HIS
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1255 GLU
Chi-restraints excluded: chain A residue 1289 VAL
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1503 VAL
Chi-restraints excluded: chain B residue  216 TRP
Chi-restraints excluded: chain B residue  303 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 133 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0670
   chunk 77 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1072 ASN
A1460 GLN
A1589 GLN
B 227 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.151141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.116898 restraints weight = 18732.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.53
r_work: 0.3371 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12736  Z= 0.135
  Angle     :  0.602   9.646  17221  Z= 0.310
  Chirality :  0.041   0.242   1915
  Planarity :  0.004   0.043   2078
  Dihedral  : 12.231  73.641   2084
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 10.83 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.22), residues: 1444
  helix:  1.45 (0.17), residues: 953
  sheet: -4.18 (1.16), residues: 10
  loop : -1.19 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 951 
 TYR   0.014   0.001   TYR A1426 
 PHE   0.018   0.001   PHE A  72 
 TRP   0.012   0.001   TRP A 119 
 HIS   0.004   0.001   HIS B 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12719)
  covalent geometry    : angle       0.58261 (17180)
  SS BOND              : bond        0.00494 (   10)
  SS BOND              : angle       2.20268 (   20)
  hydrogen bonds       : bond        0.05063 (  720)
  hydrogen bonds       : angle       4.35893 ( 2109)
  link_BETA1-4         : bond        0.00935 (    3)
  link_BETA1-4         : angle       1.57787 (    9)
  link_NAG-ASN         : bond        0.00371 (    4)
  link_NAG-ASN         : angle       4.98090 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 201
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 MET cc_start: 0.6849 (ppp) cc_final: 0.6635 (ppp)
REVERT: A  393 MET cc_start: 0.6737 (mmp) cc_final: 0.6433 (mmt)
REVERT: A  892 MET cc_start: 0.7873 (mmt) cc_final: 0.7580 (mmt)
REVERT: A  972 MET cc_start: 0.8113 (mmt) cc_final: 0.7853 (mmt)
REVERT: A 1202 LYS cc_start: 0.7581 (pttp) cc_final: 0.6812 (tppp)
REVERT: A 1302 MET cc_start: 0.7060 (ttt) cc_final: 0.6712 (tmt)
REVERT: A 1476 MET cc_start: 0.7713 (ptp) cc_final: 0.7423 (ppp)
REVERT: A 1480 LYS cc_start: 0.8507 (mptt) cc_final: 0.8285 (mptt)
REVERT: A 1513 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8920 (mmtt)
REVERT: A 1515 MET cc_start: 0.9105 (mmm) cc_final: 0.8801 (mmp)
REVERT: B  350 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7783 (mp0)
  outliers start: 39
  outliers final: 25
  residues processed: 223
  average time/residue: 0.1003
  time to fit residues: 33.0369
Evaluate side-chains
  210 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 184
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1184 ILE
Chi-restraints excluded: chain A residue 1209 HIS
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1503 VAL
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain B residue  216 TRP
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  350 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 136 optimal weight:    0.6980
   chunk 131 optimal weight:    0.9990
   chunk 101 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
A1589 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.149582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.115359 restraints weight = 18575.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.52
r_work: 0.3349 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12736  Z= 0.129
  Angle     :  0.571   8.845  17221  Z= 0.293
  Chirality :  0.040   0.195   1915
  Planarity :  0.004   0.043   2078
  Dihedral  : 11.438  77.101   2082
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.11 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.22), residues: 1444
  helix:  1.57 (0.17), residues: 959
  sheet:  None (None), residues: 0
  loop : -1.28 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 152 
 TYR   0.014   0.001   TYR A1426 
 PHE   0.020   0.001   PHE A  72 
 TRP   0.015   0.001   TRP A 119 
 HIS   0.004   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (12719)
  covalent geometry    : angle       0.55833 (17180)
  SS BOND              : bond        0.00193 (   10)
  SS BOND              : angle       1.75407 (   20)
  hydrogen bonds       : bond        0.04698 (  720)
  hydrogen bonds       : angle       4.20718 ( 2109)
  link_BETA1-4         : bond        0.00706 (    3)
  link_BETA1-4         : angle       1.62265 (    9)
  link_NAG-ASN         : bond        0.00330 (    4)
  link_NAG-ASN         : angle       3.87088 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 205
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A  388 MET cc_start: 0.6824 (ppp) cc_final: 0.6553 (ppp)
REVERT: A  393 MET cc_start: 0.6891 (mmp) cc_final: 0.6592 (mmt)
REVERT: A  616 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: A  972 MET cc_start: 0.8106 (mmt) cc_final: 0.7839 (mmt)
REVERT: A 1302 MET cc_start: 0.7253 (ttt) cc_final: 0.6891 (tmt)
REVERT: A 1335 SER cc_start: 0.9345 (p) cc_final: 0.9102 (p)
REVERT: A 1424 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8449 (mp)
REVERT: A 1468 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8530 (ttm-80)
REVERT: A 1480 LYS cc_start: 0.8493 (mptt) cc_final: 0.8249 (mptt)
REVERT: A 1513 LYS cc_start: 0.9292 (mmtt) cc_final: 0.9021 (mmtt)
REVERT: A 1515 MET cc_start: 0.9213 (mmm) cc_final: 0.8922 (mmp)
REVERT: B  216 TRP cc_start: 0.7963 (OUTLIER) cc_final: 0.4652 (t-100)
REVERT: B  233 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8215 (pm20)
REVERT: B  262 ARG cc_start: 0.7952 (tmm-80) cc_final: 0.7657 (tmm-80)
REVERT: B  270 ASP cc_start: 0.8786 (t70) cc_final: 0.8397 (t0)
REVERT: B  327 THR cc_start: 0.7412 (p) cc_final: 0.7156 (m)
REVERT: B  340 ARG cc_start: 0.8976 (mmm-85) cc_final: 0.8650 (mtt90)
  outliers start: 37
  outliers final: 24
  residues processed: 226
  average time/residue: 0.0995
  time to fit residues: 33.7599
Evaluate side-chains
  222 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1225 VAL
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain A residue 1296 ASN
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1503 VAL
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain B residue  216 TRP
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  379 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 143 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 104 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 71 optimal weight:    0.1980
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A1589 GLN
A1602 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.148144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.113605 restraints weight = 18743.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.53
r_work: 0.3324 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12736  Z= 0.147
  Angle     :  0.599   8.627  17221  Z= 0.303
  Chirality :  0.046   0.887   1915
  Planarity :  0.004   0.043   2078
  Dihedral  : 11.332  77.914   2080
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 13.10 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.22), residues: 1444
  helix:  1.59 (0.17), residues: 960
  sheet: -4.16 (1.07), residues: 10
  loop : -1.42 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 951 
 TYR   0.014   0.001   TYR A1426 
 PHE   0.018   0.001   PHE A  72 
 TRP   0.011   0.001   TRP A 119 
 HIS   0.004   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (12719)
  covalent geometry    : angle       0.58702 (17180)
  SS BOND              : bond        0.00231 (   10)
  SS BOND              : angle       2.20962 (   20)
  hydrogen bonds       : bond        0.04831 (  720)
  hydrogen bonds       : angle       4.18936 ( 2109)
  link_BETA1-4         : bond        0.00730 (    3)
  link_BETA1-4         : angle       1.49832 (    9)
  link_NAG-ASN         : bond        0.00764 (    4)
  link_NAG-ASN         : angle       3.31380 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 192
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8060 (tt0) cc_final: 0.7729 (tp30)
REVERT: A  388 MET cc_start: 0.6799 (ppp) cc_final: 0.6499 (ppp)
REVERT: A  393 MET cc_start: 0.6815 (mmp) cc_final: 0.6608 (mmt)
REVERT: A  616 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: A  972 MET cc_start: 0.8004 (mmt) cc_final: 0.7748 (mmt)
REVERT: A 1202 LYS cc_start: 0.7621 (pttm) cc_final: 0.7053 (tptt)
REVERT: A 1209 HIS cc_start: 0.6625 (OUTLIER) cc_final: 0.6414 (t-90)
REVERT: A 1302 MET cc_start: 0.7192 (ttt) cc_final: 0.6808 (tmt)
REVERT: A 1335 SER cc_start: 0.9299 (p) cc_final: 0.9036 (p)
REVERT: A 1468 ARG cc_start: 0.8745 (ttm-80) cc_final: 0.8474 (ttm-80)
REVERT: A 1480 LYS cc_start: 0.8508 (mptt) cc_final: 0.8279 (mptt)
REVERT: A 1513 LYS cc_start: 0.9300 (mmtt) cc_final: 0.9019 (mmtt)
REVERT: A 1515 MET cc_start: 0.9214 (mmm) cc_final: 0.8915 (mmp)
REVERT: B  216 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.7622 (p-90)
REVERT: B  233 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8150 (pm20)
REVERT: B  262 ARG cc_start: 0.7926 (tmm-80) cc_final: 0.7540 (tmm-80)
REVERT: B  270 ASP cc_start: 0.8676 (t70) cc_final: 0.8275 (t0)
REVERT: B  280 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8454 (mm-30)
REVERT: B  327 THR cc_start: 0.7510 (p) cc_final: 0.7275 (m)
  outliers start: 40
  outliers final: 31
  residues processed: 215
  average time/residue: 0.0998
  time to fit residues: 32.3176
Evaluate side-chains
  222 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 188
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1209 HIS
Chi-restraints excluded: chain A residue 1225 VAL
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain A residue 1296 ASN
Chi-restraints excluded: chain A residue 1476 MET
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1503 VAL
Chi-restraints excluded: chain A residue 1547 SER
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain B residue  216 TRP
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  379 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 140 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 143 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A1589 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.148513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113339 restraints weight = 18618.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.39
r_work: 0.3327 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12736  Z= 0.128
  Angle     :  0.561   8.612  17221  Z= 0.288
  Chirality :  0.040   0.272   1915
  Planarity :  0.004   0.044   2078
  Dihedral  : 10.942  77.049   2080
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 13.10 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.22), residues: 1444
  helix:  1.65 (0.17), residues: 960
  sheet:  None (None), residues: 0
  loop : -1.46 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 951 
 TYR   0.014   0.001   TYR A1426 
 PHE   0.021   0.001   PHE A  72 
 TRP   0.014   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12719)
  covalent geometry    : angle       0.55236 (17180)
  SS BOND              : bond        0.00220 (   10)
  SS BOND              : angle       1.73920 (   20)
  hydrogen bonds       : bond        0.04561 (  720)
  hydrogen bonds       : angle       4.11272 ( 2109)
  link_BETA1-4         : bond        0.00607 (    3)
  link_BETA1-4         : angle       1.43209 (    9)
  link_NAG-ASN         : bond        0.00516 (    4)
  link_NAG-ASN         : angle       2.85163 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 201
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8071 (tt0) cc_final: 0.7821 (tp30)
REVERT: A  388 MET cc_start: 0.6750 (ppp) cc_final: 0.6423 (ppp)
REVERT: A  616 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8293 (tm-30)
REVERT: A  972 MET cc_start: 0.8014 (mmt) cc_final: 0.7776 (mmt)
REVERT: A 1171 ASP cc_start: 0.7984 (m-30) cc_final: 0.7729 (m-30)
REVERT: A 1202 LYS cc_start: 0.7543 (pttm) cc_final: 0.7052 (tptt)
REVERT: A 1335 SER cc_start: 0.9283 (p) cc_final: 0.9029 (p)
REVERT: A 1424 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8512 (mp)
REVERT: A 1468 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8476 (ttm-80)
REVERT: A 1513 LYS cc_start: 0.9292 (mmtt) cc_final: 0.9028 (mmtt)
REVERT: A 1515 MET cc_start: 0.9161 (mmm) cc_final: 0.8817 (mmp)
REVERT: B  210 LYS cc_start: 0.7809 (tmmt) cc_final: 0.7541 (tmmt)
REVERT: B  216 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.4605 (t-100)
REVERT: B  233 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8132 (pm20)
REVERT: B  262 ARG cc_start: 0.7970 (tmm-80) cc_final: 0.7646 (tmm-80)
REVERT: B  270 ASP cc_start: 0.8662 (t70) cc_final: 0.8278 (t0)
REVERT: B  280 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8457 (mm-30)
  outliers start: 45
  outliers final: 32
  residues processed: 225
  average time/residue: 0.0995
  time to fit residues: 33.8349
Evaluate side-chains
  221 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 186
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1225 VAL
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain A residue 1332 MET
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1476 MET
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain B residue  216 TRP
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  379 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 133 optimal weight:    4.9990
   chunk 135 optimal weight:    0.9990
   chunk 136 optimal weight:    0.8980
   chunk 118 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 125 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0000
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 GLN
A1589 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.149338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.114391 restraints weight = 18620.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.37
r_work: 0.3344 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12736  Z= 0.117
  Angle     :  0.549   7.710  17221  Z= 0.281
  Chirality :  0.040   0.201   1915
  Planarity :  0.004   0.043   2078
  Dihedral  : 10.658  75.618   2080
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 13.63 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.22), residues: 1444
  helix:  1.73 (0.17), residues: 957
  sheet:  None (None), residues: 0
  loop : -1.47 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 951 
 TYR   0.021   0.001   TYR A 415 
 PHE   0.021   0.001   PHE A  72 
 TRP   0.013   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A1514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (12719)
  covalent geometry    : angle       0.54123 (17180)
  SS BOND              : bond        0.00135 (   10)
  SS BOND              : angle       1.67098 (   20)
  hydrogen bonds       : bond        0.04275 (  720)
  hydrogen bonds       : angle       4.06119 ( 2109)
  link_BETA1-4         : bond        0.00682 (    3)
  link_BETA1-4         : angle       1.48300 (    9)
  link_NAG-ASN         : bond        0.00510 (    4)
  link_NAG-ASN         : angle       2.70430 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 194
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8183 (tt0) cc_final: 0.7908 (tp30)
REVERT: A  244 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7592 (ptpt)
REVERT: A  388 MET cc_start: 0.6725 (ppp) cc_final: 0.6350 (ppp)
REVERT: A  616 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8295 (tm-30)
REVERT: A  875 TYR cc_start: 0.7381 (m-80) cc_final: 0.7079 (m-80)
REVERT: A  972 MET cc_start: 0.8017 (mmt) cc_final: 0.7760 (mmt)
REVERT: A 1202 LYS cc_start: 0.7552 (pttm) cc_final: 0.7067 (tptt)
REVERT: A 1302 MET cc_start: 0.7042 (ttt) cc_final: 0.6837 (tmt)
REVERT: A 1335 SER cc_start: 0.9246 (p) cc_final: 0.9013 (p)
REVERT: A 1424 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8466 (mp)
REVERT: A 1468 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8475 (ttm-80)
REVERT: A 1513 LYS cc_start: 0.9280 (mmtt) cc_final: 0.9008 (mmtt)
REVERT: B  210 LYS cc_start: 0.7820 (tmmt) cc_final: 0.7507 (tmmt)
REVERT: B  216 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.4828 (t-100)
REVERT: B  233 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8053 (pm20)
REVERT: B  262 ARG cc_start: 0.7983 (tmm-80) cc_final: 0.7528 (tmm-80)
REVERT: B  270 ASP cc_start: 0.8629 (t70) cc_final: 0.8261 (t0)
REVERT: B  283 GLU cc_start: 0.8453 (pt0) cc_final: 0.8165 (pt0)
  outliers start: 40
  outliers final: 28
  residues processed: 220
  average time/residue: 0.1003
  time to fit residues: 33.7170
Evaluate side-chains
  216 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1184 ILE
Chi-restraints excluded: chain A residue 1225 VAL
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1476 MET
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain B residue  216 TRP
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  379 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 132 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1589 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.147746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.112679 restraints weight = 18512.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.37
r_work: 0.3321 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12736  Z= 0.138
  Angle     :  0.567   7.221  17221  Z= 0.292
  Chirality :  0.040   0.195   1915
  Planarity :  0.004   0.044   2078
  Dihedral  : 10.598  73.901   2080
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.08 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.22), residues: 1444
  helix:  1.62 (0.17), residues: 966
  sheet:  None (None), residues: 0
  loop : -1.49 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 951 
 TYR   0.014   0.001   TYR A1426 
 PHE   0.021   0.001   PHE A  72 
 TRP   0.014   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (12719)
  covalent geometry    : angle       0.55904 (17180)
  SS BOND              : bond        0.00225 (   10)
  SS BOND              : angle       1.87583 (   20)
  hydrogen bonds       : bond        0.04615 (  720)
  hydrogen bonds       : angle       4.11827 ( 2109)
  link_BETA1-4         : bond        0.00683 (    3)
  link_BETA1-4         : angle       1.49515 (    9)
  link_NAG-ASN         : bond        0.00450 (    4)
  link_NAG-ASN         : angle       2.62549 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 192
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A   85 GLU cc_start: 0.8148 (tt0) cc_final: 0.7696 (tp30)
REVERT: A  152 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7131 (tpp80)
REVERT: A  244 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7606 (ptpt)
REVERT: A  274 TYR cc_start: 0.8665 (t80) cc_final: 0.8392 (t80)
REVERT: A  388 MET cc_start: 0.6799 (ppp) cc_final: 0.6393 (ppp)
REVERT: A  616 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8363 (tm-30)
REVERT: A  875 TYR cc_start: 0.7440 (m-80) cc_final: 0.7199 (m-80)
REVERT: A  972 MET cc_start: 0.8109 (mmt) cc_final: 0.7863 (mmt)
REVERT: A 1202 LYS cc_start: 0.7558 (pttm) cc_final: 0.7059 (tptt)
REVERT: A 1302 MET cc_start: 0.7162 (ttt) cc_final: 0.6882 (tmt)
REVERT: A 1335 SER cc_start: 0.9268 (p) cc_final: 0.9027 (p)
REVERT: A 1424 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8478 (mp)
REVERT: A 1513 LYS cc_start: 0.9258 (mmtt) cc_final: 0.9035 (mmtt)
REVERT: A 1515 MET cc_start: 0.8880 (mmp) cc_final: 0.8179 (mmp)
REVERT: B  210 LYS cc_start: 0.7894 (tmmt) cc_final: 0.7523 (tmmt)
REVERT: B  216 TRP cc_start: 0.7501 (p-90) cc_final: 0.4855 (t-100)
REVERT: B  233 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8043 (pm20)
REVERT: B  262 ARG cc_start: 0.7969 (tmm-80) cc_final: 0.7497 (tmm-80)
REVERT: B  270 ASP cc_start: 0.8654 (t70) cc_final: 0.8280 (t0)
  outliers start: 34
  outliers final: 26
  residues processed: 216
  average time/residue: 0.0960
  time to fit residues: 31.3180
Evaluate side-chains
  215 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1225 VAL
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain A residue 1332 MET
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1476 MET
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1547 SER
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  379 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 86 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 138 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1589 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.147803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.112804 restraints weight = 18736.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.38
r_work: 0.3323 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12736  Z= 0.134
  Angle     :  0.571  10.401  17221  Z= 0.292
  Chirality :  0.040   0.192   1915
  Planarity :  0.004   0.043   2078
  Dihedral  : 10.495  71.640   2078
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.31 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.22), residues: 1444
  helix:  1.62 (0.17), residues: 966
  sheet:  None (None), residues: 0
  loop : -1.50 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1468 
 TYR   0.015   0.001   TYR A1426 
 PHE   0.027   0.001   PHE A 389 
 TRP   0.014   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (12719)
  covalent geometry    : angle       0.56263 (17180)
  SS BOND              : bond        0.00157 (   10)
  SS BOND              : angle       1.99987 (   20)
  hydrogen bonds       : bond        0.04528 (  720)
  hydrogen bonds       : angle       4.11861 ( 2109)
  link_BETA1-4         : bond        0.00639 (    3)
  link_BETA1-4         : angle       1.47351 (    9)
  link_NAG-ASN         : bond        0.00422 (    4)
  link_NAG-ASN         : angle       2.60405 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 190
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8140 (tt0) cc_final: 0.7701 (tp30)
REVERT: A  152 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7114 (tpp80)
REVERT: A  244 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7621 (ptpt)
REVERT: A  274 TYR cc_start: 0.8688 (t80) cc_final: 0.8408 (t80)
REVERT: A  388 MET cc_start: 0.6718 (ppp) cc_final: 0.6379 (ppp)
REVERT: A  616 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: A  972 MET cc_start: 0.8152 (mmt) cc_final: 0.7936 (mmt)
REVERT: A 1009 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8287 (mt-10)
REVERT: A 1202 LYS cc_start: 0.7577 (pttm) cc_final: 0.7079 (tptt)
REVERT: A 1302 MET cc_start: 0.7071 (ttt) cc_final: 0.6802 (tmt)
REVERT: A 1335 SER cc_start: 0.9254 (p) cc_final: 0.9014 (p)
REVERT: A 1424 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8470 (mp)
REVERT: A 1513 LYS cc_start: 0.9244 (mmtt) cc_final: 0.9022 (mmtt)
REVERT: A 1515 MET cc_start: 0.8879 (mmp) cc_final: 0.8100 (mmp)
REVERT: A 1536 MET cc_start: 0.8751 (ttp) cc_final: 0.8185 (ttp)
REVERT: B  210 LYS cc_start: 0.7889 (tmmt) cc_final: 0.7612 (tmmt)
REVERT: B  216 TRP cc_start: 0.7405 (p-90) cc_final: 0.4774 (t-100)
REVERT: B  233 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8037 (pm20)
REVERT: B  270 ASP cc_start: 0.8673 (t70) cc_final: 0.8348 (t0)
  outliers start: 37
  outliers final: 29
  residues processed: 217
  average time/residue: 0.0913
  time to fit residues: 29.9402
Evaluate side-chains
  219 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 186
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1225 VAL
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain A residue 1332 MET
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1476 MET
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1547 SER
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain A residue 1589 GLN
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  379 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 111 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 97 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 143 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 79 optimal weight:    0.0870
   chunk 101 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 GLN
A1589 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.149413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.114621 restraints weight = 18629.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.38
r_work: 0.3350 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.085  12736  Z= 0.115
  Angle     :  0.559  10.729  17221  Z= 0.285
  Chirality :  0.039   0.196   1915
  Planarity :  0.004   0.043   2078
  Dihedral  : 10.312  69.343   2078
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.61 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.23), residues: 1444
  helix:  1.79 (0.17), residues: 957
  sheet:  None (None), residues: 0
  loop : -1.44 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1468 
 TYR   0.016   0.001   TYR A1426 
 PHE   0.024   0.001   PHE A 389 
 TRP   0.023   0.001   TRP A 119 
 HIS   0.002   0.001   HIS A1514 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (12719)
  covalent geometry    : angle       0.55089 (17180)
  SS BOND              : bond        0.00145 (   10)
  SS BOND              : angle       1.75265 (   20)
  hydrogen bonds       : bond        0.04137 (  720)
  hydrogen bonds       : angle       4.05059 ( 2109)
  link_BETA1-4         : bond        0.00667 (    3)
  link_BETA1-4         : angle       1.49116 (    9)
  link_NAG-ASN         : bond        0.00446 (    4)
  link_NAG-ASN         : angle       2.57344 (   12)

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

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

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2888 Ramachandran restraints generated.
    1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 191
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8103 (tt0) cc_final: 0.7701 (tp30)
REVERT: A  152 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7156 (tpp80)
REVERT: A  244 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7609 (ptpt)
REVERT: A  388 MET cc_start: 0.6698 (ppp) cc_final: 0.6350 (ppp)
REVERT: A  616 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8344 (tm-30)
REVERT: A  906 GLU cc_start: 0.8117 (mp0) cc_final: 0.7903 (mp0)
REVERT: A  972 MET cc_start: 0.8135 (mmt) cc_final: 0.7914 (mmt)
REVERT: A 1003 MET cc_start: 0.9357 (mmm) cc_final: 0.8820 (mmm)
REVERT: A 1009 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8373 (mt-10)
REVERT: A 1202 LYS cc_start: 0.7517 (pttm) cc_final: 0.7038 (tptt)
REVERT: A 1263 MET cc_start: 0.6180 (ptp) cc_final: 0.5792 (ptp)
REVERT: A 1302 MET cc_start: 0.7032 (ttt) cc_final: 0.6777 (tmt)
REVERT: A 1335 SER cc_start: 0.9204 (p) cc_final: 0.8991 (p)
REVERT: A 1424 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: A 1468 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8545 (ttm-80)
REVERT: A 1515 MET cc_start: 0.8859 (mmp) cc_final: 0.8342 (mmp)
REVERT: A 1536 MET cc_start: 0.8748 (ttp) cc_final: 0.8317 (ttp)
REVERT: A 1557 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7112 (mt-10)
REVERT: A 1589 GLN cc_start: 0.6131 (OUTLIER) cc_final: 0.5877 (pm20)
REVERT: B  210 LYS cc_start: 0.7786 (tmmt) cc_final: 0.7494 (tmmt)
REVERT: B  216 TRP cc_start: 0.7213 (p-90) cc_final: 0.4706 (t-100)
REVERT: B  233 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7982 (pm20)
REVERT: B  270 ASP cc_start: 0.8624 (t70) cc_final: 0.8192 (t0)
  outliers start: 33
  outliers final: 27
  residues processed: 215
  average time/residue: 0.0929
  time to fit residues: 30.0841
Evaluate side-chains
  216 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 183
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  152 ARG
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  943 PHE
Chi-restraints excluded: chain A residue 1086 VAL
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1225 VAL
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1476 MET
Chi-restraints excluded: chain A residue 1494 LEU
Chi-restraints excluded: chain A residue 1547 SER
Chi-restraints excluded: chain A residue 1557 GLU
Chi-restraints excluded: chain A residue 1589 GLN
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  379 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 110 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 54 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 141 optimal weight:    0.7980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1589 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.147116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.112172 restraints weight = 18639.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.37
r_work: 0.3312 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  12736  Z= 0.158
  Angle     :  0.592  10.563  17221  Z= 0.304
  Chirality :  0.041   0.190   1915
  Planarity :  0.004   0.042   2078
  Dihedral  : 10.370  69.786   2078
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.76 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.22), residues: 1444
  helix:  1.62 (0.17), residues: 966
  sheet:  None (None), residues: 0
  loop : -1.51 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 262 
 TYR   0.014   0.001   TYR A1135 
 PHE   0.025   0.002   PHE A 389 
 TRP   0.027   0.001   TRP A 119 
 HIS   0.004   0.001   HIS A 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12719)
  covalent geometry    : angle       0.58406 (17180)
  SS BOND              : bond        0.00135 (   10)
  SS BOND              : angle       2.03154 (   20)
  hydrogen bonds       : bond        0.04674 (  720)
  hydrogen bonds       : angle       4.13435 ( 2109)
  link_BETA1-4         : bond        0.00694 (    3)
  link_BETA1-4         : angle       1.51550 (    9)
  link_NAG-ASN         : bond        0.00358 (    4)
  link_NAG-ASN         : angle       2.56967 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3063.54 seconds
wall clock time: 53 minutes 1.57 seconds (3181.57 seconds total)