Starting phenix.real_space_refine
on Wed Feb  4 12:51:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j9f_61270/02_2026/9j9f_61270.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j9f_61270/02_2026/9j9f_61270.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j9f_61270/02_2026/9j9f_61270.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j9f_61270/02_2026/9j9f_61270.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j9f_61270/02_2026/9j9f_61270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j9f_61270/02_2026/9j9f_61270.map"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    6787      2.51       5
     N    1760      2.21       5
     O    1888      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10487
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1400, 10473
          Classifications: {'peptide': 1400}
          Incomplete info: {'truncation_to_alanine': 175}
          Link IDs: {'PTRANS': 50, 'TRANS': 1349}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 656
          Unresolved non-hydrogen angles: 830
          Unresolved non-hydrogen dihedrals: 523
          Unresolved non-hydrogen chiralities: 64
          Planarities with less than four sites: {'ARG:plan': 16, 'ASP:plan': 20, 'GLU:plan': 18, 'PHE:plan': 4, 'GLN:plan1': 13, 'ASN:plan1': 6, 'HIS:plan': 3, 'TRP:plan': 2, 'TYR:plan': 4}
          Unresolved non-hydrogen planarities: 367
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.98, per 1000 atoms: 0.19
  Number of scatterers: 10487
  At special positions: 0
  Unit cell: (78.02, 115.37, 156.87, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1888      8.00
     N    1760      7.00
     C    6787      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS A  32 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1601 " - " ASN A  19 "
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 471.4 milliseconds
  

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2650

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 5 sheets defined
      69.9% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 22
      removed outlier: 3.519A  pdb=" N   THR A  21 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 35
    Processing helix  chain 'A' and resid 36 through 60
      Proline residue:  A  42  - end of helix
      Proline residue:  A  51  - end of helix
    Processing helix  chain 'A' and resid 68 through 99
      removed outlier: 3.553A  pdb=" N   LYS A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ASP A  88 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 130
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 135 through 162
      removed outlier: 3.501A  pdb=" N   LYS A 162 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 190
      removed outlier: 3.579A  pdb=" N   CYS A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 220
    Processing helix  chain 'A' and resid 221 through 223
      No H-bonds generated for 'chain 'A' and resid 221 through 223'
    Processing helix  chain 'A' and resid 224 through 234
      removed outlier: 3.788A  pdb=" N   TYR A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 252
      removed outlier: 3.536A  pdb=" N   THR A 249 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   SER A 250 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU A 251 " --> pdb=" O   ASP A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 269
      removed outlier: 3.618A  pdb=" N   LEU A 257 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 322
      removed outlier: 3.525A  pdb=" N   VAL A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 339
      removed outlier: 3.906A  pdb=" N   PHE A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 355
      removed outlier: 3.678A  pdb=" N   GLU A 344 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 408
      removed outlier: 3.777A  pdb=" N   LEU A 408 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 417
    Processing helix  chain 'A' and resid 419 through 429
      removed outlier: 3.604A  pdb=" N   LEU A 426 " --> pdb=" O   GLU A 422 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   MET A 427 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 439
      removed outlier: 3.869A  pdb=" N   ALA A 438 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   THR A 439 " --> pdb=" O   MET A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 463
      Proline residue:  A 448  - end of helix
    Processing helix  chain 'A' and resid 466 through 511
      removed outlier: 3.756A  pdb=" N   VAL A 472 " --> pdb=" O   ALA A 468 " (cutoff:3.500A)
      Proline residue:  A 478  - end of helix
      removed outlier: 3.705A  pdb=" N   LYS A 488 " --> pdb=" O   ALA A 484 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA A 493 " --> pdb=" O   THR A 489 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASN A 500 " --> pdb=" O   LYS A 496 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 519
    Processing helix  chain 'A' and resid 520 through 571
      removed outlier: 3.548A  pdb=" N   PHE A 524 " --> pdb=" O   TRP A 520 " (cutoff:3.500A)
      Proline residue:  A 557  - end of helix
    Processing helix  chain 'A' and resid 584 through 621
      removed outlier: 4.618A  pdb=" N   PHE A 594 " --> pdb=" O   ASN A 590 " (cutoff:3.500A)
      Proline residue:  A 595  - end of helix
      Proline residue:  A 600  - end of helix
    Processing helix  chain 'A' and resid 683 through 692
      removed outlier: 3.567A  pdb=" N   LEU A 687 " --> pdb=" O   GLY A 683 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   LEU A 688 " --> pdb=" O   LYS A 684 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   SER A 689 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 728
    Processing helix  chain 'A' and resid 733 through 744
    Processing helix  chain 'A' and resid 746 through 751
    Processing helix  chain 'A' and resid 755 through 759
      removed outlier: 4.356A  pdb=" N   ARG A 758 " --> pdb=" O   SER A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 785
      removed outlier: 3.515A  pdb=" N   ASP A 785 " --> pdb=" O   ALA A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 798
      removed outlier: 4.116A  pdb=" N   ALA A 797 " --> pdb=" O   PRO A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 799 through 811
    Processing helix  chain 'A' and resid 831 through 835
    Processing helix  chain 'A' and resid 851 through 858
    Processing helix  chain 'A' and resid 860 through 870
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 3.781A  pdb=" N   TRP A 963 " --> pdb=" O   LEU A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 1000
    Processing helix  chain 'A' and resid 1010 through 1058
    Processing helix  chain 'A' and resid 1059 through 1066
      removed outlier: 3.718A  pdb=" N   PHE A1063 " --> pdb=" O   PRO A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1085
      removed outlier: 3.623A  pdb=" N   LEU A1071 " --> pdb=" O   PRO A1067 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLU A1078 " --> pdb=" O   ARG A1074 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   LEU A1079 " --> pdb=" O   PHE A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1111
    Processing helix  chain 'A' and resid 1117 through 1122
    Processing helix  chain 'A' and resid 1128 through 1146
    Processing helix  chain 'A' and resid 1147 through 1160
      removed outlier: 3.972A  pdb=" N   TYR A1151 " --> pdb=" O   ARG A1147 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY A1160 " --> pdb=" O   GLU A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1160 through 1167
    Processing helix  chain 'A' and resid 1169 through 1220
      removed outlier: 3.662A  pdb=" N   PHE A1173 " --> pdb=" O   GLU A1169 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A1187 " --> pdb=" O   GLU A1183 " (cutoff:3.500A)
      Proline residue:  A1190  - end of helix
      removed outlier: 3.711A  pdb=" N   SER A1220 " --> pdb=" O   PHE A1216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1227 through 1257
      removed outlier: 3.833A  pdb=" N   GLN A1238 " --> pdb=" O   SER A1234 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   THR A1240 " --> pdb=" O   SER A1236 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   THR A1241 " --> pdb=" O   LEU A1237 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ASN A1244 " --> pdb=" O   THR A1240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1263
      removed outlier: 3.719A  pdb=" N   GLU A1261 " --> pdb=" O   ILE A1257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1268
      removed outlier: 3.631A  pdb=" N   SER A1267 " --> pdb=" O   LYS A1264 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU A1268 " --> pdb=" O   GLU A1265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1264 through 1268'
    Processing helix  chain 'A' and resid 1331 through 1340
    Processing helix  chain 'A' and resid 1358 through 1360
      No H-bonds generated for 'chain 'A' and resid 1358 through 1360'
    Processing helix  chain 'A' and resid 1361 through 1367
      removed outlier: 3.500A  pdb=" N   PHE A1367 " --> pdb=" O   HIS A1363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1382 through 1388
      removed outlier: 3.690A  pdb=" N   ASN A1386 " --> pdb=" O   SER A1382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1394 through 1405
    Processing helix  chain 'A' and resid 1407 through 1413
    Processing helix  chain 'A' and resid 1423 through 1427
      removed outlier: 3.699A  pdb=" N   GLU A1427 " --> pdb=" O   GLU A1424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1430 through 1446
    Processing helix  chain 'A' and resid 1454 through 1458
    Processing helix  chain 'A' and resid 1460 through 1474
      removed outlier: 3.674A  pdb=" N   ASP A1464 " --> pdb=" O   ASP A1460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1491
      removed outlier: 3.752A  pdb=" N   ILE A1490 " --> pdb=" O   ARG A1486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1509 through 1516
    Processing helix  chain 'A' and resid 1518 through 1526
    Processing sheet with id=AA1, first strand: chain 'A' and resid 631 through 633
      removed outlier: 6.358A  pdb=" N   VAL A 702 " --> pdb=" O   GLN A 631 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   ARG A 633 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL A 704 " --> pdb=" O   ARG A 633 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 661 through 664
      removed outlier: 3.633A  pdb=" N   GLY A 663 " --> pdb=" O   ALA A 649 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   ALA A 649 " --> pdb=" O   GLY A 663 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU A 699 " --> pdb=" O   THR A 650 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   THR A 652 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   LYS A 697 " --> pdb=" O   THR A 652 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 710
      removed outlier: 6.336A  pdb=" N   ALA A 709 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ASP A 792 " --> pdb=" O   ALA A 709 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   TYR A 789 " --> pdb=" O   LEU A 823 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   VAL A 825 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LEU A 791 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET A 841 " --> pdb=" O   VAL A 677 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   VAL A 840 " --> pdb=" O   SER A 847 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1311 through 1316
      removed outlier: 4.128A  pdb=" N   ILE A1312 " --> pdb=" O   ASP A1296 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1449 through 1450
      removed outlier: 3.614A  pdb=" N   LEU A1481 " --> pdb=" O   LEU A1450 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ARG A1495 " --> pdb=" O   LYS A1321 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A1323 " --> pdb=" O   ARG A1495 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A1497 " --> pdb=" O   GLY A1323 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   VAL A1498 " --> pdb=" O   GLN A1505 " (cutoff:3.500A)

    688 hydrogen bonds defined for protein.
    2019 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: 1.67

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1672
        1.30 -     1.43: 2844
        1.43 -     1.56: 6119
        1.56 -     1.68: 0
        1.68 -     1.81: 84
  Bond restraints: 10719
  Sorted by residual:
  bond pdb=" C7  NAG A1601 "
       pdb=" N2  NAG A1601 "
    ideal  model  delta    sigma   weight residual
    1.346  1.474 -0.128 2.00e-02 2.50e+03 4.07e+01
  bond pdb=" C1  NAG A1601 "
       pdb=" O5  NAG A1601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.523 -0.117 2.00e-02 2.50e+03 3.43e+01
  bond pdb=" C2  NAG A1601 "
       pdb=" N2  NAG A1601 "
    ideal  model  delta    sigma   weight residual
    1.439  1.508 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" C5  NAG A1601 "
       pdb=" O5  NAG A1601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.470 -0.057 2.00e-02 2.50e+03 8.12e+00
  bond pdb=" C2  NAG A1601 "
       pdb=" C3  NAG A1601 "
    ideal  model  delta    sigma   weight residual
    1.526  1.482  0.044 2.00e-02 2.50e+03 4.80e+00
  ... (remaining 10714 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 14210
        1.65 -     3.30: 345
        3.30 -     4.95: 46
        4.95 -     6.60: 9
        6.60 -     8.25: 2
  Bond angle restraints: 14612
  Sorted by residual:
  angle pdb=" C   LEU A 381 "
        pdb=" N   HIS A 382 "
        pdb=" CA  HIS A 382 "
      ideal   model   delta    sigma   weight residual
     121.66  116.33    5.33 1.76e+00 3.23e-01 9.15e+00
  angle pdb=" C   PHE A1131 "
        pdb=" N   TYR A1132 "
        pdb=" CA  TYR A1132 "
      ideal   model   delta    sigma   weight residual
     121.54  116.14    5.40 1.91e+00 2.74e-01 8.00e+00
  angle pdb=" C   LEU A1056 "
        pdb=" N   ARG A1057 "
        pdb=" CA  ARG A1057 "
      ideal   model   delta    sigma   weight residual
     122.26  117.53    4.73 1.73e+00 3.34e-01 7.48e+00
  angle pdb=" N   GLY A  99 "
        pdb=" CA  GLY A  99 "
        pdb=" C   GLY A  99 "
      ideal   model   delta    sigma   weight residual
     113.18  118.84   -5.66 2.37e+00 1.78e-01 5.70e+00
  angle pdb=" N   VAL A 584 "
        pdb=" CA  VAL A 584 "
        pdb=" C   VAL A 584 "
      ideal   model   delta    sigma   weight residual
     111.90  110.02    1.88 8.10e-01 1.52e+00 5.39e+00
  ... (remaining 14607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 5737
       17.95 -    35.90: 497
       35.90 -    53.86: 82
       53.86 -    71.81: 18
       71.81 -    89.76: 8
  Dihedral angle restraints: 6342
    sinusoidal: 2253
      harmonic: 4089
  Sorted by residual:
  dihedral pdb=" CA  LEU A1224 "
           pdb=" C   LEU A1224 "
           pdb=" N   SER A1225 "
           pdb=" CA  SER A1225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.69  -25.31     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CB  CYS A   7 "
           pdb=" SG  CYS A   7 "
           pdb=" SG  CYS A  32 "
           pdb=" CB  CYS A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.64   40.36     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" CA  PHE A1127 "
           pdb=" C   PHE A1127 "
           pdb=" N   VAL A1128 "
           pdb=" CA  VAL A1128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.10   23.90     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 6339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1020
       0.034 -    0.069: 529
       0.069 -    0.103: 143
       0.103 -    0.137: 34
       0.137 -    0.171: 6
  Chirality restraints: 1732
  Sorted by residual:
  chirality pdb=" CA  HIS A 382 "
            pdb=" N   HIS A 382 "
            pdb=" C   HIS A 382 "
            pdb=" CB  HIS A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.33e-01
  chirality pdb=" C5  NAG A1601 "
            pdb=" C4  NAG A1601 "
            pdb=" C6  NAG A1601 "
            pdb=" O5  NAG A1601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.56    0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  PRO A1112 "
            pdb=" N   PRO A1112 "
            pdb=" C   PRO A1112 "
            pdb=" CB  PRO A1112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.29e-01
  ... (remaining 1729 not shown)

  Planarity restraints: 1835
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 322 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.38e+00
        pdb=" N   PRO A 323 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 323 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 323 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1148 "   -0.033 5.00e-02 4.00e+02   5.00e-02 4.00e+00
        pdb=" N   PRO A1149 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A1149 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A1149 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 382 "   -0.010 2.00e-02 2.50e+03   1.91e-02 3.65e+00
        pdb=" C   HIS A 382 "    0.033 2.00e-02 2.50e+03
        pdb=" O   HIS A 382 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLN A 383 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1832 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.50: 94
        2.50 -     3.10: 9159
        3.10 -     3.70: 16196
        3.70 -     4.30: 23133
        4.30 -     4.90: 37451
  Nonbonded interactions: 86033
  Sorted by model distance:
  nonbonded pdb=" O   SER A 328 "
            pdb=" CE1 TYR A 384 "
     model   vdw
     1.905 3.340
  nonbonded pdb=" OH  TYR A 384 "
            pdb=" ND2 ASN A 442 "
     model   vdw
     1.908 3.120
  nonbonded pdb=" OE1 GLN A  34 "
            pdb=" OG  SER A 155 "
     model   vdw
     1.967 3.040
  nonbonded pdb=" O   CYS A 265 "
            pdb=" OG  SER A 268 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" OH  TYR A 384 "
            pdb=" CG  ASN A 442 "
     model   vdw
     2.067 3.270
  ... (remaining 86028 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.840
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.120
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
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      :  0.007   0.128  10721  Z= 0.339
  Angle     :  0.645   8.246  14617  Z= 0.367
  Chirality :  0.043   0.171   1732
  Planarity :  0.005   0.063   1834
  Dihedral  : 14.279  89.760   3689
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 39.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.87 (0.19), residues: 1394
  helix: -1.89 (0.14), residues: 901
  sheet: -4.37 (0.39), residues: 69
  loop : -3.40 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1221 
 TYR   0.017   0.002   TYR A 318 
 PHE   0.018   0.002   PHE A 981 
 TRP   0.013   0.002   TRP A 242 
 HIS   0.008   0.002   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00744 (10719)
  covalent geometry    : angle       0.63969 (14612)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.04449 (    2)
  hydrogen bonds       : bond        0.13376 (  688)
  hydrogen bonds       : angle       6.45265 ( 2019)
  link_NAG-ASN         : bond        0.00639 (    1)
  link_NAG-ASN         : angle       5.71974 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 296
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 PHE cc_start: 0.8009 (m-80) cc_final: 0.7751 (m-80)
REVERT: A  154 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.7192 (ttt-90)
REVERT: A  193 ASP cc_start: 0.7996 (m-30) cc_final: 0.7726 (t0)
REVERT: A  259 LYS cc_start: 0.8359 (mtpt) cc_final: 0.8115 (mtmm)
REVERT: A  263 LYS cc_start: 0.8128 (mttt) cc_final: 0.7913 (ttmm)
REVERT: A  330 LEU cc_start: 0.8197 (tt) cc_final: 0.7893 (tp)
REVERT: A  488 LYS cc_start: 0.7498 (tmtt) cc_final: 0.7280 (tmtt)
REVERT: A  632 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7943 (mtt180)
REVERT: A  839 ILE cc_start: 0.8366 (pt) cc_final: 0.7856 (mt)
REVERT: A 1034 MET cc_start: 0.7022 (tpp) cc_final: 0.6764 (tmm)
REVERT: A 1253 MET cc_start: 0.8356 (mmm) cc_final: 0.7719 (mmm)
REVERT: A 1341 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7792 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 296
  average time/residue: 0.1036
  time to fit residues: 41.8105
Evaluate side-chains
  287 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0470
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.1980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.3878

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

Flipped N/Q/H residues before XYZ refinement:
A 412 ASN
A 461 ASN
A 491 GLN
A 656 ASN
A 719 ASN
A 985 HIS
A1184 ASN
A1244 ASN
** A1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1386 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.137258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112892 restraints weight = 15267.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.94
r_work: 0.3313 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10721  Z= 0.149
  Angle     :  0.616   9.216  14617  Z= 0.319
  Chirality :  0.042   0.168   1732
  Planarity :  0.005   0.063   1834
  Dihedral  :  4.424  28.368   1512
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.06 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.22), residues: 1394
  helix:  0.27 (0.17), residues: 912
  sheet: -3.62 (0.45), residues: 68
  loop : -1.96 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1262 
 TYR   0.032   0.002   TYR A1032 
 PHE   0.023   0.002   PHE A 558 
 TRP   0.031   0.001   TRP A1507 
 HIS   0.006   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10719)
  covalent geometry    : angle       0.60990 (14612)
  SS BOND              : bond        0.00082 (    1)
  SS BOND              : angle       0.53901 (    2)
  hydrogen bonds       : bond        0.05079 (  688)
  hydrogen bonds       : angle       4.68514 ( 2019)
  link_NAG-ASN         : bond        0.01450 (    1)
  link_NAG-ASN         : angle       6.17408 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 289
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.7768 (pt0) cc_final: 0.7538 (pt0)
REVERT: A  263 LYS cc_start: 0.8254 (mttt) cc_final: 0.8032 (ttmm)
REVERT: A  488 LYS cc_start: 0.7749 (tmtt) cc_final: 0.7509 (tmtt)
REVERT: A  515 LEU cc_start: 0.8209 (mt) cc_final: 0.7905 (mm)
REVERT: A  632 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.8131 (mtt-85)
REVERT: A  704 VAL cc_start: 0.8470 (t) cc_final: 0.8268 (p)
REVERT: A  716 TRP cc_start: 0.8582 (t60) cc_final: 0.8132 (t60)
REVERT: A  811 ILE cc_start: 0.7263 (mt) cc_final: 0.6976 (mp)
REVERT: A 1034 MET cc_start: 0.7990 (tpp) cc_final: 0.7604 (mmm)
REVERT: A 1098 PHE cc_start: 0.7984 (m-10) cc_final: 0.7761 (m-10)
REVERT: A 1253 MET cc_start: 0.8658 (mmm) cc_final: 0.8075 (mmm)
REVERT: A 1255 THR cc_start: 0.8523 (m) cc_final: 0.8307 (m)
REVERT: A 1261 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7700 (tm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 293
  average time/residue: 0.1018
  time to fit residues: 40.8672
Evaluate side-chains
  294 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 280
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  821 THR
Chi-restraints excluded: chain A residue  983 CYS
Chi-restraints excluded: chain A residue 1140 LYS
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1342 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 112 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 124 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 118 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
A 590 ASN
A 631 GLN
A 809 ASN
A 985 HIS
A1244 ASN
** A1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.136618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.112107 restraints weight = 15394.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.96
r_work: 0.3305 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10721  Z= 0.159
  Angle     :  0.566   7.757  14617  Z= 0.293
  Chirality :  0.042   0.146   1732
  Planarity :  0.005   0.067   1834
  Dihedral  :  4.199  27.236   1512
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.76 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.23), residues: 1394
  helix:  0.97 (0.17), residues: 913
  sheet: -2.63 (0.59), residues: 58
  loop : -1.53 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1262 
 TYR   0.026   0.002   TYR A1032 
 PHE   0.034   0.001   PHE A 558 
 TRP   0.017   0.001   TRP A1507 
 HIS   0.010   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10719)
  covalent geometry    : angle       0.56100 (14612)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.67535 (    2)
  hydrogen bonds       : bond        0.04954 (  688)
  hydrogen bonds       : angle       4.36682 ( 2019)
  link_NAG-ASN         : bond        0.00972 (    1)
  link_NAG-ASN         : angle       4.99631 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 288
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 ASP cc_start: 0.7449 (p0) cc_final: 0.6993 (p0)
REVERT: A   15 PHE cc_start: 0.8546 (t80) cc_final: 0.8303 (t80)
REVERT: A   17 GLU cc_start: 0.7678 (pt0) cc_final: 0.7475 (pt0)
REVERT: A   98 MET cc_start: 0.7065 (tpp) cc_final: 0.6796 (tpp)
REVERT: A  263 LYS cc_start: 0.8258 (mttt) cc_final: 0.8030 (ttmm)
REVERT: A  443 MET cc_start: 0.8266 (mmm) cc_final: 0.8010 (mmt)
REVERT: A  488 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7492 (tmtt)
REVERT: A  515 LEU cc_start: 0.8244 (mt) cc_final: 0.7961 (mm)
REVERT: A  534 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7329 (mp0)
REVERT: A  632 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.7994 (mtt180)
REVERT: A  704 VAL cc_start: 0.8454 (t) cc_final: 0.8231 (p)
REVERT: A  774 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7976 (mm-40)
REVERT: A  811 ILE cc_start: 0.7217 (mt) cc_final: 0.6961 (mp)
REVERT: A 1034 MET cc_start: 0.7977 (tpp) cc_final: 0.7634 (mmm)
REVERT: A 1253 MET cc_start: 0.8649 (mmm) cc_final: 0.8150 (mmm)
REVERT: A 1255 THR cc_start: 0.8514 (m) cc_final: 0.8274 (m)
REVERT: A 1261 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7682 (tm-30)
  outliers start: 28
  outliers final: 17
  residues processed: 300
  average time/residue: 0.1068
  time to fit residues: 44.0347
Evaluate side-chains
  300 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 282
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1479 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 80 optimal weight:    0.3980
   chunk 97 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 110 optimal weight:    0.8980
   chunk 118 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 590 ASN
A 662 HIS
** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 985 HIS
A1244 ASN
** A1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.136866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.112194 restraints weight = 15576.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.96
r_work: 0.3305 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10721  Z= 0.154
  Angle     :  0.554   8.163  14617  Z= 0.286
  Chirality :  0.042   0.234   1732
  Planarity :  0.004   0.067   1834
  Dihedral  :  4.071  25.159   1512
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.90 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.23), residues: 1394
  helix:  1.20 (0.17), residues: 918
  sheet: -2.69 (0.51), residues: 68
  loop : -1.22 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1262 
 TYR   0.022   0.002   TYR A1032 
 PHE   0.030   0.001   PHE A 558 
 TRP   0.017   0.001   TRP A 716 
 HIS   0.010   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10719)
  covalent geometry    : angle       0.54935 (14612)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       2.85120 (    2)
  hydrogen bonds       : bond        0.04827 (  688)
  hydrogen bonds       : angle       4.18784 ( 2019)
  link_NAG-ASN         : bond        0.00833 (    1)
  link_NAG-ASN         : angle       4.24678 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 282
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ASP cc_start: 0.7328 (p0) cc_final: 0.7118 (p0)
REVERT: A   15 PHE cc_start: 0.8528 (t80) cc_final: 0.8254 (t80)
REVERT: A   29 PHE cc_start: 0.8437 (m-80) cc_final: 0.8123 (m-80)
REVERT: A   98 MET cc_start: 0.7185 (tpp) cc_final: 0.6908 (tpp)
REVERT: A  263 LYS cc_start: 0.8291 (mttt) cc_final: 0.8056 (ttmm)
REVERT: A  488 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7448 (tmtt)
REVERT: A  515 LEU cc_start: 0.8248 (mt) cc_final: 0.7976 (mm)
REVERT: A  534 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7309 (mp0)
REVERT: A  702 VAL cc_start: 0.8618 (p) cc_final: 0.8401 (t)
REVERT: A  704 VAL cc_start: 0.8468 (t) cc_final: 0.8247 (p)
REVERT: A  811 ILE cc_start: 0.7171 (mt) cc_final: 0.6960 (mp)
REVERT: A  831 TYR cc_start: 0.7181 (m-10) cc_final: 0.6922 (m-10)
REVERT: A 1034 MET cc_start: 0.7963 (tpp) cc_final: 0.7618 (mmm)
REVERT: A 1071 LEU cc_start: 0.8047 (mp) cc_final: 0.7822 (mm)
REVERT: A 1253 MET cc_start: 0.8623 (mmm) cc_final: 0.8169 (mmm)
REVERT: A 1255 THR cc_start: 0.8530 (m) cc_final: 0.8302 (m)
REVERT: A 1261 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7751 (tm-30)
  outliers start: 34
  outliers final: 23
  residues processed: 300
  average time/residue: 0.1055
  time to fit residues: 43.4340
Evaluate side-chains
  303 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 279
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1241 THR
Chi-restraints excluded: chain A residue 1342 ILE
Chi-restraints excluded: chain A residue 1370 THR
Chi-restraints excluded: chain A residue 1479 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0970
   chunk 13 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 733 GLN
A 985 HIS
A 992 ASN
A1244 ASN
A1276 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.137446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112918 restraints weight = 15421.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.94
r_work: 0.3317 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10721  Z= 0.149
  Angle     :  0.534   7.129  14617  Z= 0.276
  Chirality :  0.041   0.146   1732
  Planarity :  0.004   0.065   1834
  Dihedral  :  3.958  23.085   1512
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.52 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.23), residues: 1394
  helix:  1.38 (0.17), residues: 920
  sheet: -2.33 (0.58), residues: 62
  loop : -1.08 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1262 
 TYR   0.023   0.001   TYR A1242 
 PHE   0.028   0.001   PHE A 558 
 TRP   0.024   0.002   TRP A 716 
 HIS   0.009   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10719)
  covalent geometry    : angle       0.53112 (14612)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       2.10582 (    2)
  hydrogen bonds       : bond        0.04723 (  688)
  hydrogen bonds       : angle       4.04739 ( 2019)
  link_NAG-ASN         : bond        0.00751 (    1)
  link_NAG-ASN         : angle       3.69945 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 280
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 PHE cc_start: 0.8557 (t80) cc_final: 0.8290 (t80)
REVERT: A   29 PHE cc_start: 0.8474 (m-80) cc_final: 0.8148 (m-80)
REVERT: A   66 GLN cc_start: 0.8020 (tt0) cc_final: 0.7789 (tt0)
REVERT: A   98 MET cc_start: 0.7196 (tpp) cc_final: 0.6902 (tpp)
REVERT: A  263 LYS cc_start: 0.8283 (mttt) cc_final: 0.8048 (ttmm)
REVERT: A  488 LYS cc_start: 0.7776 (tmtt) cc_final: 0.7521 (tmtt)
REVERT: A  515 LEU cc_start: 0.8247 (mt) cc_final: 0.7983 (mm)
REVERT: A  534 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: A  631 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7398 (pm20)
REVERT: A  632 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.8074 (mtp180)
REVERT: A  702 VAL cc_start: 0.8609 (p) cc_final: 0.8296 (t)
REVERT: A  704 VAL cc_start: 0.8463 (t) cc_final: 0.8255 (p)
REVERT: A  960 SER cc_start: 0.8018 (m) cc_final: 0.7782 (t)
REVERT: A 1034 MET cc_start: 0.7980 (tpp) cc_final: 0.7641 (mmm)
REVERT: A 1071 LEU cc_start: 0.8038 (mp) cc_final: 0.7818 (mm)
REVERT: A 1253 MET cc_start: 0.8624 (mmm) cc_final: 0.8048 (mmm)
REVERT: A 1255 THR cc_start: 0.8541 (m) cc_final: 0.8305 (m)
REVERT: A 1341 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8413 (ttp-170)
  outliers start: 38
  outliers final: 27
  residues processed: 296
  average time/residue: 0.0974
  time to fit residues: 39.6837
Evaluate side-chains
  310 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 281
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1342 ILE
Chi-restraints excluded: chain A residue 1370 THR
Chi-restraints excluded: chain A residue 1479 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 125 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 120 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   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 590 ASN
** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 809 ASN
A 985 HIS
A1244 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.136741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.112224 restraints weight = 15426.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.93
r_work: 0.3310 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10721  Z= 0.167
  Angle     :  0.546   7.230  14617  Z= 0.282
  Chirality :  0.041   0.140   1732
  Planarity :  0.004   0.066   1834
  Dihedral  :  3.972  21.690   1512
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.18 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.23), residues: 1394
  helix:  1.41 (0.17), residues: 920
  sheet: -2.19 (0.59), residues: 62
  loop : -0.96 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1262 
 TYR   0.026   0.002   TYR A1242 
 PHE   0.027   0.001   PHE A 558 
 TRP   0.017   0.001   TRP A1507 
 HIS   0.010   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (10719)
  covalent geometry    : angle       0.54392 (14612)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       1.52440 (    2)
  hydrogen bonds       : bond        0.04865 (  688)
  hydrogen bonds       : angle       4.03475 ( 2019)
  link_NAG-ASN         : bond        0.00695 (    1)
  link_NAG-ASN         : angle       3.47406 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 280
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 PHE cc_start: 0.8579 (t80) cc_final: 0.8308 (t80)
REVERT: A   29 PHE cc_start: 0.8466 (m-80) cc_final: 0.8092 (m-80)
REVERT: A   57 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7316 (mp)
REVERT: A   66 GLN cc_start: 0.8037 (tt0) cc_final: 0.7804 (tt0)
REVERT: A   98 MET cc_start: 0.7238 (tpp) cc_final: 0.6931 (tpp)
REVERT: A  193 ASP cc_start: 0.8326 (m-30) cc_final: 0.7995 (t0)
REVERT: A  263 LYS cc_start: 0.8291 (mttt) cc_final: 0.8054 (ttmm)
REVERT: A  488 LYS cc_start: 0.7775 (tmtt) cc_final: 0.7517 (tmtt)
REVERT: A  515 LEU cc_start: 0.8271 (mt) cc_final: 0.8009 (mm)
REVERT: A  534 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7299 (mp0)
REVERT: A  632 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.8127 (mtp180)
REVERT: A  702 VAL cc_start: 0.8656 (p) cc_final: 0.8405 (t)
REVERT: A  960 SER cc_start: 0.8017 (m) cc_final: 0.7768 (t)
REVERT: A 1034 MET cc_start: 0.8039 (tpp) cc_final: 0.7681 (mmm)
REVERT: A 1071 LEU cc_start: 0.8048 (mp) cc_final: 0.7829 (mm)
REVERT: A 1253 MET cc_start: 0.8617 (mmm) cc_final: 0.8059 (mmm)
REVERT: A 1255 THR cc_start: 0.8482 (m) cc_final: 0.8254 (m)
REVERT: A 1261 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7754 (tm-30)
REVERT: A 1341 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8412 (ttp-170)
  outliers start: 42
  outliers final: 33
  residues processed: 298
  average time/residue: 0.1165
  time to fit residues: 47.4475
Evaluate side-chains
  316 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 281
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1241 THR
Chi-restraints excluded: chain A residue 1342 ILE
Chi-restraints excluded: chain A residue 1370 THR
Chi-restraints excluded: chain A residue 1479 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   chunk 121 optimal weight:    0.3980
   chunk 131 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 123 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0970
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0670
   chunk 104 optimal weight:    0.5980
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 985 HIS
A1244 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.140019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.115656 restraints weight = 15343.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.93
r_work: 0.3348 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10721  Z= 0.117
  Angle     :  0.519   7.411  14617  Z= 0.266
  Chirality :  0.040   0.148   1732
  Planarity :  0.004   0.063   1834
  Dihedral  :  3.727  19.050   1512
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.85 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.23), residues: 1394
  helix:  1.79 (0.17), residues: 916
  sheet: -1.94 (0.54), residues: 74
  loop : -0.70 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1262 
 TYR   0.019   0.001   TYR A1242 
 PHE   0.025   0.001   PHE A 558 
 TRP   0.020   0.001   TRP A  94 
 HIS   0.010   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10719)
  covalent geometry    : angle       0.51739 (14612)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       1.00884 (    2)
  hydrogen bonds       : bond        0.04207 (  688)
  hydrogen bonds       : angle       3.83545 ( 2019)
  link_NAG-ASN         : bond        0.00737 (    1)
  link_NAG-ASN         : angle       2.86723 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 287
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 PHE cc_start: 0.8481 (t80) cc_final: 0.8280 (t80)
REVERT: A   17 GLU cc_start: 0.7664 (pt0) cc_final: 0.7457 (pt0)
REVERT: A   29 PHE cc_start: 0.8405 (m-80) cc_final: 0.8051 (m-80)
REVERT: A   66 GLN cc_start: 0.7971 (tt0) cc_final: 0.7722 (tt0)
REVERT: A   67 MET cc_start: 0.7911 (mmm) cc_final: 0.7689 (mpp)
REVERT: A   98 MET cc_start: 0.7239 (tpp) cc_final: 0.6843 (tpt)
REVERT: A  193 ASP cc_start: 0.8315 (m-30) cc_final: 0.7992 (t0)
REVERT: A  263 LYS cc_start: 0.8270 (mttt) cc_final: 0.8036 (ttmm)
REVERT: A  488 LYS cc_start: 0.7758 (tmtt) cc_final: 0.7500 (tmtt)
REVERT: A  515 LEU cc_start: 0.8248 (mt) cc_final: 0.7995 (mm)
REVERT: A  534 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7129 (mp0)
REVERT: A  632 ARG cc_start: 0.8278 (mtt-85) cc_final: 0.7942 (mtt-85)
REVERT: A  702 VAL cc_start: 0.8677 (p) cc_final: 0.8414 (t)
REVERT: A  811 ILE cc_start: 0.6981 (mm) cc_final: 0.6685 (mt)
REVERT: A  960 SER cc_start: 0.7974 (m) cc_final: 0.7772 (t)
REVERT: A  981 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6769 (t80)
REVERT: A 1034 MET cc_start: 0.8017 (tpp) cc_final: 0.7572 (mmm)
REVERT: A 1071 LEU cc_start: 0.7981 (mp) cc_final: 0.7745 (mm)
REVERT: A 1253 MET cc_start: 0.8616 (mmm) cc_final: 0.8016 (mmm)
REVERT: A 1255 THR cc_start: 0.8524 (m) cc_final: 0.8287 (m)
  outliers start: 35
  outliers final: 19
  residues processed: 302
  average time/residue: 0.0981
  time to fit residues: 40.3094
Evaluate side-chains
  299 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 278
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue  981 PHE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1140 LYS
Chi-restraints excluded: chain A residue 1241 THR
Chi-restraints excluded: chain A residue 1342 ILE
Chi-restraints excluded: chain A residue 1370 THR
Chi-restraints excluded: chain A residue 1479 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0870
   chunk 89 optimal weight:    0.9990
   chunk 132 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0050
   chunk 139 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.4172

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN
A 461 ASN
** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 HIS
A 985 HIS
A1244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.139678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115114 restraints weight = 15359.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.95
r_work: 0.3339 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10721  Z= 0.124
  Angle     :  0.528   8.006  14617  Z= 0.269
  Chirality :  0.040   0.149   1732
  Planarity :  0.004   0.064   1834
  Dihedral  :  3.704  18.115   1512
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.37 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.23), residues: 1394
  helix:  1.82 (0.17), residues: 922
  sheet: -1.87 (0.55), residues: 74
  loop : -0.62 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1262 
 TYR   0.028   0.001   TYR A1242 
 PHE   0.038   0.001   PHE A 558 
 TRP   0.018   0.001   TRP A  94 
 HIS   0.014   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10719)
  covalent geometry    : angle       0.52681 (14612)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       0.96569 (    2)
  hydrogen bonds       : bond        0.04304 (  688)
  hydrogen bonds       : angle       3.81672 ( 2019)
  link_NAG-ASN         : bond        0.00676 (    1)
  link_NAG-ASN         : angle       2.64730 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 282
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 PHE cc_start: 0.8517 (t80) cc_final: 0.8248 (t80)
REVERT: A   29 PHE cc_start: 0.8425 (m-80) cc_final: 0.8078 (m-80)
REVERT: A   31 LYS cc_start: 0.8005 (mmmm) cc_final: 0.7754 (mmtm)
REVERT: A   66 GLN cc_start: 0.7939 (tt0) cc_final: 0.7667 (tt0)
REVERT: A   98 MET cc_start: 0.7215 (tpp) cc_final: 0.6977 (tpp)
REVERT: A  193 ASP cc_start: 0.8322 (m-30) cc_final: 0.7997 (t0)
REVERT: A  263 LYS cc_start: 0.8271 (mttt) cc_final: 0.8037 (ttmm)
REVERT: A  443 MET cc_start: 0.8248 (mmm) cc_final: 0.8033 (mmt)
REVERT: A  488 LYS cc_start: 0.7747 (tmtt) cc_final: 0.7470 (tmtt)
REVERT: A  515 LEU cc_start: 0.8247 (mt) cc_final: 0.7990 (mm)
REVERT: A  534 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7141 (mp0)
REVERT: A  631 GLN cc_start: 0.7600 (pt0) cc_final: 0.7300 (pm20)
REVERT: A  811 ILE cc_start: 0.7016 (mm) cc_final: 0.6755 (mt)
REVERT: A  981 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6814 (t80)
REVERT: A 1034 MET cc_start: 0.8002 (tpp) cc_final: 0.7572 (mmm)
REVERT: A 1071 LEU cc_start: 0.7995 (mp) cc_final: 0.7767 (mm)
REVERT: A 1253 MET cc_start: 0.8615 (mmm) cc_final: 0.8051 (mmm)
  outliers start: 27
  outliers final: 20
  residues processed: 292
  average time/residue: 0.1067
  time to fit residues: 42.6567
Evaluate side-chains
  299 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 277
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  665 THR
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue  981 PHE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1342 ILE
Chi-restraints excluded: chain A residue 1370 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 125 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 138 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 91 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 113 optimal weight:    0.8980
   chunk 89 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN
A 590 ASN
** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 809 ASN
A 985 HIS
A1244 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.114073 restraints weight = 15316.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.94
r_work: 0.3321 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10721  Z= 0.153
  Angle     :  0.560   8.651  14617  Z= 0.283
  Chirality :  0.041   0.148   1732
  Planarity :  0.004   0.065   1834
  Dihedral  :  3.779  18.671   1512
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.80 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.23), residues: 1394
  helix:  1.76 (0.17), residues: 922
  sheet: -1.80 (0.57), residues: 74
  loop : -0.62 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1262 
 TYR   0.033   0.001   TYR A1242 
 PHE   0.037   0.001   PHE A 558 
 TRP   0.016   0.001   TRP A  94 
 HIS   0.015   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10719)
  covalent geometry    : angle       0.55855 (14612)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       1.06036 (    2)
  hydrogen bonds       : bond        0.04616 (  688)
  hydrogen bonds       : angle       3.84572 ( 2019)
  link_NAG-ASN         : bond        0.00630 (    1)
  link_NAG-ASN         : angle       2.62423 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 282
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 PHE cc_start: 0.8552 (t80) cc_final: 0.8259 (t80)
REVERT: A   29 PHE cc_start: 0.8412 (m-80) cc_final: 0.8047 (m-80)
REVERT: A   31 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7789 (mptt)
REVERT: A   66 GLN cc_start: 0.7925 (tt0) cc_final: 0.7673 (tt0)
REVERT: A   67 MET cc_start: 0.7871 (mmm) cc_final: 0.7668 (mpp)
REVERT: A   98 MET cc_start: 0.7179 (tpp) cc_final: 0.6901 (tpt)
REVERT: A  193 ASP cc_start: 0.8313 (m-30) cc_final: 0.7969 (t0)
REVERT: A  263 LYS cc_start: 0.8295 (mttt) cc_final: 0.8060 (ttmm)
REVERT: A  488 LYS cc_start: 0.7760 (tmtt) cc_final: 0.7499 (tmtt)
REVERT: A  515 LEU cc_start: 0.8258 (mt) cc_final: 0.8000 (mm)
REVERT: A  534 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7229 (mp0)
REVERT: A  811 ILE cc_start: 0.7134 (mm) cc_final: 0.6756 (mt)
REVERT: A  981 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6891 (t80)
REVERT: A 1034 MET cc_start: 0.7990 (tpp) cc_final: 0.7564 (mmm)
REVERT: A 1071 LEU cc_start: 0.7999 (mp) cc_final: 0.7783 (mm)
REVERT: A 1253 MET cc_start: 0.8613 (mmm) cc_final: 0.8064 (mmm)
  outliers start: 33
  outliers final: 25
  residues processed: 292
  average time/residue: 0.1139
  time to fit residues: 45.5360
Evaluate side-chains
  307 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 280
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue  981 PHE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1342 ILE
Chi-restraints excluded: chain A residue 1370 THR
Chi-restraints excluded: chain A residue 1479 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 95 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0770
   chunk 63 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 47 optimal weight:    0.3980
   chunk 111 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN
A 590 ASN
** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 985 HIS
A1244 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.139486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.114857 restraints weight = 15193.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.94
r_work: 0.3335 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10721  Z= 0.136
  Angle     :  0.567   9.592  14617  Z= 0.284
  Chirality :  0.040   0.150   1732
  Planarity :  0.004   0.064   1834
  Dihedral  :  3.757  18.271   1512
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 21.08 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.23), residues: 1394
  helix:  1.81 (0.17), residues: 924
  sheet: -1.62 (0.62), residues: 63
  loop : -0.57 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 194 
 TYR   0.037   0.001   TYR A1242 
 PHE   0.035   0.001   PHE A 558 
 TRP   0.018   0.001   TRP A  94 
 HIS   0.013   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10719)
  covalent geometry    : angle       0.56583 (14612)
  SS BOND              : bond        0.00316 (    1)
  SS BOND              : angle       0.96565 (    2)
  hydrogen bonds       : bond        0.04446 (  688)
  hydrogen bonds       : angle       3.81207 ( 2019)
  link_NAG-ASN         : bond        0.00665 (    1)
  link_NAG-ASN         : angle       2.42425 (    3)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 275
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 PHE cc_start: 0.8535 (t80) cc_final: 0.8249 (t80)
REVERT: A   29 PHE cc_start: 0.8414 (m-80) cc_final: 0.8035 (m-80)
REVERT: A   31 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7783 (mptt)
REVERT: A   66 GLN cc_start: 0.7937 (tt0) cc_final: 0.7662 (tt0)
REVERT: A   98 MET cc_start: 0.7152 (tpp) cc_final: 0.6864 (tpt)
REVERT: A  193 ASP cc_start: 0.8317 (m-30) cc_final: 0.7982 (t0)
REVERT: A  263 LYS cc_start: 0.8290 (mttt) cc_final: 0.8056 (ttmm)
REVERT: A  488 LYS cc_start: 0.7763 (tmtt) cc_final: 0.7492 (tmtt)
REVERT: A  515 LEU cc_start: 0.8239 (mt) cc_final: 0.7979 (mm)
REVERT: A  534 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7212 (mp0)
REVERT: A  774 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8056 (mt0)
REVERT: A  811 ILE cc_start: 0.7017 (mm) cc_final: 0.6754 (mt)
REVERT: A  981 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6863 (t80)
REVERT: A 1034 MET cc_start: 0.7977 (tpp) cc_final: 0.7565 (mmm)
REVERT: A 1071 LEU cc_start: 0.7984 (mp) cc_final: 0.7763 (mm)
REVERT: A 1253 MET cc_start: 0.8607 (mmm) cc_final: 0.8056 (mmm)
  outliers start: 33
  outliers final: 26
  residues processed: 285
  average time/residue: 0.1146
  time to fit residues: 44.8698
Evaluate side-chains
  303 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 275
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  265 CYS
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  793 ASP
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue  981 PHE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1241 THR
Chi-restraints excluded: chain A residue 1342 ILE
Chi-restraints excluded: chain A residue 1370 THR
Chi-restraints excluded: chain A residue 1479 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 60 optimal weight:    0.1980
   chunk 14 optimal weight:    1.9990
   chunk 128 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 127 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 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 985 HIS
A1244 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.138171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.113301 restraints weight = 15405.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.96
r_work: 0.3313 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10721  Z= 0.168
  Angle     :  0.587  10.249  14617  Z= 0.296
  Chirality :  0.042   0.147   1732
  Planarity :  0.005   0.065   1834
  Dihedral  :  3.851  19.090   1512
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.99 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.23), residues: 1394
  helix:  1.66 (0.17), residues: 929
  sheet: -1.59 (0.63), residues: 63
  loop : -0.62 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 822 
 TYR   0.043   0.002   TYR A1242 
 PHE   0.036   0.001   PHE A 558 
 TRP   0.016   0.001   TRP A  94 
 HIS   0.015   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10719)
  covalent geometry    : angle       0.58607 (14612)
  SS BOND              : bond        0.00352 (    1)
  SS BOND              : angle       1.08213 (    2)
  hydrogen bonds       : bond        0.04789 (  688)
  hydrogen bonds       : angle       3.87467 ( 2019)
  link_NAG-ASN         : bond        0.00618 (    1)
  link_NAG-ASN         : angle       2.43568 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2886.13 seconds
wall clock time: 50 minutes 1.00 seconds (3001.00 seconds total)