Starting phenix.real_space_refine
on Thu Jun  4 05:56:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lg8_63057/06_2026/9lg8_63057_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lg8_63057/06_2026/9lg8_63057.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lg8_63057/06_2026/9lg8_63057_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lg8_63057/06_2026/9lg8_63057_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lg8_63057/06_2026/9lg8_63057.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lg8_63057/06_2026/9lg8_63057.map"
  }
  resolution = 3.55
  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=   0.020
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      58      5.16       5
     C    6900      2.51       5
     N    1754      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 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10600
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1329, 10556
          Classifications: {'peptide': 1329}
          Link IDs: {'PTRANS': 49, 'TRANS': 1279}
          Chain breaks: 8
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 44
          Unusual residues: {'FY5': 1, 'GSH': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.90, per 1000 atoms: 0.27
  Number of scatterers: 10600
  At special positions: 0
  Unit cell: (81, 114, 149, 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      58     16.00
     O    1888      8.00
     N    1754      7.00
     C    6900      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 572.6 milliseconds
  

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2516

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 4 sheets defined
      72.4% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 22
      removed outlier: 3.543A  pdb=" N   THR A  21 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 60
      removed outlier: 3.959A  pdb=" N   LEU A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   VAL A  39 " --> pdb=" O   ASN A  35 " (cutoff:3.500A)
      Proline residue:  A  42  - end of helix
      Proline residue:  A  51  - end of helix
      removed outlier: 3.866A  pdb=" N   LEU A  55 " --> pdb=" O   PRO A  51 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR A  56 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 94
      removed outlier: 3.696A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 130
      removed outlier: 3.578A  pdb=" N   VAL A 108 " --> pdb=" O   PRO A 104 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 136 through 160
      removed outlier: 4.582A  pdb=" N   TRP A 142 " --> pdb=" O   MET A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 191
      removed outlier: 3.544A  pdb=" N   PHE A 175 " --> pdb=" O   ARG A 171 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   PHE A 191 " --> pdb=" O   VAL A 187 " (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: 3.585A  pdb=" N   TYR A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 268
      Proline residue:  A 255  - end of helix
    Processing helix  chain 'A' and resid 312 through 321
      removed outlier: 3.754A  pdb=" N   VAL A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 326 through 355
      removed outlier: 3.797A  pdb=" N   LEU A 330 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY A 342 " --> pdb=" O   MET A 338 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 359 through 408
      removed outlier: 4.404A  pdb=" N   GLY A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 408 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 419 through 429
      removed outlier: 3.898A  pdb=" N   MET A 427 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 439
      removed outlier: 3.815A  pdb=" N   THR A 439 " --> pdb=" O   MET A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 462
      Proline residue:  A 448  - end of helix
      removed outlier: 3.611A  pdb=" N   ALA A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 475
      removed outlier: 3.840A  pdb=" N   GLY A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 510
      removed outlier: 3.673A  pdb=" N   LYS A 503 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU A 504 " --> pdb=" O   ASN A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 519
    Processing helix  chain 'A' and resid 520 through 555
      removed outlier: 3.662A  pdb=" N   LYS A 541 " --> pdb=" O   LYS A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 572
      removed outlier: 4.244A  pdb=" N   ASP A 572 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 592
      removed outlier: 4.039A  pdb=" N   VAL A 584 " --> pdb=" O   GLN A 580 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   SER A 585 " --> pdb=" O   LYS A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 621
      removed outlier: 3.539A  pdb=" N   ASN A 597 " --> pdb=" O   ARG A 593 " (cutoff:3.500A)
      Proline residue:  A 600  - end of helix
    Processing helix  chain 'A' and resid 626 through 630
    Processing helix  chain 'A' and resid 683 through 692
      removed outlier: 3.552A  pdb=" N   LEU A 688 " --> pdb=" O   LYS A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 728
    Processing helix  chain 'A' and resid 733 through 744
      removed outlier: 4.370A  pdb=" N   GLU A 742 " --> pdb=" O   LYS A 738 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 743 " --> pdb=" O   ALA A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 753
    Processing helix  chain 'A' and resid 755 through 759
      removed outlier: 3.659A  pdb=" N   ARG A 758 " --> pdb=" O   SER A 755 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR A 759 " --> pdb=" O   GLY A 756 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 755 through 759'
    Processing helix  chain 'A' and resid 769 through 785
    Processing helix  chain 'A' and resid 799 through 810
    Processing helix  chain 'A' and resid 831 through 835
    Processing helix  chain 'A' and resid 851 through 859
    Processing helix  chain 'A' and resid 860 through 869
      removed outlier: 4.015A  pdb=" N   TYR A 869 " --> pdb=" O   PHE A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
    Processing helix  chain 'A' and resid 970 through 999
    Processing helix  chain 'A' and resid 1011 through 1058
    Processing helix  chain 'A' and resid 1059 through 1066
      removed outlier: 3.529A  pdb=" N   PHE A1063 " --> pdb=" O   PRO A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1076
      removed outlier: 3.589A  pdb=" N   PHE A1075 " --> pdb=" O   LEU A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1085
    Processing helix  chain 'A' and resid 1085 through 1111
    Processing helix  chain 'A' and resid 1112 through 1116
      removed outlier: 3.569A  pdb=" N   VAL A1116 " --> pdb=" O   MET A1113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1160
      removed outlier: 3.616A  pdb=" N   VAL A1133 " --> pdb=" O   GLN A1129 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A1137 " --> pdb=" O   VAL A1133 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLN A1138 " --> pdb=" O   ALA A1134 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   SER A1144 " --> pdb=" O   LYS A1140 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   SER A1148 " --> pdb=" O   SER A1144 " (cutoff:3.500A)
      Proline residue:  A1149  - end of helix
    Processing helix  chain 'A' and resid 1160 through 1167
    Processing helix  chain 'A' and resid 1169 through 1220
      removed outlier: 3.670A  pdb=" N   ALA A1187 " --> pdb=" O   GLU A1183 " (cutoff:3.500A)
      Proline residue:  A1190  - end of helix
      removed outlier: 3.501A  pdb=" N   VAL A1205 " --> pdb=" O   ARG A1201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1225 through 1264
      removed outlier: 3.643A  pdb=" N   THR A1240 " --> pdb=" O   SER A1236 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   THR A1241 " --> pdb=" O   LEU A1237 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASN A1244 " --> pdb=" O   THR A1240 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ALA A1259 " --> pdb=" O   THR A1255 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LYS A1264 " --> pdb=" O   VAL A1260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1331 through 1340
      removed outlier: 3.833A  pdb=" N   THR A1336 " --> pdb=" O   LYS A1332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1361 through 1368
    Processing helix  chain 'A' and resid 1382 through 1388
    Processing helix  chain 'A' and resid 1394 through 1405
    Processing helix  chain 'A' and resid 1407 through 1412
    Processing helix  chain 'A' and resid 1416 through 1420
      removed outlier: 3.864A  pdb=" N   HIS A1420 " --> pdb=" O   LYS A1417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1430 through 1446
      removed outlier: 3.638A  pdb=" N   LYS A1446 " --> pdb=" O   ALA A1442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1463 through 1474
      removed outlier: 3.976A  pdb=" N   GLN A1474 " --> pdb=" O   THR A1470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1493
      removed outlier: 3.879A  pdb=" N   ILE A1490 " --> pdb=" O   ARG A1486 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   ASP A1492 " --> pdb=" O   ASN A1488 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   TYR A1493 " --> pdb=" O   THR A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1509 through 1514
    Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 668
      removed outlier: 7.038A  pdb=" N   HIS A 662 " --> pdb=" O   THR A 650 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   THR A 650 " --> pdb=" O   HIS A 662 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ILE A 664 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL A 646 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   VAL A 702 " --> pdb=" O   VAL A 646 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ASN A 648 " --> pdb=" O   GLY A 700 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY A 700 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   THR A 650 " --> pdb=" O   VAL A 698 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711
      removed outlier: 6.431A  pdb=" N   VAL A 674 " --> pdb=" O   LEU A 824 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   LEU A 673 " --> pdb=" O   VAL A 837 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE A 839 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ALA A 675 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1312 through 1316
      removed outlier: 7.422A  pdb=" N   VAL A1314 " --> pdb=" O   ARG A1295 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   ARG A1295 " --> pdb=" O   VAL A1314 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   ILE A1316 " --> pdb=" O   GLU A1293 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   GLU A1293 " --> pdb=" O   ILE A1316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1369 through 1372
      removed outlier: 6.389A  pdb=" N   LEU A1450 " --> pdb=" O   LEU A1481 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   ILE A1483 " --> pdb=" O   LEU A1450 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   LEU A1452 " --> pdb=" O   ILE A1483 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLY A1323 " --> pdb=" O   ILE A1497 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   LEU A1499 " --> pdb=" O   GLY A1323 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   VAL A1325 " --> pdb=" O   LEU A1499 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   VAL A1496 " --> pdb=" O   TRP A1507 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   TRP A1507 " --> pdb=" O   VAL A1496 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL A1498 " --> pdb=" O   GLN A1505 " (cutoff:3.500A)

    682 hydrogen bonds defined for protein.
    2010 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2048
        1.33 -     1.45: 2587
        1.45 -     1.57: 6110
        1.57 -     1.70: 1
        1.70 -     1.82: 92
  Bond restraints: 10838
  Sorted by residual:
  bond pdb=" N   VAL A1289 "
       pdb=" CA  VAL A1289 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 8.60e-03 1.35e+04 1.46e+01
  bond pdb=" N   VAL A  20 "
       pdb=" CA  VAL A  20 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.08e-02 8.57e+03 1.28e+01
  bond pdb=" O20 FY5 A1601 "
       pdb=" S21 FY5 A1601 "
    ideal  model  delta    sigma   weight residual
    1.673  1.602  0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" N   TRP A1286 "
       pdb=" CA  TRP A1286 "
    ideal  model  delta    sigma   weight residual
    1.462  1.487 -0.025 7.70e-03 1.69e+04 1.07e+01
  bond pdb=" N   ILE A1355 "
       pdb=" CA  ILE A1355 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.19e-02 7.06e+03 9.96e+00
  ... (remaining 10833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 13514
        1.69 -     3.39: 1064
        3.39 -     5.08: 119
        5.08 -     6.77: 15
        6.77 -     8.46: 5
  Bond angle restraints: 14717
  Sorted by residual:
  angle pdb=" N   VAL A1289 "
        pdb=" CA  VAL A1289 "
        pdb=" C   VAL A1289 "
      ideal   model   delta    sigma   weight residual
     113.71  107.57    6.14 9.50e-01 1.11e+00 4.18e+01
  angle pdb=" N   ILE A 441 "
        pdb=" CA  ILE A 441 "
        pdb=" C   ILE A 441 "
      ideal   model   delta    sigma   weight residual
     110.72  105.43    5.29 1.01e+00 9.80e-01 2.74e+01
  angle pdb=" N   PRO A1389 "
        pdb=" CA  PRO A1389 "
        pdb=" C   PRO A1389 "
      ideal   model   delta    sigma   weight residual
     113.40  107.18    6.22 1.34e+00 5.57e-01 2.15e+01
  angle pdb=" N   ASN A 412 "
        pdb=" CA  ASN A 412 "
        pdb=" C   ASN A 412 "
      ideal   model   delta    sigma   weight residual
     111.07  106.43    4.64 1.07e+00 8.73e-01 1.88e+01
  angle pdb=" N   ILE A1342 "
        pdb=" CA  ILE A1342 "
        pdb=" C   ILE A1342 "
      ideal   model   delta    sigma   weight residual
     110.62  106.26    4.36 1.02e+00 9.61e-01 1.83e+01
  ... (remaining 14712 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 5687
       17.88 -    35.77: 586
       35.77 -    53.65: 145
       53.65 -    71.53: 39
       71.53 -    89.42: 14
  Dihedral angle restraints: 6471
    sinusoidal: 2590
      harmonic: 3881
  Sorted by residual:
  dihedral pdb=" CG  ARG A1472 "
           pdb=" CD  ARG A1472 "
           pdb=" NE  ARG A1472 "
           pdb=" CZ  ARG A1472 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -40.17  -49.83     2      1.50e+01 4.44e-03 1.25e+01
  dihedral pdb=" CA  ASP A 785 "
           pdb=" CB  ASP A 785 "
           pdb=" CG  ASP A 785 "
           pdb=" OD1 ASP A 785 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.14   58.14     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CA  VAL A1480 "
           pdb=" C   VAL A1480 "
           pdb=" N   LEU A1481 "
           pdb=" CA  LEU A1481 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.76   16.24     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 6468 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1137
       0.046 -    0.091: 336
       0.091 -    0.136: 153
       0.136 -    0.182: 74
       0.182 -    0.227: 14
  Chirality restraints: 1714
  Sorted by residual:
  chirality pdb=" CA  ARG A 593 "
            pdb=" N   ARG A 593 "
            pdb=" C   ARG A 593 "
            pdb=" CB  ARG A 593 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  ILE A1003 "
            pdb=" N   ILE A1003 "
            pdb=" C   ILE A1003 "
            pdb=" CB  ILE A1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  ILE A1342 "
            pdb=" N   ILE A1342 "
            pdb=" C   ILE A1342 "
            pdb=" CB  ILE A1342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1711 not shown)

  Planarity restraints: 1817
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG1 GSH A1602 "    0.152 2.00e-02 2.50e+03   1.67e-01 3.47e+02
        pdb=" CD1 GSH A1602 "   -0.071 2.00e-02 2.50e+03
        pdb=" OE1 GSH A1602 "   -0.022 2.00e-02 2.50e+03
        pdb=" CA2 GSH A1602 "    0.204 2.00e-02 2.50e+03
        pdb=" N2  GSH A1602 "   -0.262 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  GSH A1602 "    0.038 2.00e-02 2.50e+03   6.00e-02 4.50e+01
        pdb=" CA2 GSH A1602 "   -0.060 2.00e-02 2.50e+03
        pdb=" CA3 GSH A1602 "   -0.073 2.00e-02 2.50e+03
        pdb=" N3  GSH A1602 "    0.086 2.00e-02 2.50e+03
        pdb=" O2  GSH A1602 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 523 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   ALA A 523 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ALA A 523 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PHE A 524 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1814 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2205
        2.78 -     3.31: 11136
        3.31 -     3.84: 18145
        3.84 -     4.37: 21169
        4.37 -     4.90: 35483
  Nonbonded interactions: 88138
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 582 "
            pdb=" OG  SER A 585 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   ALA A 566 "
            pdb=" OG1 THR A 570 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OE2 GLU A 127 "
            pdb=" OG  SER A 135 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OH  TYR A 568 "
            pdb=" O   ILE A 576 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" OH  TYR A 404 "
            pdb=" OG1 THR A1157 "
     model   vdw
     2.362 3.040
  ... (remaining 88133 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.020
  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:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.890
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
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   0.071  10838  Z= 0.472
  Angle     :  0.904   8.464  14717  Z= 0.644
  Chirality :  0.059   0.227   1714
  Planarity :  0.010   0.167   1817
  Dihedral  : 16.239  89.417   3955
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 20.29 %
    Favored  : 79.45 %
  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: -0.15 (0.23), residues: 1311
  helix:  0.47 (0.18), residues: 850
  sheet: -0.30 (0.60), residues: 70
  loop : -1.14 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 735 
 TYR   0.023   0.001   TYR A 318 
 PHE   0.028   0.001   PHE A 865 
 TRP   0.018   0.002   TRP A 445 
 HIS   0.006   0.001   HIS A 985 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00667 /  0.47 (10838)
  covalent geometry    : angle       0.90357 /  0.64 (14717)
  hydrogen bonds       : bond        0.17422 / 10.72 (  682)
  hydrogen bonds       : angle       6.85199 /  5.06 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 336
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 ASP cc_start: 0.8022 (t0) cc_final: 0.7591 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 338
  average time/residue: 0.1055
  time to fit residues: 50.5503
Evaluate side-chains
  193 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN
A 774 GLN
** A 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1363 HIS
A1485 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.162828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.122861 restraints weight = 16931.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.120807 restraints weight = 9774.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.122011 restraints weight = 8809.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.122650 restraints weight = 6503.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.123015 restraints weight = 5895.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10838  Z= 0.275
  Angle     :  0.722  12.529  14717  Z= 0.370
  Chirality :  0.046   0.195   1714
  Planarity :  0.005   0.052   1817
  Dihedral  :  6.536  89.318   1489
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 21.58 %
    Favored  : 72.95 %
  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:  0.57 (0.23), residues: 1311
  helix:  1.12 (0.17), residues: 869
  sheet: -0.91 (0.53), residues: 80
  loop : -0.99 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 775 
 TYR   0.019   0.002   TYR A1018 
 PHE   0.021   0.002   PHE A1212 
 TRP   0.020   0.002   TRP A 994 
 HIS   0.008   0.002   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00635 /  0.28 (10838)
  covalent geometry    : angle       0.72153 /  0.37 (14717)
  hydrogen bonds       : bond        0.05264 /  3.42 (  682)
  hydrogen bonds       : angle       4.77868 /  3.46 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 211
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.7501 (ptp) cc_final: 0.6467 (mmt)
REVERT: A  502 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7677 (pt)
REVERT: A  686 SER cc_start: 0.8715 (m) cc_final: 0.8198 (t)
REVERT: A  831 TYR cc_start: 0.8229 (m-80) cc_final: 0.7930 (m-10)
REVERT: A  984 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8362 (t0)
REVERT: A 1108 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (mt)
REVERT: A 1280 MET cc_start: 0.6742 (mpp) cc_final: 0.6275 (ptp)
REVERT: A 1385 MET cc_start: 0.8278 (ptm) cc_final: 0.8052 (ptt)
  outliers start: 64
  outliers final: 32
  residues processed: 254
  average time/residue: 0.0866
  time to fit residues: 33.3501
Evaluate side-chains
  200 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 165
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  811 ILE
Chi-restraints excluded: chain A residue  824 LEU
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue  984 ASN
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1073 ASN
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1239 VAL
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1363 HIS
Chi-restraints excluded: chain A residue 1370 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 130 optimal weight:   20.0000
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A  71 ASN
A 494 HIS
A 580 GLN
** A 984 ASN ** 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 = 0.4135 r_free = 0.4135 target = 0.164213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.123123 restraints weight = 16932.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.122792 restraints weight = 9882.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.123380 restraints weight = 7377.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.124098 restraints weight = 5984.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.124382 restraints weight = 5468.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10838  Z= 0.167
  Angle     :  0.620  10.638  14717  Z= 0.312
  Chirality :  0.042   0.173   1714
  Planarity :  0.004   0.040   1817
  Dihedral  :  6.343  88.315   1489
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 22.95 %
    Favored  : 72.95 %
  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:  0.91 (0.23), residues: 1311
  helix:  1.38 (0.17), residues: 872
  sheet: -0.61 (0.56), residues: 81
  loop : -0.93 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 775 
 TYR   0.021   0.001   TYR A 178 
 PHE   0.019   0.002   PHE A 865 
 TRP   0.020   0.001   TRP A  82 
 HIS   0.007   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.17 (10838)
  covalent geometry    : angle       0.61970 /  0.31 (14717)
  hydrogen bonds       : bond        0.04769 /  3.09 (  682)
  hydrogen bonds       : angle       4.44443 /  3.20 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 184
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TRP cc_start: 0.5806 (t60) cc_final: 0.5465 (t60)
REVERT: A  354 ASN cc_start: 0.7600 (t0) cc_final: 0.7393 (t0)
REVERT: A  436 ASP cc_start: 0.7557 (t0) cc_final: 0.7268 (m-30)
REVERT: A  443 MET cc_start: 0.9052 (tpp) cc_final: 0.8781 (tpp)
REVERT: A  485 MET cc_start: 0.7515 (ptp) cc_final: 0.6421 (mmt)
REVERT: A  686 SER cc_start: 0.8634 (m) cc_final: 0.8068 (t)
REVERT: A 1179 LEU cc_start: 0.8470 (tt) cc_final: 0.8245 (tp)
REVERT: A 1280 MET cc_start: 0.6776 (mpp) cc_final: 0.6283 (ptp)
  outliers start: 48
  outliers final: 34
  residues processed: 213
  average time/residue: 0.0871
  time to fit residues: 28.2948
Evaluate side-chains
  197 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  185 GLN
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  811 ILE
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1416 ASP
Chi-restraints excluded: chain A residue 1431 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 56 optimal weight:    0.2980
   chunk 6 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 128 optimal weight:    0.8980
   chunk 127 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A1363 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.164383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.122289 restraints weight = 17143.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.123750 restraints weight = 9301.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.124379 restraints weight = 6923.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.125261 restraints weight = 5501.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.125309 restraints weight = 4912.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10838  Z= 0.149
  Angle     :  0.589  10.247  14717  Z= 0.296
  Chirality :  0.041   0.189   1714
  Planarity :  0.004   0.039   1817
  Dihedral  :  6.114  85.007   1489
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 23.03 %
    Favored  : 72.60 %
  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:  1.07 (0.23), residues: 1311
  helix:  1.53 (0.17), residues: 870
  sheet: -0.43 (0.58), residues: 81
  loop : -0.98 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 775 
 TYR   0.025   0.002   TYR A1242 
 PHE   0.037   0.002   PHE A 558 
 TRP   0.018   0.001   TRP A1286 
 HIS   0.006   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 (10838)
  covalent geometry    : angle       0.58944 /  0.30 (14717)
  hydrogen bonds       : bond        0.04394 /  2.85 (  682)
  hydrogen bonds       : angle       4.29757 /  3.10 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 183
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 TRP cc_start: 0.5950 (t60) cc_final: 0.5424 (t60)
REVERT: A  354 ASN cc_start: 0.7547 (t0) cc_final: 0.7308 (m-40)
REVERT: A  436 ASP cc_start: 0.7478 (t0) cc_final: 0.7223 (m-30)
REVERT: A  443 MET cc_start: 0.9000 (tpp) cc_final: 0.8781 (tpp)
REVERT: A  485 MET cc_start: 0.7397 (ptp) cc_final: 0.6284 (mmt)
REVERT: A  502 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7667 (pt)
REVERT: A  798 VAL cc_start: 0.8051 (m) cc_final: 0.7759 (t)
REVERT: A 1280 MET cc_start: 0.6802 (mpp) cc_final: 0.6256 (ptp)
REVERT: A 1435 GLN cc_start: 0.7953 (mp10) cc_final: 0.7751 (mp10)
  outliers start: 51
  outliers final: 34
  residues processed: 218
  average time/residue: 0.0885
  time to fit residues: 29.3938
Evaluate side-chains
  195 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 160
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  811 ILE
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1094 MET
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1209 ILE
Chi-restraints excluded: chain A residue 1239 VAL
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1335 LEU
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1416 ASP
Chi-restraints excluded: chain A residue 1431 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 9 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 24 optimal weight:    0.5980
   chunk 109 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A1099 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.163991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.122945 restraints weight = 16888.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.123177 restraints weight = 9883.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.123626 restraints weight = 7529.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.124370 restraints weight = 6034.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.124629 restraints weight = 5538.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10838  Z= 0.157
  Angle     :  0.602   9.691  14717  Z= 0.304
  Chirality :  0.041   0.238   1714
  Planarity :  0.004   0.037   1817
  Dihedral  :  6.083  83.962   1489
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 23.63 %
    Favored  : 71.32 %
  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:  1.11 (0.23), residues: 1311
  helix:  1.56 (0.18), residues: 869
  sheet: -0.48 (0.59), residues: 81
  loop : -0.94 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 775 
 TYR   0.033   0.002   TYR A1242 
 PHE   0.018   0.001   PHE A 865 
 TRP   0.015   0.001   TRP A1286 
 HIS   0.006   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.16 (10838)
  covalent geometry    : angle       0.60195 /  0.30 (14717)
  hydrogen bonds       : bond        0.04354 /  2.83 (  682)
  hydrogen bonds       : angle       4.25252 /  3.07 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 170
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7549 (t0) cc_final: 0.7298 (m-40)
REVERT: A  436 ASP cc_start: 0.7506 (t0) cc_final: 0.7220 (m-30)
REVERT: A  443 MET cc_start: 0.9003 (tpp) cc_final: 0.8796 (tpp)
REVERT: A  485 MET cc_start: 0.7516 (ptp) cc_final: 0.6334 (mmt)
REVERT: A  502 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7726 (pt)
REVERT: A  545 LEU cc_start: 0.8565 (mt) cc_final: 0.8287 (tp)
REVERT: A 1280 MET cc_start: 0.6883 (mpp) cc_final: 0.6347 (ptp)
REVERT: A 1435 GLN cc_start: 0.8010 (mp10) cc_final: 0.7710 (mp10)
REVERT: A 1491 MET cc_start: 0.8134 (mmm) cc_final: 0.7919 (mmt)
  outliers start: 59
  outliers final: 43
  residues processed: 211
  average time/residue: 0.0848
  time to fit residues: 27.4698
Evaluate side-chains
  202 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 158
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  811 ILE
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1013 VAL
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1209 ILE
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1335 LEU
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1439 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 129 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 116 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 127 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 992 ASN
** A1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1222 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.157721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.109754 restraints weight = 17260.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.113514 restraints weight = 8629.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.115946 restraints weight = 5626.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.117320 restraints weight = 4343.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.117993 restraints weight = 3767.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.5434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  10838  Z= 0.315
  Angle     :  0.739   9.915  14717  Z= 0.378
  Chirality :  0.046   0.251   1714
  Planarity :  0.005   0.044   1817
  Dihedral  :  6.671  89.853   1489
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 23.72 %
    Favored  : 70.21 %
  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:  0.60 (0.23), residues: 1311
  helix:  1.10 (0.17), residues: 865
  sheet: -0.88 (0.57), residues: 81
  loop : -0.87 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A1295 
 TYR   0.042   0.002   TYR A1242 
 PHE   0.020   0.002   PHE A 558 
 TRP   0.020   0.002   TRP A 520 
 HIS   0.010   0.002   HIS A1153 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00730 /  0.32 (10838)
  covalent geometry    : angle       0.73931 /  0.38 (14717)
  hydrogen bonds       : bond        0.05086 /  3.31 (  682)
  hydrogen bonds       : angle       4.61871 /  3.34 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 168
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7842 (t0) cc_final: 0.7527 (m-40)
REVERT: A  436 ASP cc_start: 0.7563 (t0) cc_final: 0.7218 (m-30)
REVERT: A  673 LEU cc_start: 0.8478 (tp) cc_final: 0.8222 (tp)
REVERT: A  798 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7767 (t)
REVERT: A 1238 GLN cc_start: 0.7333 (pt0) cc_final: 0.7118 (pt0)
REVERT: A 1280 MET cc_start: 0.6939 (mpp) cc_final: 0.6390 (ptp)
REVERT: A 1390 PHE cc_start: 0.7883 (m-10) cc_final: 0.7430 (m-10)
REVERT: A 1491 MET cc_start: 0.8356 (mmm) cc_final: 0.8085 (mmt)
  outliers start: 71
  outliers final: 47
  residues processed: 219
  average time/residue: 0.0832
  time to fit residues: 28.2626
Evaluate side-chains
  202 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 154
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1013 VAL
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1073 ASN
Chi-restraints excluded: chain A residue 1085 MET
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1255 THR
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1335 LEU
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1416 ASP
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1439 LEU
Chi-restraints excluded: chain A residue 1514 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 115 optimal weight:   10.0000
   chunk 121 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 114 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 130 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A1099 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.160271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.119621 restraints weight = 17182.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.118455 restraints weight = 9953.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.119257 restraints weight = 8782.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.119812 restraints weight = 6695.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.119959 restraints weight = 6289.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.5606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  10838  Z= 0.194
  Angle     :  0.653   9.984  14717  Z= 0.326
  Chirality :  0.042   0.179   1714
  Planarity :  0.004   0.044   1817
  Dihedral  :  6.339  88.215   1487
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 26.03 %
    Favored  : 69.52 %
  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:  0.70 (0.23), residues: 1311
  helix:  1.21 (0.17), residues: 866
  sheet: -0.78 (0.58), residues: 81
  loop : -0.95 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1165 
 TYR   0.039   0.002   TYR A1242 
 PHE   0.031   0.002   PHE A1390 
 TRP   0.020   0.002   TRP A1286 
 HIS   0.007   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.19 (10838)
  covalent geometry    : angle       0.65270 /  0.33 (14717)
  hydrogen bonds       : bond        0.04633 /  3.01 (  682)
  hydrogen bonds       : angle       4.45186 /  3.21 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 166
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 TRP cc_start: 0.7727 (m100) cc_final: 0.7462 (m100)
REVERT: A  318 TYR cc_start: 0.7359 (p90) cc_final: 0.6668 (p90)
REVERT: A  436 ASP cc_start: 0.7522 (t0) cc_final: 0.7157 (m-30)
REVERT: A  596 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8285 (tp)
REVERT: A  673 LEU cc_start: 0.8490 (tp) cc_final: 0.8189 (tp)
REVERT: A  798 VAL cc_start: 0.8072 (m) cc_final: 0.7859 (t)
REVERT: A 1280 MET cc_start: 0.7127 (mpp) cc_final: 0.6608 (ptp)
REVERT: A 1390 PHE cc_start: 0.7678 (m-10) cc_final: 0.7399 (m-10)
  outliers start: 52
  outliers final: 41
  residues processed: 200
  average time/residue: 0.0816
  time to fit residues: 25.5236
Evaluate side-chains
  196 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 154
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  339 MET
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain A residue 1013 VAL
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1072 VAL
Chi-restraints excluded: chain A residue 1073 ASN
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1439 LEU
Chi-restraints excluded: chain A residue 1514 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    0.0020
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.4980
   chunk 129 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 121 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.157000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.115224 restraints weight = 17111.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.116196 restraints weight = 9133.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.116517 restraints weight = 7931.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.117048 restraints weight = 5994.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.117247 restraints weight = 5689.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.5703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10838  Z= 0.143
  Angle     :  0.639  10.889  14717  Z= 0.311
  Chirality :  0.041   0.239   1714
  Planarity :  0.004   0.040   1817
  Dihedral  :  6.079  84.137   1487
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 26.88 %
    Favored  : 69.43 %
  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:  0.87 (0.23), residues: 1311
  helix:  1.37 (0.17), residues: 866
  sheet: -0.63 (0.60), residues: 81
  loop : -0.96 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.020   0.001   TYR A 178 
 PHE   0.023   0.001   PHE A1390 
 TRP   0.027   0.002   TRP A  40 
 HIS   0.005   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 (10838)
  covalent geometry    : angle       0.63887 /  0.31 (14717)
  hydrogen bonds       : bond        0.04329 /  2.82 (  682)
  hydrogen bonds       : angle       4.32399 /  3.12 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 169
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 TRP cc_start: 0.7713 (m100) cc_final: 0.7384 (m100)
REVERT: A   65 ILE cc_start: 0.8766 (mm) cc_final: 0.8377 (pt)
REVERT: A   82 TRP cc_start: 0.6087 (t60) cc_final: 0.5285 (t60)
REVERT: A  318 TYR cc_start: 0.7394 (p90) cc_final: 0.6648 (p90)
REVERT: A  346 LEU cc_start: 0.8996 (tp) cc_final: 0.8712 (tp)
REVERT: A  436 ASP cc_start: 0.7657 (t0) cc_final: 0.7309 (m-30)
REVERT: A  485 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6327 (mmt)
REVERT: A 1280 MET cc_start: 0.7183 (mpp) cc_final: 0.6647 (ptp)
REVERT: A 1286 TRP cc_start: 0.8055 (t60) cc_final: 0.7847 (t60)
REVERT: A 1390 PHE cc_start: 0.7618 (m-10) cc_final: 0.7282 (m-10)
  outliers start: 43
  outliers final: 37
  residues processed: 199
  average time/residue: 0.0821
  time to fit residues: 25.7282
Evaluate side-chains
  194 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 156
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 TRP
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  339 MET
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain A residue 1013 VAL
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1073 ASN
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1241 THR
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1439 LEU
Chi-restraints excluded: chain A residue 1514 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 122 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 16 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** A1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.156567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.115907 restraints weight = 17216.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.113636 restraints weight = 10687.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114241 restraints weight = 9202.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.115138 restraints weight = 7084.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.115482 restraints weight = 6451.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10838  Z= 0.152
  Angle     :  0.650  13.362  14717  Z= 0.317
  Chirality :  0.042   0.250   1714
  Planarity :  0.004   0.041   1817
  Dihedral  :  6.058  82.643   1487
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 27.40 %
    Favored  : 68.84 %
  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:  0.96 (0.23), residues: 1311
  helix:  1.40 (0.18), residues: 874
  sheet: -0.58 (0.60), residues: 81
  loop : -0.89 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.018   0.001   TYR A 178 
 PHE   0.048   0.002   PHE A 558 
 TRP   0.039   0.002   TRP A  40 
 HIS   0.005   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (10838)
  covalent geometry    : angle       0.65017 /  0.32 (14717)
  hydrogen bonds       : bond        0.04315 /  2.79 (  682)
  hydrogen bonds       : angle       4.32233 /  3.13 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 162
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9086 (t) cc_final: 0.8634 (p)
REVERT: A   47 TRP cc_start: 0.7801 (m100) cc_final: 0.7488 (m100)
REVERT: A   65 ILE cc_start: 0.8789 (mm) cc_final: 0.8359 (pt)
REVERT: A   82 TRP cc_start: 0.6237 (t60) cc_final: 0.5453 (t60)
REVERT: A  318 TYR cc_start: 0.7378 (p90) cc_final: 0.6671 (p90)
REVERT: A  436 ASP cc_start: 0.7718 (t0) cc_final: 0.7343 (m-30)
REVERT: A  485 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6344 (mmt)
REVERT: A 1280 MET cc_start: 0.7312 (mpp) cc_final: 0.6748 (ptp)
REVERT: A 1390 PHE cc_start: 0.7571 (m-10) cc_final: 0.7193 (m-10)
  outliers start: 44
  outliers final: 37
  residues processed: 191
  average time/residue: 0.0831
  time to fit residues: 24.7211
Evaluate side-chains
  189 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 151
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 TRP
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain A residue 1013 VAL
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1073 ASN
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1241 THR
Chi-restraints excluded: chain A residue 1249 MET
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1439 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 131 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   chunk 130 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.155932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.114203 restraints weight = 17221.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114774 restraints weight = 9338.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.115171 restraints weight = 8204.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.115761 restraints weight = 6110.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.116129 restraints weight = 5666.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10838  Z= 0.162
  Angle     :  0.671  12.771  14717  Z= 0.326
  Chirality :  0.042   0.233   1714
  Planarity :  0.004   0.040   1817
  Dihedral  :  6.033  81.679   1487
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 28.00 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.23), residues: 1311
  helix:  1.36 (0.17), residues: 878
  sheet: -0.62 (0.59), residues: 81
  loop : -0.89 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1165 
 TYR   0.021   0.001   TYR A 178 
 PHE   0.045   0.002   PHE A 558 
 TRP   0.031   0.002   TRP A1286 
 HIS   0.006   0.001   HIS A 335 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00373 /  0.16 (10838)
  covalent geometry    : angle       0.67121 /  0.33 (14717)
  hydrogen bonds       : bond        0.04321 /  2.80 (  682)
  hydrogen bonds       : angle       4.32087 /  3.12 ( 2010)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 163
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9061 (t) cc_final: 0.8629 (p)
REVERT: A   47 TRP cc_start: 0.7770 (m100) cc_final: 0.7477 (m100)
REVERT: A   82 TRP cc_start: 0.6166 (t60) cc_final: 0.5520 (t60)
REVERT: A  318 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6594 (p90)
REVERT: A  436 ASP cc_start: 0.7606 (t0) cc_final: 0.7254 (m-30)
REVERT: A  485 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6338 (mmt)
REVERT: A  673 LEU cc_start: 0.8390 (tp) cc_final: 0.8017 (tp)
REVERT: A 1280 MET cc_start: 0.7095 (mpp) cc_final: 0.6761 (ptp)
REVERT: A 1390 PHE cc_start: 0.7523 (m-10) cc_final: 0.7163 (m-10)
  outliers start: 41
  outliers final: 35
  residues processed: 189
  average time/residue: 0.0843
  time to fit residues: 24.6546
Evaluate side-chains
  192 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 155
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 TRP
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  318 TYR
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain A residue 1013 VAL
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1105 ILE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1162 SER
Chi-restraints excluded: chain A residue 1241 THR
Chi-restraints excluded: chain A residue 1249 MET
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1416 ASP
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1439 LEU
Chi-restraints excluded: chain A residue 1514 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 65 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0970
   chunk 58 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 129 optimal weight:    0.8980
   chunk 131 optimal weight:    6.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.156910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.115850 restraints weight = 17363.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.113967 restraints weight = 9927.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.114808 restraints weight = 9059.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.115364 restraints weight = 6765.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.115864 restraints weight = 5764.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.6094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10838  Z= 0.150
  Angle     :  0.667  10.027  14717  Z= 0.324
  Chirality :  0.042   0.259   1714
  Planarity :  0.004   0.041   1817
  Dihedral  :  5.940  78.991   1487
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 28.60 %
    Favored  : 68.32 %
  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:  1.00 (0.23), residues: 1311
  helix:  1.41 (0.18), residues: 878
  sheet: -0.57 (0.59), residues: 81
  loop : -0.85 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.023   0.001   TYR A 178 
 PHE   0.047   0.002   PHE A 558 
 TRP   0.024   0.002   TRP A1286 
 HIS   0.004   0.001   HIS A 335 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (10838)
  covalent geometry    : angle       0.66718 /  0.32 (14717)
  hydrogen bonds       : bond        0.04212 /  2.73 (  682)
  hydrogen bonds       : angle       4.28466 /  3.09 ( 2010)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1944.70 seconds
wall clock time: 34 minutes 32.86 seconds (2072.86 seconds total)