Starting phenix.real_space_refine
on Wed Feb  4 13:30:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lg8_63057/02_2026/9lg8_63057_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lg8_63057/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lg8_63057/02_2026/9lg8_63057.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lg8_63057/02_2026/9lg8_63057.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lg8_63057/02_2026/9lg8_63057_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lg8_63057/02_2026/9lg8_63057_neut.cif"
  }
  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-2.0-5952/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: 2.45, per 1000 atoms: 0.23
  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 623.5 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: 0.36
  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: 1.22 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=" C1  GSH A1602 "
       pdb=" O11 GSH A1602 "
    ideal  model  delta    sigma   weight residual
    1.213  1.247 -0.034 1.00e-02 1.00e+04 1.19e+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
  ... (remaining 10833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 13513
        1.69 -     3.39: 1063
        3.39 -     5.08: 119
        5.08 -     6.77: 17
        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: 5689
       17.88 -    35.77: 581
       35.77 -    53.65: 146
       53.65 -    71.53: 39
       71.53 -    89.42: 14
  Dihedral angle restraints: 6469
    sinusoidal: 2588
      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 6466 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1135
       0.046 -    0.091: 337
       0.091 -    0.136: 154
       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:             3.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.480
  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:             0.010
  Load rotamer database and sin/cos tables:1.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.660
-------------------------------------------------------------------------------
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= 0.476
  Angle     :  0.905   8.464  14717  Z= 0.645
  Chirality :  0.060   0.227   1714
  Planarity :  0.010   0.167   1817
  Dihedral  : 16.228  89.417   3953
  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
  covalent geometry    : bond        0.00672 (10838)
  covalent geometry    : angle       0.90518 (14717)
  hydrogen bonds       : bond        0.17422 (  682)
  hydrogen bonds       : angle       6.85199 ( 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  : 0.395 
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: 0.1007
  time to fit residues: 48.0302
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  : 0.414 
-------------------------------------------------------------------------------
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
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 = 0.4127 r_free = 0.4127 target = 0.162664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.122874 restraints weight = 16974.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.120519 restraints weight = 10129.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.121762 restraints weight = 8922.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.122441 restraints weight = 6570.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.122808 restraints weight = 5945.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  10838  Z= 0.273
  Angle     :  0.726  12.264  14717  Z= 0.372
  Chirality :  0.046   0.206   1714
  Planarity :  0.005   0.056   1817
  Dihedral  :  6.859  89.356   1487
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 21.40 %
    Favored  : 72.77 %
  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:  0.47 (0.23), residues: 1311
  helix:  1.03 (0.17), residues: 875
  sheet: -0.92 (0.53), residues: 80
  loop : -1.05 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 775 
 TYR   0.019   0.002   TYR A1018 
 PHE   0.023   0.002   PHE A1212 
 TRP   0.022   0.002   TRP A 994 
 HIS   0.008   0.002   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00631 (10838)
  covalent geometry    : angle       0.72580 (14717)
  hydrogen bonds       : bond        0.05349 (  682)
  hydrogen bonds       : angle       4.79143 ( 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
  268 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 200
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 LEU cc_start: 0.8319 (tp) cc_final: 0.8086 (tp)
REVERT: A  485 MET cc_start: 0.7487 (ptp) cc_final: 0.6476 (mmt)
REVERT: A  502 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7725 (pt)
REVERT: A  686 SER cc_start: 0.8746 (m) cc_final: 0.8212 (t)
REVERT: A  831 TYR cc_start: 0.8242 (m-80) cc_final: 0.7877 (m-10)
REVERT: A  984 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8389 (t0)
REVERT: A 1034 MET cc_start: 0.8042 (mmm) cc_final: 0.7722 (mmm)
REVERT: A 1108 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8415 (mt)
REVERT: A 1280 MET cc_start: 0.6838 (mpp) cc_final: 0.6279 (ptp)
REVERT: A 1324 ILE cc_start: 0.8413 (mp) cc_final: 0.8209 (mm)
  outliers start: 68
  outliers final: 35
  residues processed: 247
  average time/residue: 0.0752
  time to fit residues: 28.2861
Evaluate side-chains
  202 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
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  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 1082 VAL
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
Chi-restraints excluded: chain A residue 1431 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 106 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 130 optimal weight:   20.0000
   chunk 34 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 56 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A  71 ASN
A 494 HIS
A1363 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.164429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.123735 restraints weight = 17011.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.123770 restraints weight = 9972.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.124308 restraints weight = 7329.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.125061 restraints weight = 5914.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.125303 restraints weight = 5390.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10838  Z= 0.163
  Angle     :  0.613   9.944  14717  Z= 0.309
  Chirality :  0.041   0.179   1714
  Planarity :  0.004   0.039   1817
  Dihedral  :  6.634  87.803   1487
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.12 %
    Favored  : 72.86 %
  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:  1.38 (0.17), residues: 872
  sheet: -0.69 (0.55), residues: 81
  loop : -0.91 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 775 
 TYR   0.020   0.001   TYR A 178 
 PHE   0.020   0.001   PHE A 865 
 TRP   0.020   0.002   TRP A  82 
 HIS   0.007   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (10838)
  covalent geometry    : angle       0.61313 (14717)
  hydrogen bonds       : bond        0.04739 (  682)
  hydrogen bonds       : angle       4.43954 ( 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
  238 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 191
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TRP cc_start: 0.5786 (t60) cc_final: 0.5461 (t60)
REVERT: A  354 ASN cc_start: 0.7557 (t0) cc_final: 0.7355 (t0)
REVERT: A  436 ASP cc_start: 0.7542 (t0) cc_final: 0.7207 (m-30)
REVERT: A  443 MET cc_start: 0.9063 (tpp) cc_final: 0.8780 (tpp)
REVERT: A  485 MET cc_start: 0.7547 (ptp) cc_final: 0.6434 (mmt)
REVERT: A  545 LEU cc_start: 0.8548 (mt) cc_final: 0.8260 (tp)
REVERT: A 1179 LEU cc_start: 0.8436 (tt) cc_final: 0.8236 (tp)
REVERT: A 1280 MET cc_start: 0.6751 (mpp) cc_final: 0.6302 (ptp)
REVERT: A 1390 PHE cc_start: 0.7711 (m-10) cc_final: 0.7383 (m-10)
  outliers start: 47
  outliers final: 31
  residues processed: 222
  average time/residue: 0.0802
  time to fit residues: 26.8849
Evaluate side-chains
  197 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 166
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0570
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9990
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
** A 984 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 = 0.4138 r_free = 0.4138 target = 0.164464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.123154 restraints weight = 17192.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.123512 restraints weight = 9967.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.123987 restraints weight = 7437.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.124734 restraints weight = 5926.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.124984 restraints weight = 5400.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.4587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10838  Z= 0.155
  Angle     :  0.591  10.582  14717  Z= 0.298
  Chirality :  0.041   0.211   1714
  Planarity :  0.004   0.039   1817
  Dihedral  :  6.563  85.324   1487
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 23.37 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.23), residues: 1311
  helix:  1.49 (0.17), residues: 864
  sheet: -0.58 (0.57), residues: 81
  loop : -0.96 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1341 
 TYR   0.028   0.002   TYR A1242 
 PHE   0.022   0.001   PHE A 865 
 TRP   0.016   0.001   TRP A1286 
 HIS   0.007   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10838)
  covalent geometry    : angle       0.59095 (14717)
  hydrogen bonds       : bond        0.04473 (  682)
  hydrogen bonds       : angle       4.32130 ( 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
  232 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 176
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TRP cc_start: 0.5903 (t60) cc_final: 0.5465 (t60)
REVERT: A  354 ASN cc_start: 0.7584 (t0) cc_final: 0.7362 (m-40)
REVERT: A  436 ASP cc_start: 0.7536 (t0) cc_final: 0.7190 (m-30)
REVERT: A  443 MET cc_start: 0.9033 (tpp) cc_final: 0.8799 (tpp)
REVERT: A  485 MET cc_start: 0.7547 (ptp) cc_final: 0.6377 (mmt)
REVERT: A  502 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7616 (pt)
REVERT: A  515 LEU cc_start: 0.9017 (tp) cc_final: 0.8445 (tp)
REVERT: A  798 VAL cc_start: 0.8107 (m) cc_final: 0.7815 (t)
REVERT: A 1280 MET cc_start: 0.6845 (mpp) cc_final: 0.6188 (ptp)
REVERT: A 1349 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.5903 (pt0)
REVERT: A 1491 MET cc_start: 0.8024 (mmm) cc_final: 0.7786 (mmt)
  outliers start: 56
  outliers final: 38
  residues processed: 216
  average time/residue: 0.0836
  time to fit residues: 27.6726
Evaluate side-chains
  197 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 157
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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   75 THR
Chi-restraints excluded: chain A residue  107 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  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  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  811 ILE
Chi-restraints excluded: chain A residue  839 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 1047 LEU
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 1336 THR
Chi-restraints excluded: chain A residue 1349 GLU
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:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 24 optimal weight:    0.5980
   chunk 109 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1099 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.163637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.123539 restraints weight = 16819.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.122118 restraints weight = 9875.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.123096 restraints weight = 7486.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.123831 restraints weight = 5977.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.124072 restraints weight = 5591.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10838  Z= 0.150
  Angle     :  0.600   9.858  14717  Z= 0.302
  Chirality :  0.040   0.192   1714
  Planarity :  0.004   0.038   1817
  Dihedral  :  6.501  83.176   1487
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 24.23 %
    Favored  : 70.63 %
  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:  1.55 (0.17), residues: 863
  sheet: -0.51 (0.58), residues: 81
  loop : -0.98 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.044   0.002   TYR A1242 
 PHE   0.039   0.001   PHE A 558 
 TRP   0.015   0.001   TRP A1286 
 HIS   0.006   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (10838)
  covalent geometry    : angle       0.60009 (14717)
  hydrogen bonds       : bond        0.04325 (  682)
  hydrogen bonds       : angle       4.26280 ( 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
  235 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 175
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  436 ASP cc_start: 0.7483 (t0) cc_final: 0.7144 (m-30)
REVERT: A  473 MET cc_start: 0.8057 (mmm) cc_final: 0.7531 (mmm)
REVERT: A  483 MET cc_start: 0.6275 (tmm) cc_final: 0.5150 (tmm)
REVERT: A  485 MET cc_start: 0.7525 (ptp) cc_final: 0.6375 (mmt)
REVERT: A  502 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7602 (pt)
REVERT: A  515 LEU cc_start: 0.8984 (tp) cc_final: 0.8722 (tp)
REVERT: A  545 LEU cc_start: 0.8519 (mt) cc_final: 0.7687 (tp)
REVERT: A 1280 MET cc_start: 0.6872 (mpp) cc_final: 0.6338 (ptp)
REVERT: A 1295 ARG cc_start: 0.7995 (mpp80) cc_final: 0.7511 (mpp80)
REVERT: A 1349 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6255 (pt0)
REVERT: A 1435 GLN cc_start: 0.8058 (mp10) cc_final: 0.7767 (mp10)
  outliers start: 60
  outliers final: 46
  residues processed: 216
  average time/residue: 0.0727
  time to fit residues: 24.0437
Evaluate side-chains
  210 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 162
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
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   75 THR
Chi-restraints excluded: chain A residue  107 LEU
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  185 GLN
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  330 LEU
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  474 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  616 LEU
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  824 LEU
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 1053 HIS
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 1209 ILE
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 1349 GLU
Chi-restraints excluded: chain A residue 1416 ASP
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:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 116 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 127 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1099 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.160841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.119860 restraints weight = 17103.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.119632 restraints weight = 10080.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.120355 restraints weight = 7847.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.121018 restraints weight = 5951.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.121328 restraints weight = 5465.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  10838  Z= 0.206
  Angle     :  0.641   9.979  14717  Z= 0.322
  Chirality :  0.042   0.244   1714
  Planarity :  0.004   0.038   1817
  Dihedral  :  6.631  84.848   1487
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 24.23 %
    Favored  : 70.38 %
  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:  0.85 (0.23), residues: 1311
  helix:  1.35 (0.17), residues: 867
  sheet: -0.66 (0.57), residues: 81
  loop : -0.97 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1165 
 TYR   0.044   0.002   TYR A1242 
 PHE   0.039   0.002   PHE A 558 
 TRP   0.015   0.002   TRP A  40 
 HIS   0.007   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (10838)
  covalent geometry    : angle       0.64142 (14717)
  hydrogen bonds       : bond        0.04578 (  682)
  hydrogen bonds       : angle       4.36266 ( 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
  230 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 167
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 TYR cc_start: 0.7409 (p90) cc_final: 0.6757 (p90)
REVERT: A  436 ASP cc_start: 0.7534 (t0) cc_final: 0.7172 (m-30)
REVERT: A  502 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7704 (pt)
REVERT: A 1121 LEU cc_start: 0.9172 (mt) cc_final: 0.8592 (mt)
REVERT: A 1280 MET cc_start: 0.6899 (mpp) cc_final: 0.6475 (ptp)
REVERT: A 1295 ARG cc_start: 0.8024 (mpp80) cc_final: 0.7615 (mpp80)
REVERT: A 1349 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.5943 (pt0)
  outliers start: 63
  outliers final: 47
  residues processed: 214
  average time/residue: 0.0766
  time to fit residues: 25.2349
Evaluate side-chains
  199 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 150
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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  107 LEU
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  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  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  482 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  514 VAL
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  616 LEU
Chi-restraints excluded: chain A residue  618 VAL
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 1053 HIS
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 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 1349 GLU
Chi-restraints excluded: chain A residue 1416 ASP
Chi-restraints excluded: chain A residue 1431 VAL
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:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 121 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 114 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 130 optimal weight:   20.0000
   chunk 62 optimal weight:    0.2980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1406 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.163021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.123351 restraints weight = 17067.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121567 restraints weight = 9496.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.122635 restraints weight = 8370.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.123219 restraints weight = 6126.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.123427 restraints weight = 5857.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.5423

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= 0.149
  Angle     :  0.624  11.067  14717  Z= 0.306
  Chirality :  0.041   0.198   1714
  Planarity :  0.004   0.037   1817
  Dihedral  :  6.526  82.262   1487
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 25.43 %
    Favored  : 70.12 %
  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:  0.97 (0.23), residues: 1311
  helix:  1.47 (0.17), residues: 866
  sheet: -0.61 (0.58), residues: 81
  loop : -1.00 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1366 
 TYR   0.021   0.001   TYR A 178 
 PHE   0.043   0.001   PHE A 558 
 TRP   0.022   0.002   TRP A1286 
 HIS   0.005   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10838)
  covalent geometry    : angle       0.62441 (14717)
  hydrogen bonds       : bond        0.04328 (  682)
  hydrogen bonds       : angle       4.26884 ( 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  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ILE cc_start: 0.8742 (mm) cc_final: 0.8382 (pt)
REVERT: A  318 TYR cc_start: 0.7344 (p90) cc_final: 0.6666 (p90)
REVERT: A  436 ASP cc_start: 0.7547 (t0) cc_final: 0.7183 (m-30)
REVERT: A  502 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7419 (pt)
REVERT: A  545 LEU cc_start: 0.8445 (mt) cc_final: 0.8111 (tp)
REVERT: A  964 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7383 (t0)
REVERT: A 1280 MET cc_start: 0.7080 (mpp) cc_final: 0.6570 (ptp)
REVERT: A 1491 MET cc_start: 0.8198 (mmm) cc_final: 0.7910 (mmt)
  outliers start: 52
  outliers final: 41
  residues processed: 206
  average time/residue: 0.0684
  time to fit residues: 22.3263
Evaluate side-chains
  200 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 157
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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  107 LEU
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  185 GLN
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  482 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  514 VAL
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  964 ASP
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 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 1198 LEU
Chi-restraints excluded: chain A residue 1209 ILE
Chi-restraints excluded: chain A residue 1239 VAL
Chi-restraints excluded: chain A residue 1241 THR
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 1514 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    0.0060
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 129 optimal weight:    8.9990
   chunk 104 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 984 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 = 0.4127 r_free = 0.4127 target = 0.163664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.122953 restraints weight = 16980.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.123284 restraints weight = 10048.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.123675 restraints weight = 7974.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.124471 restraints weight = 5885.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.124562 restraints weight = 5469.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10838  Z= 0.142
  Angle     :  0.617  10.817  14717  Z= 0.301
  Chirality :  0.041   0.191   1714
  Planarity :  0.004   0.038   1817
  Dihedral  :  6.446  79.217   1487
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 26.03 %
    Favored  : 69.86 %
  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:  1.01 (0.23), residues: 1311
  helix:  1.51 (0.17), residues: 868
  sheet: -0.63 (0.59), residues: 81
  loop : -1.03 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.019   0.001   TYR A 178 
 PHE   0.043   0.002   PHE A 558 
 TRP   0.027   0.002   TRP A  40 
 HIS   0.004   0.001   HIS A1406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10838)
  covalent geometry    : angle       0.61747 (14717)
  hydrogen bonds       : bond        0.04235 (  682)
  hydrogen bonds       : angle       4.22838 ( 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
  213 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 165
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 ILE cc_start: 0.8628 (mm) cc_final: 0.8186 (pt)
REVERT: A   82 TRP cc_start: 0.5989 (t60) cc_final: 0.5244 (t60)
REVERT: A  318 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6664 (p90)
REVERT: A  436 ASP cc_start: 0.7512 (t0) cc_final: 0.7150 (m-30)
REVERT: A  502 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7394 (pt)
REVERT: A  964 ASP cc_start: 0.7634 (t70) cc_final: 0.7359 (t0)
REVERT: A 1280 MET cc_start: 0.6905 (mpp) cc_final: 0.6514 (ptp)
REVERT: A 1392 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8421 (pm20)
REVERT: A 1491 MET cc_start: 0.8080 (mmm) cc_final: 0.7801 (mmt)
  outliers start: 48
  outliers final: 40
  residues processed: 199
  average time/residue: 0.0702
  time to fit residues: 22.0320
Evaluate side-chains
  196 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 153
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  107 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  339 MET
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  441 ILE
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  502 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  984 ASN
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 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 1198 LEU
Chi-restraints excluded: chain A residue 1239 VAL
Chi-restraints excluded: chain A residue 1258 VAL
Chi-restraints excluded: chain A residue 1392 GLN
Chi-restraints excluded: chain A residue 1431 VAL
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:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 122 optimal weight:    5.9990
   chunk 130 optimal weight:   20.0000
   chunk 72 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0970
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.7578

-------------------------------------------------------------------------------
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 = 0.4122 r_free = 0.4122 target = 0.163127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.123742 restraints weight = 17119.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.121707 restraints weight = 9731.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.122907 restraints weight = 8788.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.123476 restraints weight = 6426.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.123688 restraints weight = 6056.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.5696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10838  Z= 0.154
  Angle     :  0.654  12.275  14717  Z= 0.315
  Chirality :  0.042   0.233   1714
  Planarity :  0.004   0.039   1817
  Dihedral  :  6.447  77.870   1487
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 26.54 %
    Favored  : 69.26 %
  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:  1.05 (0.23), residues: 1311
  helix:  1.51 (0.17), residues: 874
  sheet: -0.62 (0.59), residues: 81
  loop : -0.94 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.021   0.001   TYR A 178 
 PHE   0.046   0.001   PHE A 558 
 TRP   0.035   0.002   TRP A  40 
 HIS   0.005   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10838)
  covalent geometry    : angle       0.65403 (14717)
  hydrogen bonds       : bond        0.04268 (  682)
  hydrogen bonds       : angle       4.28873 ( 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
  214 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 165
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 TRP cc_start: 0.7659 (m100) cc_final: 0.7250 (m100)
REVERT: A   65 ILE cc_start: 0.8711 (mm) cc_final: 0.8228 (pt)
REVERT: A   82 TRP cc_start: 0.6122 (t60) cc_final: 0.5444 (t60)
REVERT: A  138 MET cc_start: 0.8953 (tmm) cc_final: 0.8297 (tpt)
REVERT: A  318 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6636 (p90)
REVERT: A  436 ASP cc_start: 0.7444 (t0) cc_final: 0.7082 (m-30)
REVERT: A  485 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6465 (mmt)
REVERT: A  502 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7385 (pt)
REVERT: A  964 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7376 (t0)
REVERT: A 1016 SER cc_start: 0.8785 (m) cc_final: 0.8537 (m)
REVERT: A 1280 MET cc_start: 0.6986 (mpp) cc_final: 0.6570 (ptp)
REVERT: A 1491 MET cc_start: 0.8193 (mmm) cc_final: 0.7888 (mmt)
  outliers start: 49
  outliers final: 41
  residues processed: 197
  average time/residue: 0.0759
  time to fit residues: 23.2193
Evaluate side-chains
  201 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 156
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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  107 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  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  441 ILE
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  485 MET
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue  984 ASN
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 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 1198 LEU
Chi-restraints excluded: chain A residue 1239 VAL
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 1514 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 131 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0980
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.163788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.124076 restraints weight = 17006.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.124498 restraints weight = 8956.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.125027 restraints weight = 8518.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.125696 restraints weight = 5936.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.126009 restraints weight = 5457.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.5804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10838  Z= 0.142
  Angle     :  0.644  11.749  14717  Z= 0.311
  Chirality :  0.041   0.216   1714
  Planarity :  0.004   0.039   1817
  Dihedral  :  6.392  74.854   1487
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 27.14 %
    Favored  : 69.09 %
  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:  1.54 (0.18), residues: 879
  sheet: -0.56 (0.59), residues: 81
  loop : -0.93 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.020   0.001   TYR A 178 
 PHE   0.046   0.002   PHE A 558 
 TRP   0.031   0.002   TRP A  40 
 HIS   0.004   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10838)
  covalent geometry    : angle       0.64428 (14717)
  hydrogen bonds       : bond        0.04134 (  682)
  hydrogen bonds       : angle       4.27616 ( 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
  202 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 158
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9083 (t) cc_final: 0.8674 (p)
REVERT: A   47 TRP cc_start: 0.7617 (m100) cc_final: 0.7247 (m100)
REVERT: A   65 ILE cc_start: 0.8554 (mm) cc_final: 0.8119 (pt)
REVERT: A   82 TRP cc_start: 0.5972 (t60) cc_final: 0.5396 (t60)
REVERT: A  117 MET cc_start: 0.7617 (ttm) cc_final: 0.7414 (ttm)
REVERT: A  318 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6562 (p90)
REVERT: A  346 LEU cc_start: 0.8769 (tp) cc_final: 0.8469 (tp)
REVERT: A  436 ASP cc_start: 0.7381 (t0) cc_final: 0.7024 (m-30)
REVERT: A  483 MET cc_start: 0.6295 (tmm) cc_final: 0.5626 (tmm)
REVERT: A  485 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6492 (mmt)
REVERT: A  502 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7326 (pt)
REVERT: A  964 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7343 (t0)
REVERT: A 1016 SER cc_start: 0.8798 (m) cc_final: 0.8543 (m)
REVERT: A 1280 MET cc_start: 0.6870 (mpp) cc_final: 0.6596 (ptp)
REVERT: A 1286 TRP cc_start: 0.8000 (t60) cc_final: 0.7775 (t60)
REVERT: A 1491 MET cc_start: 0.8026 (mmm) cc_final: 0.7764 (mmt)
  outliers start: 44
  outliers final: 36
  residues processed: 188
  average time/residue: 0.0709
  time to fit residues: 20.8153
Evaluate side-chains
  192 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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   70 LEU
Chi-restraints excluded: chain A residue  107 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  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  441 ILE
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  485 MET
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  703 THR
Chi-restraints excluded: chain A residue  964 ASP
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 1198 LEU
Chi-restraints excluded: chain A residue 1239 VAL
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 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:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 122 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0970
   chunk 31 optimal weight:    1.9990
   chunk 129 optimal weight:    0.9990
   chunk 131 optimal weight:    6.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.4113 r_free = 0.4113 target = 0.162201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.121675 restraints weight = 17182.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.122800 restraints weight = 9270.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.123039 restraints weight = 8311.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.123654 restraints weight = 6107.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.123844 restraints weight = 5631.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.5936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10838  Z= 0.171
  Angle     :  0.684  12.958  14717  Z= 0.332
  Chirality :  0.042   0.227   1714
  Planarity :  0.004   0.040   1817
  Dihedral  :  6.410  75.787   1487
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 27.31 %
    Favored  : 68.41 %
  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:  1.10 (0.23), residues: 1311
  helix:  1.50 (0.17), residues: 877
  sheet: -0.61 (0.59), residues: 81
  loop : -0.82 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.018   0.001   TYR A 178 
 PHE   0.047   0.002   PHE A 558 
 TRP   0.028   0.002   TRP A  40 
 HIS   0.005   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (10838)
  covalent geometry    : angle       0.68445 (14717)
  hydrogen bonds       : bond        0.04276 (  682)
  hydrogen bonds       : angle       4.31328 ( 2010)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1627.90 seconds
wall clock time: 28 minutes 57.44 seconds (1737.44 seconds total)