Starting phenix.real_space_refine
on Sat Aug 23 09:50:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qls_53233/08_2025/9qls_53233.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qls_53233/08_2025/9qls_53233.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qls_53233/08_2025/9qls_53233.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qls_53233/08_2025/9qls_53233.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qls_53233/08_2025/9qls_53233.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qls_53233/08_2025/9qls_53233.map"
  }
  resolution = 3.54
  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=  -0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      56      5.16       5
     C    7114      2.51       5
     N    1898      2.21       5
     O    2026      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11100
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1370, 11094
          Classifications: {'peptide': 1370}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 4, 'PTRANS': 86, 'TRANS': 1279}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Unusual residues: {' CA': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 2.99, per 1000 atoms: 0.27
  Number of scatterers: 11100
  At special positions: 0
  Unit cell: (102.24, 149.04, 92.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      6     19.99
     S      56     16.00
     O    2026      8.00
     N    1898      7.00
     C    7114      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: 1.13
  Conformation dependent library (CDL) restraints added in 532.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2576

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 19 sheets defined
      18.0% alpha, 27.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 273 through 278
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 311 through 315
      removed outlier: 3.633A  pdb=" N   ALA A 315 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 332
      removed outlier: 3.708A  pdb=" N   GLY A 332 " --> pdb=" O   PHE A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 485
      No H-bonds generated for 'chain 'A' and resid 483 through 485'
    Processing helix  chain 'A' and resid 539 through 545
      removed outlier: 3.567A  pdb=" N   GLY A 545 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 582
      removed outlier: 3.912A  pdb=" N   LEU A 581 " --> pdb=" O   ALA A 577 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ARG A 582 " --> pdb=" O   ASP A 578 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 577 through 582'
    Processing helix  chain 'A' and resid 583 through 586
    Processing helix  chain 'A' and resid 668 through 698
      removed outlier: 3.550A  pdb=" N   THR A 674 " --> pdb=" O   HIS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 721
      removed outlier: 3.646A  pdb=" N   GLU A 715 " --> pdb=" O   GLN A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 761
    Processing helix  chain 'A' and resid 764 through 783
      removed outlier: 3.735A  pdb=" N   GLN A 771 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 814
    Processing helix  chain 'A' and resid 863 through 865
      No H-bonds generated for 'chain 'A' and resid 863 through 865'
    Processing helix  chain 'A' and resid 866 through 871
      removed outlier: 4.192A  pdb=" N   PHE A 870 " --> pdb=" O   GLU A 866 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 918
      removed outlier: 3.604A  pdb=" N   SER A 917 " --> pdb=" O   PRO A 914 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   PHE A 918 " --> pdb=" O   LYS A 915 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 914 through 918'
    Processing helix  chain 'A' and resid 1104 through 1112
      removed outlier: 3.833A  pdb=" N   ALA A1107 " --> pdb=" O   THR A1104 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A1108 " --> pdb=" O   GLY A1105 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL A1109 " --> pdb=" O   PRO A1106 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   PHE A1110 " --> pdb=" O   ALA A1107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1220
    Processing helix  chain 'A' and resid 1476 through 1486
      removed outlier: 3.753A  pdb=" N   LYS A1480 " --> pdb=" O   ASP A1476 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE A1485 " --> pdb=" O   PHE A1481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1487 through 1492
    Processing helix  chain 'A' and resid 1493 through 1495
      No H-bonds generated for 'chain 'A' and resid 1493 through 1495'
    Processing helix  chain 'A' and resid 1508 through 1512
      removed outlier: 3.671A  pdb=" N   ASN A1511 " --> pdb=" O   GLN A1508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1613 through 1618
      removed outlier: 3.635A  pdb=" N   TYR A1618 " --> pdb=" O   GLN A1615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1666 through 1672
      removed outlier: 3.808A  pdb=" N   LEU A1670 " --> pdb=" O   LEU A1666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1697 through 1709
    Processing helix  chain 'A' and resid 1731 through 1733
      No H-bonds generated for 'chain 'A' and resid 1731 through 1733'
    Processing helix  chain 'A' and resid 1745 through 1758
    Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 271
      removed outlier: 6.730A  pdb=" N   LYS A 338 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   GLY A 229 " --> pdb=" O   TYR A 336 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   TYR A 336 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 245
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 248 through 249
    current: chain 'A' and resid 295 through 299
    Processing sheet with id=AA3, first strand: chain 'A' and resid 518 through 527
      removed outlier: 6.258A  pdb=" N   LEU A 558 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   TYR A 522 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU A 556 " --> pdb=" O   TYR A 522 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   ASN A 524 " --> pdb=" O   GLY A 554 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   GLY A 554 " --> pdb=" O   ASN A 524 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   TYR A 526 " --> pdb=" O   TYR A 552 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   TYR A 552 " --> pdb=" O   TYR A 526 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ARG A 555 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ALA A 388 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU A 557 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ARG A 387 " --> pdb=" O   TRP A 442 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   TRP A 442 " --> pdb=" O   ARG A 387 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A 571 " --> pdb=" O   THR A 447 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 430
      removed outlier: 6.269A  pdb=" N   MET A 459 " --> pdb=" O   TYR A 479 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   TYR A 479 " --> pdb=" O   MET A 459 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE A 461 " --> pdb=" O   THR A 477 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   THR A 477 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ILE A 463 " --> pdb=" O   VAL A 475 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 835
      removed outlier: 6.159A  pdb=" N   GLN A 851 " --> pdb=" O   ALA A 601 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ALA A 601 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ARG A 853 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   SER A 600 " --> pdb=" O   VAL A 655 " (cutoff:3.500A)
      removed outlier: 11.464A  pdb=" N   VAL A 655 " --> pdb=" O   SER A 600 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ILE A1142 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 611 through 617
      removed outlier: 5.873A  pdb=" N   ILE A 793 " --> pdb=" O   ARG A 808 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ARG A 808 " --> pdb=" O   ILE A 793 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE A 795 " --> pdb=" O   TYR A 806 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   TYR A 806 " --> pdb=" O   ILE A 795 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   MET A 797 " --> pdb=" O   VAL A 804 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 641 through 642
    Processing sheet with id=AA8, first strand: chain 'A' and resid 879 through 886
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 904 through 905
    current: chain 'A' and resid 1079 through 1080
    Processing sheet with id=AA9, first strand: chain 'A' and resid 924 through 926
    Processing sheet with id=AB1, first strand: chain 'A' and resid 948 through 951
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 948 through 951
    current: chain 'A' and resid 1037 through 1048
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1148 through 1162
      removed outlier: 6.660A  pdb=" N   ASN A1150 " --> pdb=" O   GLU A1209 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   GLU A1209 " --> pdb=" O   ASN A1150 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   TYR A1152 " --> pdb=" O   GLU A1207 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLU A1207 " --> pdb=" O   TYR A1152 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1201 through 1210
    current: chain 'A' and resid 1266 through 1278
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1184 through 1187
      removed outlier: 3.807A  pdb=" N   GLY A1241 " --> pdb=" O   LEU A1228 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   ASP A1230 " --> pdb=" O   PHE A1239 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   PHE A1239 " --> pdb=" O   ASP A1230 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1313 through 1315
      removed outlier: 3.634A  pdb=" N   GLU A1315 " --> pdb=" O   ILE A1318 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1384 through 1391
      removed outlier: 5.281A  pdb=" N   ILE A1334 " --> pdb=" O   TYR A1552 " (cutoff:3.500A)
      removed outlier: 7.404A  pdb=" N   TYR A1552 " --> pdb=" O   ILE A1334 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ILE A1336 " --> pdb=" O   LYS A1550 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   LYS A1550 " --> pdb=" O   ILE A1336 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   ALA A1338 " --> pdb=" O   LEU A1548 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   LEU A1548 " --> pdb=" O   ALA A1338 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A1340 " --> pdb=" O   LYS A1546 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLY A1543 " --> pdb=" O   LEU A1527 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1364 through 1370
      removed outlier: 4.266A  pdb=" N   CYS A1361 " --> pdb=" O   GLN A1364 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   LEU A1357 " --> pdb=" O   SER A1368 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   VAL A1370 " --> pdb=" O   PRO A1355 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   THR A1402 " --> pdb=" O   GLU A1360 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP A1407 " --> pdb=" O   VAL A1416 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   VAL A1416 " --> pdb=" O   ASP A1407 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1503 through 1505
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1629 through 1636
      removed outlier: 3.717A  pdb=" N   ILE A1584 " --> pdb=" O   LYS A1629 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A1585 " --> pdb=" O   GLN A1784 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   GLN A1784 " --> pdb=" O   VAL A1585 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   ALA A1587 " --> pdb=" O   LYS A1782 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   LYS A1782 " --> pdb=" O   ALA A1587 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   GLY A1781 " --> pdb=" O   LEU A1770 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1610 through 1611
      removed outlier: 3.931A  pdb=" N   SER A1606 " --> pdb=" O   LYS A1644 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   LYS A1644 " --> pdb=" O   SER A1606 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LEU A1643 " --> pdb=" O   VAL A1663 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL A1663 " --> pdb=" O   LEU A1643 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ILE A1645 " --> pdb=" O   GLU A1661 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   GLU A1661 " --> pdb=" O   ILE A1645 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   LEU A1647 " --> pdb=" O   ILE A1659 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1720 through 1723

    303 hydrogen bonds defined for protein.
    804 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: 2.48

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3597
        1.34 -     1.46: 2633
        1.46 -     1.58: 5067
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 11379
  Sorted by residual:
  bond pdb=" C   ARG A1697 "
       pdb=" N   PRO A1698 "
    ideal  model  delta    sigma   weight residual
    1.335  1.370 -0.035 1.28e-02 6.10e+03 7.47e+00
  bond pdb=" CA  ARG A1413 "
       pdb=" C   ARG A1413 "
    ideal  model  delta    sigma   weight residual
    1.522  1.557 -0.034 1.43e-02 4.89e+03 5.78e+00
  bond pdb=" CB  ASP A1381 "
       pdb=" CG  ASP A1381 "
    ideal  model  delta    sigma   weight residual
    1.516  1.574 -0.058 2.50e-02 1.60e+03 5.47e+00
  bond pdb=" CB  ASP A 706 "
       pdb=" CG  ASP A 706 "
    ideal  model  delta    sigma   weight residual
    1.516  1.567 -0.051 2.50e-02 1.60e+03 4.11e+00
  bond pdb=" N   MET A 626 "
       pdb=" CA  MET A 626 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.76e+00
  ... (remaining 11374 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 15121
        2.85 -     5.70: 247
        5.70 -     8.55: 44
        8.55 -    11.40: 12
       11.40 -    14.25: 6
  Bond angle restraints: 15430
  Sorted by residual:
  angle pdb=" C   SER A1767 "
        pdb=" N   ARG A1768 "
        pdb=" CA  ARG A1768 "
      ideal   model   delta    sigma   weight residual
     120.83  128.96   -8.13 1.43e+00 4.89e-01 3.23e+01
  angle pdb=" N   PHE A 262 "
        pdb=" CA  PHE A 262 "
        pdb=" C   PHE A 262 "
      ideal   model   delta    sigma   weight residual
     111.11  117.02   -5.91 1.20e+00 6.94e-01 2.42e+01
  angle pdb=" C   LEU A 261 "
        pdb=" N   PHE A 262 "
        pdb=" CA  PHE A 262 "
      ideal   model   delta    sigma   weight residual
     120.54  126.60   -6.06 1.35e+00 5.49e-01 2.02e+01
  angle pdb=" CA  ASP A1381 "
        pdb=" CB  ASP A1381 "
        pdb=" CG  ASP A1381 "
      ideal   model   delta    sigma   weight residual
     112.60  116.89   -4.29 1.00e+00 1.00e+00 1.84e+01
  angle pdb=" CA  MET A 451 "
        pdb=" CB  MET A 451 "
        pdb=" CG  MET A 451 "
      ideal   model   delta    sigma   weight residual
     114.10  122.63   -8.53 2.00e+00 2.50e-01 1.82e+01
  ... (remaining 15425 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 6037
       17.82 -    35.65: 621
       35.65 -    53.47: 144
       53.47 -    71.30: 22
       71.30 -    89.12: 17
  Dihedral angle restraints: 6841
    sinusoidal: 2850
      harmonic: 3991
  Sorted by residual:
  dihedral pdb=" CA  GLU A1013 "
           pdb=" C   GLU A1013 "
           pdb=" N   TYR A1014 "
           pdb=" CA  TYR A1014 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.55  -27.45     0      5.00e+00 4.00e-02 3.01e+01
  dihedral pdb=" CA  ARG A1342 "
           pdb=" C   ARG A1342 "
           pdb=" N   ASN A1343 "
           pdb=" CA  ASN A1343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.84   23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  GLU A 978 "
           pdb=" C   GLU A 978 "
           pdb=" N   LYS A 979 "
           pdb=" CA  LYS A 979 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.58  -21.42     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 6838 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1297
       0.055 -    0.110: 262
       0.110 -    0.166: 85
       0.166 -    0.221: 9
       0.221 -    0.276: 3
  Chirality restraints: 1656
  Sorted by residual:
  chirality pdb=" CB  ILE A1208 "
            pdb=" CA  ILE A1208 "
            pdb=" CG1 ILE A1208 "
            pdb=" CG2 ILE A1208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CB  ILE A1401 "
            pdb=" CA  ILE A1401 "
            pdb=" CG1 ILE A1401 "
            pdb=" CG2 ILE A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CG  LEU A 341 "
            pdb=" CB  LEU A 341 "
            pdb=" CD1 LEU A 341 "
            pdb=" CD2 LEU A 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 1653 not shown)

  Planarity restraints: 1995
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1094 "    0.030 2.00e-02 2.50e+03   2.47e-02 1.52e+01
        pdb=" CG  TRP A1094 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1094 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1094 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1094 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1094 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1094 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1094 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1094 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1094 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 775 "    0.024 2.00e-02 2.50e+03   2.43e-02 1.48e+01
        pdb=" CG  TRP A 775 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 775 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 775 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 775 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 775 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 775 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 775 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 775 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 775 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 608 "    0.015 2.00e-02 2.50e+03   3.00e-02 8.97e+00
        pdb=" CG  ASP A 608 "   -0.052 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 608 "    0.019 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 608 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1992 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 3875
        2.91 -     3.40: 10281
        3.40 -     3.90: 18655
        3.90 -     4.40: 20434
        4.40 -     4.90: 34576
  Nonbonded interactions: 87821
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A1168 "
            pdb="CA    CA A2101 "
     model   vdw
     2.406 2.510
  nonbonded pdb=" OD1 ASP A1232 "
            pdb="CA    CA A2101 "
     model   vdw
     2.409 2.510
  nonbonded pdb=" OD2 ASP A1174 "
            pdb="CA    CA A2101 "
     model   vdw
     2.424 2.510
  nonbonded pdb=" OD1 ASP A1232 "
            pdb="CA    CA A2104 "
     model   vdw
     2.427 2.510
  nonbonded pdb=" OD2 ASP A1232 "
            pdb="CA    CA A2104 "
     model   vdw
     2.436 2.510
  ... (remaining 87816 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:             9.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.020
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11379  Z= 0.205
  Angle     :  0.982  14.252  15430  Z= 0.528
  Chirality :  0.052   0.276   1656
  Planarity :  0.008   0.085   1995
  Dihedral  : 15.524  89.122   4265
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.75 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.13 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.21), residues: 1346
  helix: -3.81 (0.18), residues: 186
  sheet: -1.20 (0.25), residues: 428
  loop : -1.31 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1693 
 TYR   0.018   0.002   TYR A 552 
 PHE   0.033   0.002   PHE A 954 
 TRP   0.067   0.003   TRP A1094 
 HIS   0.004   0.001   HIS A 812 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (11379)
  covalent geometry    : angle       0.98245 (15430)
  hydrogen bonds       : bond        0.24973 (  303)
  hydrogen bonds       : angle      10.48950 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 MET cc_start: 0.7099 (pmm) cc_final: 0.5548 (ttt)
REVERT: A  309 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7194 (t80)
REVERT: A  827 ASN cc_start: 0.8325 (m-40) cc_final: 0.7662 (m110)
REVERT: A  844 PRO cc_start: 0.7407 (Cg_exo) cc_final: 0.6995 (Cg_endo)
REVERT: A  848 MET cc_start: 0.6843 (tpp) cc_final: 0.6236 (tpp)
REVERT: A 1159 TYR cc_start: 0.7373 (t80) cc_final: 0.7136 (t80)
REVERT: A 1390 MET cc_start: 0.8893 (mmp) cc_final: 0.8618 (mpp)
REVERT: A 1391 LEU cc_start: 0.8091 (mt) cc_final: 0.7795 (mt)
REVERT: A 1419 GLN cc_start: 0.8192 (mp10) cc_final: 0.7883 (pp30)
REVERT: A 1630 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6070 (mmt)
REVERT: A 1725 ASP cc_start: 0.7001 (m-30) cc_final: 0.6264 (p0)
  outliers start: 19
  outliers final: 10
  residues processed: 185
  average time/residue: 0.1432
  time to fit residues: 35.5686
Evaluate side-chains
  117 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue 1007 VAL
Chi-restraints excluded: chain A residue 1357 LEU
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1630 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:   30.0000
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 GLN
A 771 GLN
A 812 HIS
A1753 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.147636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.102517 restraints weight = 35083.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.101753 restraints weight = 19779.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.103471 restraints weight = 13382.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.103328 restraints weight = 11157.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.103359 restraints weight = 10026.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.077  11379  Z= 0.361
  Angle     :  0.834  12.393  15430  Z= 0.428
  Chirality :  0.050   0.219   1656
  Planarity :  0.007   0.061   1995
  Dihedral  :  6.621  49.082   1521
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.53 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 15.87 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.22), residues: 1346
  helix: -0.74 (0.36), residues: 179
  sheet: -1.29 (0.25), residues: 423
  loop : -0.91 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 462 
 TYR   0.024   0.002   TYR A 664 
 PHE   0.026   0.002   PHE A1239 
 TRP   0.044   0.002   TRP A 775 
 HIS   0.012   0.002   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00817 (11379)
  covalent geometry    : angle       0.83410 (15430)
  hydrogen bonds       : bond        0.04738 (  303)
  hydrogen bonds       : angle       7.39718 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 99
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  552 TYR cc_start: 0.8723 (t80) cc_final: 0.8463 (t80)
REVERT: A  827 ASN cc_start: 0.8574 (m-40) cc_final: 0.8120 (m-40)
REVERT: A  832 GLN cc_start: 0.8321 (tt0) cc_final: 0.8023 (tt0)
REVERT: A  848 MET cc_start: 0.7968 (tpp) cc_final: 0.7608 (tpp)
REVERT: A  953 VAL cc_start: 0.5935 (OUTLIER) cc_final: 0.5153 (t)
REVERT: A 1039 ARG cc_start: 0.5279 (OUTLIER) cc_final: 0.5062 (mtt90)
REVERT: A 1387 MET cc_start: 0.0974 (ptt) cc_final: 0.0730 (ptt)
REVERT: A 1404 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7473 (mmtt)
REVERT: A 1419 GLN cc_start: 0.8745 (mp10) cc_final: 0.7864 (tm-30)
REVERT: A 1725 ASP cc_start: 0.7063 (m-30) cc_final: 0.6736 (t0)
REVERT: A 1766 GLU cc_start: 0.8477 (mp0) cc_final: 0.8233 (pm20)
  outliers start: 51
  outliers final: 31
  residues processed: 137
  average time/residue: 0.1233
  time to fit residues: 23.8597
Evaluate side-chains
  115 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 81
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  457 GLU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  465 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  760 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue  949 PHE
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1039 ARG
Chi-restraints excluded: chain A residue 1109 VAL
Chi-restraints excluded: chain A residue 1204 ILE
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1404 LYS
Chi-restraints excluded: chain A residue 1406 ILE
Chi-restraints excluded: chain A residue 1580 VAL
Chi-restraints excluded: chain A residue 1753 HIS
Chi-restraints excluded: chain A residue 1785 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 98 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 103 optimal weight:    7.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 636 GLN
A1802 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.148854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.104061 restraints weight = 34949.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.103360 restraints weight = 19845.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.103727 restraints weight = 14846.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.104451 restraints weight = 13396.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.104485 restraints weight = 12259.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11379  Z= 0.187
  Angle     :  0.676  11.666  15430  Z= 0.338
  Chirality :  0.045   0.186   1656
  Planarity :  0.005   0.049   1995
  Dihedral  :  5.858  41.639   1513
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 17.52 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.23), residues: 1346
  helix:  0.22 (0.39), residues: 173
  sheet: -1.32 (0.24), residues: 430
  loop : -0.84 (0.23), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1251 
 TYR   0.013   0.001   TYR A1159 
 PHE   0.010   0.001   PHE A 867 
 TRP   0.026   0.001   TRP A 999 
 HIS   0.008   0.001   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (11379)
  covalent geometry    : angle       0.67612 (15430)
  hydrogen bonds       : bond        0.03845 (  303)
  hydrogen bonds       : angle       6.72278 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 88
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7844 (t80)
REVERT: A  832 GLN cc_start: 0.8245 (tt0) cc_final: 0.8011 (tt0)
REVERT: A 1039 ARG cc_start: 0.5297 (OUTLIER) cc_final: 0.5051 (mtt90)
REVERT: A 1095 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7668 (mtm110)
REVERT: A 1159 TYR cc_start: 0.8047 (t80) cc_final: 0.7805 (t80)
REVERT: A 1366 VAL cc_start: 0.2806 (OUTLIER) cc_final: 0.2366 (t)
REVERT: A 1387 MET cc_start: 0.0906 (ptt) cc_final: 0.0369 (ptt)
REVERT: A 1419 GLN cc_start: 0.8719 (mp10) cc_final: 0.7822 (tm-30)
REVERT: A 1425 LEU cc_start: 0.9104 (tp) cc_final: 0.8883 (pp)
REVERT: A 1725 ASP cc_start: 0.7300 (m-30) cc_final: 0.7009 (t0)
REVERT: A 1766 GLU cc_start: 0.8509 (mp0) cc_final: 0.8071 (pm20)
  outliers start: 54
  outliers final: 27
  residues processed: 127
  average time/residue: 0.1146
  time to fit residues: 20.8278
Evaluate side-chains
  113 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  760 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue  949 PHE
Chi-restraints excluded: chain A residue 1007 VAL
Chi-restraints excluded: chain A residue 1039 ARG
Chi-restraints excluded: chain A residue 1210 ILE
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1366 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1406 ILE
Chi-restraints excluded: chain A residue 1663 VAL
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1753 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 133 optimal weight:    9.9990
   chunk 120 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 109 optimal weight:   20.0000
   chunk 74 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 6 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 15 optimal weight:    0.7980
   chunk 60 optimal weight:   20.0000
   chunk 8 optimal weight:    3.9990
   overall best weight:    3.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 691 GLN
A 722 GLN
** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1753 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.146186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.100262 restraints weight = 35089.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.099371 restraints weight = 20478.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.099858 restraints weight = 15954.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.100220 restraints weight = 13189.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.100223 restraints weight = 12017.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  11379  Z= 0.312
  Angle     :  0.749  11.731  15430  Z= 0.381
  Chirality :  0.047   0.188   1656
  Planarity :  0.006   0.060   1995
  Dihedral  :  5.988  49.171   1511
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 17.27 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.61 (0.23), residues: 1346
  helix:  0.09 (0.38), residues: 191
  sheet: -1.42 (0.25), residues: 416
  loop : -1.10 (0.23), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A1251 
 TYR   0.033   0.002   TYR A 552 
 PHE   0.017   0.002   PHE A 419 
 TRP   0.020   0.002   TRP A 775 
 HIS   0.010   0.002   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00704 (11379)
  covalent geometry    : angle       0.74868 (15430)
  hydrogen bonds       : bond        0.04147 (  303)
  hydrogen bonds       : angle       6.76852 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 86
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7876 (t80)
REVERT: A  968 MET cc_start: 0.3790 (mtm) cc_final: 0.3370 (mpp)
REVERT: A 1366 VAL cc_start: 0.2632 (OUTLIER) cc_final: 0.2293 (t)
REVERT: A 1387 MET cc_start: 0.1208 (ptt) cc_final: 0.0671 (ptt)
REVERT: A 1419 GLN cc_start: 0.8797 (mp10) cc_final: 0.7791 (tm-30)
REVERT: A 1425 LEU cc_start: 0.9150 (tp) cc_final: 0.8746 (pp)
REVERT: A 1785 MET cc_start: 0.5388 (tmm) cc_final: 0.4528 (tmm)
  outliers start: 58
  outliers final: 36
  residues processed: 131
  average time/residue: 0.1154
  time to fit residues: 21.5282
Evaluate side-chains
  121 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  760 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue 1093 ARG
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1109 VAL
Chi-restraints excluded: chain A residue 1204 ILE
Chi-restraints excluded: chain A residue 1210 ILE
Chi-restraints excluded: chain A residue 1227 GLU
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1366 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1406 ILE
Chi-restraints excluded: chain A residue 1663 VAL
Chi-restraints excluded: chain A residue 1670 LEU
Chi-restraints excluded: chain A residue 1703 HIS
Chi-restraints excluded: chain A residue 1711 VAL
Chi-restraints excluded: chain A residue 1753 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 130 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 113 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 73 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 722 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.149067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.104911 restraints weight = 35023.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.104727 restraints weight = 20761.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.104732 restraints weight = 13950.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.105093 restraints weight = 13295.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.105276 restraints weight = 11838.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.4020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11379  Z= 0.135
  Angle     :  0.651  13.429  15430  Z= 0.322
  Chirality :  0.046   0.315   1656
  Planarity :  0.005   0.047   1995
  Dihedral  :  5.518  47.879   1509
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.26 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.23), residues: 1346
  helix:  0.73 (0.40), residues: 177
  sheet: -1.39 (0.25), residues: 432
  loop : -0.81 (0.23), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1251 
 TYR   0.033   0.001   TYR A 552 
 PHE   0.020   0.001   PHE A 452 
 TRP   0.046   0.002   TRP A 999 
 HIS   0.007   0.001   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11379)
  covalent geometry    : angle       0.65139 (15430)
  hydrogen bonds       : bond        0.03322 (  303)
  hydrogen bonds       : angle       6.22428 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 91
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7855 (t80)
REVERT: A  968 MET cc_start: 0.3932 (mtm) cc_final: 0.3600 (mpp)
REVERT: A 1159 TYR cc_start: 0.7841 (t80) cc_final: 0.7513 (t80)
REVERT: A 1419 GLN cc_start: 0.8711 (mp10) cc_final: 0.7782 (tm-30)
REVERT: A 1665 ASP cc_start: 0.8616 (p0) cc_final: 0.8362 (p0)
REVERT: A 1785 MET cc_start: 0.5077 (tmm) cc_final: 0.4622 (tmm)
  outliers start: 40
  outliers final: 27
  residues processed: 121
  average time/residue: 0.1135
  time to fit residues: 19.8794
Evaluate side-chains
  109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  614 GLU
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  760 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue 1093 ARG
Chi-restraints excluded: chain A residue 1227 GLU
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1663 VAL
Chi-restraints excluded: chain A residue 1711 VAL
Chi-restraints excluded: chain A residue 1753 HIS
Chi-restraints excluded: chain A residue 1787 VAL
Chi-restraints excluded: chain A residue 1801 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 132 optimal weight:    7.9990
   chunk 109 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 136 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 129 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 71 optimal weight:   30.0000
   chunk 95 optimal weight:   10.0000
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1753 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.147870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.103431 restraints weight = 35260.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.102260 restraints weight = 19053.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.102798 restraints weight = 13303.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.103172 restraints weight = 11679.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.103161 restraints weight = 10286.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.4267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11379  Z= 0.182
  Angle     :  0.660  12.828  15430  Z= 0.326
  Chirality :  0.045   0.215   1656
  Planarity :  0.005   0.045   1995
  Dihedral  :  5.490  51.273   1509
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.26 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.23), residues: 1346
  helix:  0.81 (0.39), residues: 184
  sheet: -1.39 (0.25), residues: 423
  loop : -0.81 (0.23), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1162 
 TYR   0.013   0.001   TYR A1528 
 PHE   0.011   0.001   PHE A 419 
 TRP   0.020   0.001   TRP A 999 
 HIS   0.008   0.001   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (11379)
  covalent geometry    : angle       0.65967 (15430)
  hydrogen bonds       : bond        0.03341 (  303)
  hydrogen bonds       : angle       6.16485 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 89
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7950 (t80)
REVERT: A 1033 MET cc_start: 0.5111 (pmm) cc_final: 0.3189 (tpp)
REVERT: A 1067 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.4029 (pt0)
REVERT: A 1159 TYR cc_start: 0.7816 (t80) cc_final: 0.7522 (t80)
REVERT: A 1366 VAL cc_start: 0.2956 (OUTLIER) cc_final: 0.2492 (t)
REVERT: A 1419 GLN cc_start: 0.8706 (mp10) cc_final: 0.7845 (tm-30)
REVERT: A 1665 ASP cc_start: 0.8551 (p0) cc_final: 0.8240 (p0)
REVERT: A 1785 MET cc_start: 0.5093 (tmm) cc_final: 0.4873 (tmm)
  outliers start: 43
  outliers final: 31
  residues processed: 121
  average time/residue: 0.1148
  time to fit residues: 20.2570
Evaluate side-chains
  118 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  614 GLU
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  760 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue 1067 GLU
Chi-restraints excluded: chain A residue 1210 ILE
Chi-restraints excluded: chain A residue 1227 GLU
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1366 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1501 THR
Chi-restraints excluded: chain A residue 1663 VAL
Chi-restraints excluded: chain A residue 1711 VAL
Chi-restraints excluded: chain A residue 1753 HIS
Chi-restraints excluded: chain A residue 1787 VAL
Chi-restraints excluded: chain A residue 1801 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 121 optimal weight:   20.0000
   chunk 72 optimal weight:    2.9990
   chunk 132 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 119 optimal weight:    8.9990
   chunk 2 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   overall best weight:    3.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 543 ASN
** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 GLN
A 762 HIS
A1753 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.145529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.098473 restraints weight = 34917.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.099731 restraints weight = 20032.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.100081 restraints weight = 12278.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.100444 restraints weight = 12091.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.100404 restraints weight = 10772.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.4780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  11379  Z= 0.324
  Angle     :  0.770  14.066  15430  Z= 0.384
  Chirality :  0.048   0.249   1656
  Planarity :  0.005   0.061   1995
  Dihedral  :  5.883  58.735   1509
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 17.93 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.23), residues: 1346
  helix:  0.38 (0.39), residues: 192
  sheet: -1.41 (0.25), residues: 415
  loop : -1.03 (0.23), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1093 
 TYR   0.017   0.002   TYR A1528 
 PHE   0.016   0.002   PHE A 419 
 TRP   0.061   0.002   TRP A 999 
 HIS   0.010   0.002   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 (11379)
  covalent geometry    : angle       0.76970 (15430)
  hydrogen bonds       : bond        0.03977 (  303)
  hydrogen bonds       : angle       6.53136 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 78
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7903 (t80)
REVERT: A 1033 MET cc_start: 0.5077 (pmm) cc_final: 0.3158 (tpp)
REVERT: A 1067 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.3977 (pt0)
REVERT: A 1102 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7054 (mp0)
REVERT: A 1366 VAL cc_start: 0.2842 (OUTLIER) cc_final: 0.2475 (t)
REVERT: A 1419 GLN cc_start: 0.8829 (mp10) cc_final: 0.7880 (tm-30)
REVERT: A 1665 ASP cc_start: 0.8455 (p0) cc_final: 0.8133 (p0)
REVERT: A 1695 GLN cc_start: 0.5810 (OUTLIER) cc_final: 0.5301 (mt0)
REVERT: A 1785 MET cc_start: 0.5077 (tmm) cc_final: 0.4867 (tmm)
  outliers start: 49
  outliers final: 36
  residues processed: 117
  average time/residue: 0.0971
  time to fit residues: 17.3234
Evaluate side-chains
  114 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 73
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  416 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  614 GLU
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  760 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue 1067 GLU
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1204 ILE
Chi-restraints excluded: chain A residue 1227 GLU
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1366 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1422 ILE
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1663 VAL
Chi-restraints excluded: chain A residue 1695 GLN
Chi-restraints excluded: chain A residue 1711 VAL
Chi-restraints excluded: chain A residue 1753 HIS
Chi-restraints excluded: chain A residue 1801 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 134 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1753 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.147130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.100783 restraints weight = 34676.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.101853 restraints weight = 21980.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.102507 restraints weight = 13623.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.102918 restraints weight = 11606.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.103038 restraints weight = 10839.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.4785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11379  Z= 0.189
  Angle     :  0.707  13.332  15430  Z= 0.344
  Chirality :  0.046   0.169   1656
  Planarity :  0.005   0.046   1995
  Dihedral  :  5.680  58.895   1509
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 19.01 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.23), residues: 1346
  helix:  0.69 (0.39), residues: 190
  sheet: -1.39 (0.25), residues: 409
  loop : -0.97 (0.23), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1162 
 TYR   0.015   0.001   TYR A1159 
 PHE   0.027   0.001   PHE A 452 
 TRP   0.048   0.002   TRP A 999 
 HIS   0.008   0.001   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (11379)
  covalent geometry    : angle       0.70717 (15430)
  hydrogen bonds       : bond        0.03456 (  303)
  hydrogen bonds       : angle       6.21822 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 84
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7952 (t80)
REVERT: A  946 HIS cc_start: 0.5889 (OUTLIER) cc_final: 0.5274 (m-70)
REVERT: A 1033 MET cc_start: 0.5158 (pmm) cc_final: 0.3434 (tpp)
REVERT: A 1067 GLU cc_start: 0.5550 (OUTLIER) cc_final: 0.4092 (pt0)
REVERT: A 1102 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7003 (mp0)
REVERT: A 1366 VAL cc_start: 0.3089 (OUTLIER) cc_final: 0.2676 (t)
REVERT: A 1419 GLN cc_start: 0.8747 (mp10) cc_final: 0.7841 (tm-30)
REVERT: A 1665 ASP cc_start: 0.8529 (p0) cc_final: 0.8207 (p0)
REVERT: A 1785 MET cc_start: 0.5005 (tmm) cc_final: 0.4765 (tmm)
  outliers start: 39
  outliers final: 31
  residues processed: 113
  average time/residue: 0.1053
  time to fit residues: 17.8977
Evaluate side-chains
  116 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 80
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  614 GLU
Chi-restraints excluded: chain A residue  617 ILE
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  760 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue 1067 GLU
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1210 ILE
Chi-restraints excluded: chain A residue 1227 GLU
Chi-restraints excluded: chain A residue 1287 ILE
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1366 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1403 VAL
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1663 VAL
Chi-restraints excluded: chain A residue 1711 VAL
Chi-restraints excluded: chain A residue 1753 HIS
Chi-restraints excluded: chain A residue 1801 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 44 optimal weight:    0.0870
   chunk 66 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 125 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0980
   chunk 89 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 108 optimal weight:    5.9990
   chunk 102 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0770
   chunk 55 optimal weight:    0.1980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1753 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.149054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.104962 restraints weight = 34753.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.105404 restraints weight = 19604.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.104999 restraints weight = 13645.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.105436 restraints weight = 12898.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.105737 restraints weight = 11256.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.4709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11379  Z= 0.120
  Angle     :  0.683  15.216  15430  Z= 0.327
  Chirality :  0.046   0.168   1656
  Planarity :  0.004   0.047   1995
  Dihedral  :  5.429  57.874   1509
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.08 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.23), residues: 1346
  helix:  0.79 (0.38), residues: 191
  sheet: -1.18 (0.26), residues: 395
  loop : -0.97 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1242 
 TYR   0.023   0.001   TYR A1159 
 PHE   0.012   0.001   PHE A 642 
 TRP   0.049   0.001   TRP A 999 
 HIS   0.013   0.001   HIS A1753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (11379)
  covalent geometry    : angle       0.68347 (15430)
  hydrogen bonds       : bond        0.03146 (  303)
  hydrogen bonds       : angle       5.87372 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  946 HIS cc_start: 0.5773 (OUTLIER) cc_final: 0.5166 (m-70)
REVERT: A 1033 MET cc_start: 0.5055 (pmm) cc_final: 0.3373 (tpp)
REVERT: A 1102 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7176 (mp0)
REVERT: A 1390 MET cc_start: 0.8934 (mmm) cc_final: 0.8452 (mpp)
REVERT: A 1419 GLN cc_start: 0.8726 (mp10) cc_final: 0.7833 (tm-30)
REVERT: A 1665 ASP cc_start: 0.8505 (p0) cc_final: 0.8152 (p0)
  outliers start: 31
  outliers final: 24
  residues processed: 114
  average time/residue: 0.1122
  time to fit residues: 18.6415
Evaluate side-chains
  112 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  614 GLU
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1227 GLU
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1501 THR
Chi-restraints excluded: chain A residue 1663 VAL
Chi-restraints excluded: chain A residue 1711 VAL
Chi-restraints excluded: chain A residue 1753 HIS
Chi-restraints excluded: chain A residue 1801 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 122 optimal weight:   20.0000
   chunk 54 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0870
   chunk 115 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
A1753 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.149022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.105391 restraints weight = 35060.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.104019 restraints weight = 21019.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.105534 restraints weight = 14331.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.105545 restraints weight = 10623.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.105780 restraints weight = 10324.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.4782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11379  Z= 0.134
  Angle     :  0.707  14.472  15430  Z= 0.341
  Chirality :  0.046   0.205   1656
  Planarity :  0.004   0.046   1995
  Dihedral  :  5.394  55.963   1509
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.66 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.23), residues: 1346
  helix:  0.81 (0.38), residues: 191
  sheet: -1.15 (0.25), residues: 415
  loop : -0.93 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1710 
 TYR   0.019   0.001   TYR A1159 
 PHE   0.010   0.001   PHE A 642 
 TRP   0.049   0.001   TRP A 999 
 HIS   0.007   0.001   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11379)
  covalent geometry    : angle       0.70702 (15430)
  hydrogen bonds       : bond        0.03197 (  303)
  hydrogen bonds       : angle       5.83369 (  804)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 87
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 ARG cc_start: 0.8261 (mpp-170) cc_final: 0.8013 (mpp-170)
REVERT: A  515 LEU cc_start: 0.8246 (mt) cc_final: 0.7913 (pt)
REVERT: A  643 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.6888 (p0)
REVERT: A  946 HIS cc_start: 0.5742 (OUTLIER) cc_final: 0.5255 (m-70)
REVERT: A 1033 MET cc_start: 0.5070 (pmm) cc_final: 0.3459 (tpp)
REVERT: A 1102 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7181 (mp0)
REVERT: A 1103 LYS cc_start: 0.8513 (tptt) cc_final: 0.8240 (tptp)
REVERT: A 1387 MET cc_start: 0.1627 (ppp) cc_final: 0.1424 (ppp)
REVERT: A 1419 GLN cc_start: 0.8728 (mp10) cc_final: 0.7851 (tm-30)
REVERT: A 1665 ASP cc_start: 0.8528 (p0) cc_final: 0.8172 (p0)
  outliers start: 29
  outliers final: 24
  residues processed: 109
  average time/residue: 0.1020
  time to fit residues: 16.6579
Evaluate side-chains
  113 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain A residue  614 GLU
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  655 VAL
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  724 LEU
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain A residue 1102 GLU
Chi-restraints excluded: chain A residue 1210 ILE
Chi-restraints excluded: chain A residue 1227 GLU
Chi-restraints excluded: chain A residue 1359 VAL
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1402 THR
Chi-restraints excluded: chain A residue 1501 THR
Chi-restraints excluded: chain A residue 1663 VAL
Chi-restraints excluded: chain A residue 1753 HIS
Chi-restraints excluded: chain A residue 1801 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 131 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0170
   chunk 67 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.4022

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

Flipped N/Q/H residues before XYZ refinement:
A1753 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.148158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.103904 restraints weight = 35258.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.102945 restraints weight = 19693.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.104505 restraints weight = 13944.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.104685 restraints weight = 10503.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.104625 restraints weight = 9874.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.4890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11379  Z= 0.164
  Angle     :  0.710  14.593  15430  Z= 0.342
  Chirality :  0.046   0.197   1656
  Planarity :  0.005   0.046   1995
  Dihedral  :  5.422  52.979   1509
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.33 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.23), residues: 1346
  helix:  0.85 (0.39), residues: 191
  sheet: -1.07 (0.25), residues: 409
  loop : -0.93 (0.23), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1710 
 TYR   0.021   0.001   TYR A1159 
 PHE   0.018   0.001   PHE A 878 
 TRP   0.045   0.001   TRP A 999 
 HIS   0.008   0.001   HIS A 746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (11379)
  covalent geometry    : angle       0.70964 (15430)
  hydrogen bonds       : bond        0.03247 (  303)
  hydrogen bonds       : angle       5.84790 (  804)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2563.51 seconds
wall clock time: 45 minutes 2.89 seconds (2702.89 seconds total)