Starting phenix.real_space_refine
on Sat Aug 23 06:29:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ils_35545/08_2025/8ils_35545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ils_35545/08_2025/8ils_35545.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ils_35545/08_2025/8ils_35545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ils_35545/08_2025/8ils_35545.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ils_35545/08_2025/8ils_35545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ils_35545/08_2025/8ils_35545.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.102
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      73      5.16       5
     C    6602      2.51       5
     N    1792      2.21       5
     O    1907      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  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: 10374
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7980
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 977, 7980
          Classifications: {'peptide': 977}
          Link IDs: {'PTRANS': 47, 'TRANS': 929}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2346
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 4, 'TRANS': 271}
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 48
          Unusual residues: {'7U5': 1}
          Classifications: {'undetermined': 1, 'water': 8}
          Link IDs: {None: 8}
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  BGLU A 950 " occ=0.46
      ... (7 atoms not shown)
      pdb=" OE2BGLU A 950 " occ=0.46
    residue:
      pdb=" N  BARG A 951 " occ=0.46
      ... (9 atoms not shown)
      pdb=" NH2BARG A 951 " occ=0.46
    residue:
      pdb=" N  BVAL A 952 " occ=0.46
      ... (4 atoms not shown)
      pdb=" CG2BVAL A 952 " occ=0.46
    residue:
      pdb=" N  BPRO A 953 " occ=0.46
      ... (5 atoms not shown)
      pdb=" CD BPRO A 953 " occ=0.46
    residue:
      pdb=" N  BVAL A 955 " occ=0.46
      ... (5 atoms not shown)
      pdb=" CG2BVAL A 955 " occ=0.46
    residue:
      pdb=" N  BLEU A 956 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CD2BLEU A 956 " occ=0.50
  Time building chain proxies: 2.57, per 1000 atoms: 0.25
  Number of scatterers: 10374
  At special positions: 0
  Unit cell: (85.696, 131.456, 109.824, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      73     16.00
     O    1907      8.00
     N    1792      7.00
     C    6602      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: 1.03
  Conformation dependent library (CDL) restraints added in 414.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2398

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 12 sheets defined
      51.7% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 88 through 93
      removed outlier: 3.557A  pdb=" N   LEU A  92 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ARG A  93 " --> pdb=" O   CYS A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 121
      removed outlier: 4.106A  pdb=" N   ARG A 115 " --> pdb=" O   LYS A 111 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU A 116 " --> pdb=" O   ILE A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 131
      removed outlier: 3.549A  pdb=" N   VAL A 131 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 143
      removed outlier: 3.526A  pdb=" N   ARG A 141 " --> pdb=" O   GLN A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 154
      removed outlier: 3.611A  pdb=" N   CYS A 147 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 167
      removed outlier: 3.787A  pdb=" N   ARG A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 199 through 202
    Processing helix  chain 'A' and resid 216 through 229
      removed outlier: 3.569A  pdb=" N   LYS A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 289 through 297
      removed outlier: 3.535A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLN A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 488 through 496
    Processing helix  chain 'A' and resid 528 through 536
      removed outlier: 3.502A  pdb=" N   THR A 536 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
      removed outlier: 3.562A  pdb=" N   SER A 553 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 563
      removed outlier: 3.645A  pdb=" N   THR A 560 " --> pdb=" O   TYR A 557 " (cutoff:3.500A)
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 571
      removed outlier: 3.650A  pdb=" N   LEU A 570 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 588
      removed outlier: 3.606A  pdb=" N   GLN A 582 " --> pdb=" O   ASP A 578 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   CYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.607A  pdb=" N   LYS A 621 " --> pdb=" O   ARG A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 629
    Processing helix  chain 'A' and resid 631 through 638
      removed outlier: 3.680A  pdb=" N   GLN A 637 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 658
    Processing helix  chain 'A' and resid 660 through 673
      removed outlier: 3.504A  pdb=" N   PHE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 697 through 722
      removed outlier: 4.016A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 740
    Processing helix  chain 'A' and resid 741 through 748
    Processing helix  chain 'A' and resid 765 through 769
    Processing helix  chain 'A' and resid 787 through 791
      removed outlier: 4.543A  pdb=" N   GLU A 791 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 828
      removed outlier: 3.546A  pdb=" N   LEU A 812 " --> pdb=" O   ARG A 808 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN A 815 " --> pdb=" O   MET A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 864
    Processing helix  chain 'A' and resid 875 through 885
    Processing helix  chain 'A' and resid 889 through 912
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 3.659A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 994
      removed outlier: 3.695A  pdb=" N   HIS A 994 " --> pdb=" O   ALA A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1004
      removed outlier: 3.686A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE A1002 " --> pdb=" O   PHE A 998 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1009
      removed outlier: 4.102A  pdb=" N   GLY A1009 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1026
      removed outlier: 3.683A  pdb=" N   ARG A1023 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1047
      removed outlier: 3.583A  pdb=" N   HIS A1047 " --> pdb=" O   MET A1043 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 331
    Processing helix  chain 'B' and resid 339 through 348
    Processing helix  chain 'B' and resid 400 through 409
    Processing helix  chain 'B' and resid 433 through 437
      removed outlier: 3.791A  pdb=" N   VAL B 436 " --> pdb=" O   GLN B 433 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL B 437 " --> pdb=" O   ASP B 434 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 433 through 437'
    Processing helix  chain 'B' and resid 441 through 505
      removed outlier: 3.554A  pdb=" N   VAL B 445 " --> pdb=" O   ASN B 441 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY B 446 " --> pdb=" O   ILE B 442 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLU B 502 " --> pdb=" O   CYS B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 515
      removed outlier: 3.738A  pdb=" N   LYS B 511 " --> pdb=" O   GLU B 507 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU B 515 " --> pdb=" O   LYS B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 587
      removed outlier: 3.541A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLU B 547 " --> pdb=" O   ARG B 543 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
      removed outlier: 3.778A  pdb=" N   THR B 585 " --> pdb=" O   LEU B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 598
      removed outlier: 4.066A  pdb=" N   LEU B 594 " --> pdb=" O   ARG B 590 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLU B 596 " --> pdb=" O   LYS B 592 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35
      removed outlier: 3.542A  pdb=" N   VAL A  32 " --> pdb=" O   CYS A  24 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   GLU A  23 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 73
    Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 212
      removed outlier: 8.329A  pdb=" N   LEU A 285 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   TRP A 195 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A 252 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326
    Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 392
      removed outlier: 9.884A  pdb=" N   GLU A 385 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 8.633A  pdb=" N   CYS A 340 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   LEU A 387 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   ILE A 338 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   TYR A 389 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   ILE A 336 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   ILE A 391 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.910A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 371 through 372
      removed outlier: 3.634A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 751 through 752
    Processing sheet with id=AA9, first strand: chain 'A' and resid 779 through 782
    Processing sheet with id=AB1, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AB2, first strand: chain 'B' and resid 377 through 381
      removed outlier: 3.895A  pdb=" N   THR B 354 " --> pdb=" O   ARG B 373 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 384 through 385

    480 hydrogen bonds defined for protein.
    1347 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.79

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2212
        1.33 -     1.45: 2311
        1.45 -     1.57: 5950
        1.57 -     1.69: 0
        1.69 -     1.81: 114
  Bond restraints: 10587
  Sorted by residual:
  bond pdb=" CA  SER A 773 "
       pdb=" C   SER A 773 "
    ideal  model  delta    sigma   weight residual
    1.522  1.470  0.052 1.40e-02 5.10e+03 1.37e+01
  bond pdb=" N   LYS A 776 "
       pdb=" CA  LYS A 776 "
    ideal  model  delta    sigma   weight residual
    1.457  1.418  0.039 1.10e-02 8.26e+03 1.28e+01
  bond pdb=" CA  SER A 774 "
       pdb=" C   SER A 774 "
    ideal  model  delta    sigma   weight residual
    1.523  1.487  0.037 1.34e-02 5.57e+03 7.46e+00
  bond pdb=" C   LEU A 755 "
       pdb=" N   ASN A 756 "
    ideal  model  delta    sigma   weight residual
    1.332  1.311  0.020 7.50e-03 1.78e+04 7.26e+00
  bond pdb=" C14 7U5 A1101 "
       pdb=" N13 7U5 A1101 "
    ideal  model  delta    sigma   weight residual
    1.309  1.359 -0.050 2.00e-02 2.50e+03 6.34e+00
  ... (remaining 10582 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 14136
        2.14 -     4.28: 139
        4.28 -     6.42: 4
        6.42 -     8.55: 0
        8.55 -    10.69: 1
  Bond angle restraints: 14280
  Sorted by residual:
  angle pdb=" N   ALA A 775 "
        pdb=" CA  ALA A 775 "
        pdb=" C   ALA A 775 "
      ideal   model   delta    sigma   weight residual
     110.80  121.49  -10.69 2.13e+00 2.20e-01 2.52e+01
  angle pdb=" C   TRP A 383 "
        pdb=" N   ASN A 384 "
        pdb=" CA  ASN A 384 "
      ideal   model   delta    sigma   weight residual
     122.05  118.05    4.00 1.48e+00 4.57e-01 7.32e+00
  angle pdb=" C   ALA A 775 "
        pdb=" N   LYS A 776 "
        pdb=" CA  LYS A 776 "
      ideal   model   delta    sigma   weight residual
     122.83  118.84    3.99 1.54e+00 4.22e-01 6.71e+00
  angle pdb=" O   MET A 772 "
        pdb=" C   MET A 772 "
        pdb=" N   SER A 773 "
      ideal   model   delta    sigma   weight residual
     122.81  119.66    3.15 1.23e+00 6.61e-01 6.56e+00
  angle pdb=" CA  LYS A 776 "
        pdb=" C   LYS A 776 "
        pdb=" O   LYS A 776 "
      ideal   model   delta    sigma   weight residual
     120.15  116.86    3.29 1.29e+00 6.01e-01 6.50e+00
  ... (remaining 14275 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5716
       17.98 -    35.97: 638
       35.97 -    53.95: 81
       53.95 -    71.94: 22
       71.94 -    89.92: 11
  Dihedral angle restraints: 6468
    sinusoidal: 2773
      harmonic: 3695
  Sorted by residual:
  dihedral pdb=" CA  LYS A 111 "
           pdb=" C   LYS A 111 "
           pdb=" N   ILE A 112 "
           pdb=" CA  ILE A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.95   30.05     0      5.00e+00 4.00e-02 3.61e+01
  dihedral pdb=" CA  SER A 158 "
           pdb=" C   SER A 158 "
           pdb=" N   PRO A 159 "
           pdb=" CA  PRO A 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.14   17.86     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  GLY A 828 "
           pdb=" C   GLY A 828 "
           pdb=" N   LEU A 829 "
           pdb=" CA  LEU A 829 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.34  -17.66     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 6465 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1306
       0.057 -    0.114: 211
       0.114 -    0.170: 19
       0.170 -    0.227: 0
       0.227 -    0.284: 1
  Chirality restraints: 1537
  Sorted by residual:
  chirality pdb=" CA  ALA A 775 "
            pdb=" N   ALA A 775 "
            pdb=" C   ALA A 775 "
            pdb=" CB  ALA A 775 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.20    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  ILE A 561 "
            pdb=" N   ILE A 561 "
            pdb=" C   ILE A 561 "
            pdb=" CB  ILE A 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  LYS A 111 "
            pdb=" N   LYS A 111 "
            pdb=" C   LYS A 111 "
            pdb=" CB  LYS A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.29e-01
  ... (remaining 1534 not shown)

  Planarity restraints: 1835
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C29 7U5 A1101 "   -0.095 2.00e-02 2.50e+03   4.77e-02 6.81e+01
        pdb=" C30 7U5 A1101 "   -0.017 2.00e-02 2.50e+03
        pdb=" C31 7U5 A1101 "    0.039 2.00e-02 2.50e+03
        pdb=" C32 7U5 A1101 "    0.024 2.00e-02 2.50e+03
        pdb=" C33 7U5 A1101 "    0.019 2.00e-02 2.50e+03
        pdb=" C34 7U5 A1101 "    0.073 2.00e-02 2.50e+03
        pdb=" C35 7U5 A1101 "    0.048 2.00e-02 2.50e+03
        pdb=" C36 7U5 A1101 "    0.018 2.00e-02 2.50e+03
        pdb=" C38 7U5 A1101 "   -0.065 2.00e-02 2.50e+03
        pdb=" C39 7U5 A1101 "   -0.040 2.00e-02 2.50e+03
        pdb=" N37 7U5 A1101 "   -0.031 2.00e-02 2.50e+03
        pdb=" N40 7U5 A1101 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C22 7U5 A1101 "    0.107 2.00e-02 2.50e+03   5.00e-02 5.63e+01
        pdb=" C23 7U5 A1101 "   -0.018 2.00e-02 2.50e+03
        pdb=" C24 7U5 A1101 "   -0.039 2.00e-02 2.50e+03
        pdb=" C25 7U5 A1101 "   -0.034 2.00e-02 2.50e+03
        pdb=" C26 7U5 A1101 "   -0.039 2.00e-02 2.50e+03
        pdb=" C27 7U5 A1101 "   -0.040 2.00e-02 2.50e+03
        pdb=" C28 7U5 A1101 "   -0.022 2.00e-02 2.50e+03
        pdb=" C29 7U5 A1101 "    0.022 2.00e-02 2.50e+03
        pdb=" C30 7U5 A1101 "    0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 7U5 A1101 "    0.042 2.00e-02 2.50e+03   3.01e-02 2.94e+01
        pdb=" C09 7U5 A1101 "    0.028 2.00e-02 2.50e+03
        pdb=" C10 7U5 A1101 "   -0.005 2.00e-02 2.50e+03
        pdb=" C11 7U5 A1101 "   -0.050 2.00e-02 2.50e+03
        pdb=" C12 7U5 A1101 "   -0.028 2.00e-02 2.50e+03
        pdb=" C14 7U5 A1101 "    0.012 2.00e-02 2.50e+03
        pdb=" C15 7U5 A1101 "    0.067 2.00e-02 2.50e+03
        pdb=" C16 7U5 A1101 "   -0.010 2.00e-02 2.50e+03
        pdb=" C17 7U5 A1101 "   -0.014 2.00e-02 2.50e+03
        pdb=" C19 7U5 A1101 "   -0.019 2.00e-02 2.50e+03
        pdb=" C20 7U5 A1101 "    0.006 2.00e-02 2.50e+03
        pdb=" N13 7U5 A1101 "   -0.004 2.00e-02 2.50e+03
        pdb=" N18 7U5 A1101 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1832 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 82
        2.57 -     3.16: 8935
        3.16 -     3.74: 15191
        3.74 -     4.32: 22927
        4.32 -     4.90: 37713
  Nonbonded interactions: 84848
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 428 "
            pdb=" NE2 GLN A 643 "
     model   vdw
     1.993 3.120
  nonbonded pdb=" OE2 GLU A 642 "
            pdb=" O   HOH A1201 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ASP A 138 "
            pdb=" ND2 ASN A 142 "
     model   vdw
     2.110 3.120
  nonbonded pdb=" N   SER B 399 "
            pdb=" OE2 GLU B 403 "
     model   vdw
     2.124 3.120
  nonbonded pdb=" O   ALA B 331 "
            pdb=" NZ  LYS B 430 "
     model   vdw
     2.150 3.120
  ... (remaining 84843 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.46 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.340
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
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      :  0.006   0.052  10587  Z= 0.262
  Angle     :  0.549  10.692  14280  Z= 0.298
  Chirality :  0.042   0.284   1537
  Planarity :  0.004   0.050   1835
  Dihedral  : 14.928  89.920   4070
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 25.16
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.57 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.52 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.20 (0.24), residues: 1239
  helix: -0.26 (0.22), residues: 550
  sheet: -1.56 (0.40), residues: 168
  loop : -0.96 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  87 
 TYR   0.011   0.001   TYR A 432 
 PHE   0.016   0.002   PHE A 430 
 TRP   0.013   0.001   TRP B 597 
 HIS   0.003   0.001   HIS A 917 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 (10587)
  covalent geometry    : angle       0.54861 (14280)
  hydrogen bonds       : bond        0.25740 (  480)
  hydrogen bonds       : angle       8.04967 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 179
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 MET cc_start: 0.7614 (ttp) cc_final: 0.7346 (ttp)
REVERT: A  488 ASP cc_start: 0.7504 (p0) cc_final: 0.7053 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1210
  time to fit residues: 30.2455
Evaluate side-chains
  153 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 384 ASN
A 682 GLN
A 749 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.172492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.111404 restraints weight = 11782.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.44
r_work: 0.2872 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10587  Z= 0.186
  Angle     :  0.611   7.147  14280  Z= 0.316
  Chirality :  0.044   0.196   1537
  Planarity :  0.004   0.057   1835
  Dihedral  :  4.457  32.358   1388
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.38 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  7.83 %
    Favored  : 91.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.56 (0.24), residues: 1239
  helix:  0.62 (0.21), residues: 568
  sheet: -1.30 (0.40), residues: 164
  loop : -1.10 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 503 
 TYR   0.014   0.001   TYR A 904 
 PHE   0.022   0.002   PHE A  70 
 TRP   0.013   0.001   TRP B 597 
 HIS   0.004   0.001   HIS A1047 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (10587)
  covalent geometry    : angle       0.61127 (14280)
  hydrogen bonds       : bond        0.05678 (  480)
  hydrogen bonds       : angle       4.70168 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   30 MET cc_start: 0.6109 (mmp) cc_final: 0.5733 (mmm)
REVERT: A   93 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7426 (ttm170)
REVERT: A  100 LYS cc_start: 0.7251 (tttt) cc_final: 0.6948 (tttt)
REVERT: A  162 ARG cc_start: 0.8545 (tpp80) cc_final: 0.7702 (mtm180)
REVERT: A  164 MET cc_start: 0.9099 (mmm) cc_final: 0.8870 (mmm)
REVERT: A  347 ASN cc_start: 0.7511 (t0) cc_final: 0.7049 (t0)
REVERT: A  352 ASP cc_start: 0.7674 (m-30) cc_final: 0.7184 (m-30)
REVERT: A  488 ASP cc_start: 0.7540 (p0) cc_final: 0.6957 (p0)
REVERT: A  545 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8358 (mm-30)
REVERT: A  733 LYS cc_start: 0.8563 (ptpt) cc_final: 0.8070 (ptmm)
REVERT: A  976 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7671 (mm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 165
  average time/residue: 0.1253
  time to fit residues: 27.9869
Evaluate side-chains
  151 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 101 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 94 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 113 optimal weight:    8.9990
   chunk 111 optimal weight:    8.9990
   chunk 6 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0570
   overall best weight:    1.3102

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 384 ASN
A 643 GLN
A1047 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.172864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.116105 restraints weight = 11785.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.20
r_work: 0.2952 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2815
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10587  Z= 0.147
  Angle     :  0.539   6.671  14280  Z= 0.280
  Chirality :  0.042   0.151   1537
  Planarity :  0.004   0.065   1835
  Dihedral  :  4.329  28.051   1388
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.79 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.78 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.24), residues: 1239
  helix:  1.03 (0.22), residues: 572
  sheet: -1.19 (0.39), residues: 159
  loop : -1.13 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 503 
 TYR   0.013   0.001   TYR A 904 
 PHE   0.020   0.002   PHE A 734 
 TRP   0.012   0.001   TRP A 479 
 HIS   0.003   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10587)
  covalent geometry    : angle       0.53897 (14280)
  hydrogen bonds       : bond        0.04907 (  480)
  hydrogen bonds       : angle       4.31291 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.6132 (mmp) cc_final: 0.5771 (mmm)
REVERT: A   58 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5982 (mp)
REVERT: A  162 ARG cc_start: 0.8604 (tpp80) cc_final: 0.7700 (mtm180)
REVERT: A  164 MET cc_start: 0.9028 (mmm) cc_final: 0.8775 (mmm)
REVERT: A  352 ASP cc_start: 0.7654 (m-30) cc_final: 0.7140 (m-30)
REVERT: A  488 ASP cc_start: 0.7407 (p0) cc_final: 0.6879 (p0)
REVERT: A  697 MET cc_start: 0.8958 (ttt) cc_final: 0.8680 (mmt)
REVERT: A  733 LYS cc_start: 0.8562 (ptpt) cc_final: 0.8059 (ptmm)
REVERT: A  976 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7471 (mm-30)
REVERT: B  525 MET cc_start: 0.8235 (mmp) cc_final: 0.6977 (tpt)
  outliers start: 14
  outliers final: 9
  residues processed: 163
  average time/residue: 0.1279
  time to fit residues: 28.7033
Evaluate side-chains
  156 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  643 GLN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 111 optimal weight:    8.9990
   chunk 102 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 3 optimal weight:   20.0000
   chunk 98 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0870
   chunk 77 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.2962

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 384 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.173725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.111123 restraints weight = 11869.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.49
r_work: 0.2931 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10587  Z= 0.142
  Angle     :  0.528   7.411  14280  Z= 0.272
  Chirality :  0.042   0.144   1537
  Planarity :  0.004   0.066   1835
  Dihedral  :  4.229  28.939   1388
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.63 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.39 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.24), residues: 1239
  helix:  1.22 (0.22), residues: 572
  sheet: -1.11 (0.39), residues: 159
  loop : -1.13 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 777 
 TYR   0.013   0.001   TYR B 470 
 PHE   0.024   0.002   PHE A 734 
 TRP   0.011   0.001   TRP A 479 
 HIS   0.003   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10587)
  covalent geometry    : angle       0.52766 (14280)
  hydrogen bonds       : bond        0.04583 (  480)
  hydrogen bonds       : angle       4.11334 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.6147 (mmp) cc_final: 0.5661 (mmm)
REVERT: A  162 ARG cc_start: 0.8661 (tpp80) cc_final: 0.7781 (mtm180)
REVERT: A  164 MET cc_start: 0.9017 (mmm) cc_final: 0.8761 (mmm)
REVERT: A  352 ASP cc_start: 0.7662 (m-30) cc_final: 0.7115 (m-30)
REVERT: A  476 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7737 (tm-30)
REVERT: A  488 ASP cc_start: 0.7422 (p0) cc_final: 0.6890 (p0)
REVERT: A  697 MET cc_start: 0.8995 (ttt) cc_final: 0.8730 (mmt)
REVERT: B  525 MET cc_start: 0.8149 (mmp) cc_final: 0.7188 (tpp)
  outliers start: 14
  outliers final: 11
  residues processed: 165
  average time/residue: 0.1143
  time to fit residues: 26.1249
Evaluate side-chains
  154 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 102 optimal weight:    0.3980
   chunk 64 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 115 optimal weight:   20.0000
   chunk 101 optimal weight:    7.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 450 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.175927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.113816 restraints weight = 11798.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.39
r_work: 0.2960 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10587  Z= 0.106
  Angle     :  0.487   6.396  14280  Z= 0.254
  Chirality :  0.041   0.151   1537
  Planarity :  0.004   0.066   1835
  Dihedral  :  4.037  26.626   1388
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.46 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.35 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.24), residues: 1239
  helix:  1.37 (0.22), residues: 574
  sheet: -0.98 (0.39), residues: 159
  loop : -1.10 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 765 
 TYR   0.013   0.001   TYR B 470 
 PHE   0.021   0.001   PHE A 734 
 TRP   0.010   0.001   TRP A 479 
 HIS   0.004   0.000   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (10587)
  covalent geometry    : angle       0.48713 (14280)
  hydrogen bonds       : bond        0.04087 (  480)
  hydrogen bonds       : angle       3.94046 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.8969 (mmm) cc_final: 0.8718 (mmm)
REVERT: A  352 ASP cc_start: 0.7663 (m-30) cc_final: 0.7138 (m-30)
REVERT: A  476 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7693 (tm-30)
REVERT: A  488 ASP cc_start: 0.7295 (p0) cc_final: 0.6820 (p0)
REVERT: A  599 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8883 (mtp)
REVERT: A  697 MET cc_start: 0.8912 (ttt) cc_final: 0.8642 (mmt)
REVERT: B  403 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6677 (mm-30)
REVERT: B  525 MET cc_start: 0.8037 (mmp) cc_final: 0.6816 (tpt)
REVERT: B  584 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6284 (tt)
  outliers start: 16
  outliers final: 8
  residues processed: 172
  average time/residue: 0.1128
  time to fit residues: 26.9541
Evaluate side-chains
  160 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 107 optimal weight:    4.9990
   chunk 115 optimal weight:   30.0000
   chunk 100 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 110 optimal weight:    8.9990
   chunk 89 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 80 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 384 ASN
A 643 GLN
A 803 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.170567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.110740 restraints weight = 11927.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 2.38
r_work: 0.2887 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055  10587  Z= 0.298
  Angle     :  0.645   8.712  14280  Z= 0.325
  Chirality :  0.046   0.162   1537
  Planarity :  0.004   0.069   1835
  Dihedral  :  4.445  28.724   1388
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.76 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.52 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.23), residues: 1239
  helix:  0.99 (0.21), residues: 574
  sheet: -1.13 (0.38), residues: 161
  loop : -1.33 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 765 
 TYR   0.016   0.002   TYR B 470 
 PHE   0.022   0.003   PHE A 734 
 TRP   0.014   0.002   TRP A 195 
 HIS   0.006   0.001   HIS A1047 

Details of bonding type rmsd
  covalent geometry    : bond        0.00740 (10587)
  covalent geometry    : angle       0.64545 (14280)
  hydrogen bonds       : bond        0.05164 (  480)
  hydrogen bonds       : angle       4.16850 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 PHE cc_start: 0.7941 (m-80) cc_final: 0.7574 (m-80)
REVERT: A  162 ARG cc_start: 0.8676 (tpp80) cc_final: 0.7827 (mtm180)
REVERT: A  352 ASP cc_start: 0.7699 (m-30) cc_final: 0.7105 (m-30)
REVERT: A  476 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7771 (tm-30)
REVERT: A  488 ASP cc_start: 0.7435 (p0) cc_final: 0.6868 (p0)
REVERT: A  697 MET cc_start: 0.9108 (ttt) cc_final: 0.8872 (mmt)
REVERT: A  739 MET cc_start: 0.9156 (mtm) cc_final: 0.8687 (mtm)
REVERT: B  403 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6708 (mm-30)
REVERT: B  525 MET cc_start: 0.8020 (mmp) cc_final: 0.6743 (tpt)
  outliers start: 27
  outliers final: 19
  residues processed: 172
  average time/residue: 0.1149
  time to fit residues: 26.7098
Evaluate side-chains
  162 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  659 THR
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0980
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 384 ASN
A 450 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.175170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.115756 restraints weight = 11753.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.50
r_work: 0.2959 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10587  Z= 0.109
  Angle     :  0.496   6.552  14280  Z= 0.257
  Chirality :  0.041   0.146   1537
  Planarity :  0.004   0.066   1835
  Dihedral  :  4.118  25.600   1388
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.46 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.65 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.24), residues: 1239
  helix:  1.25 (0.22), residues: 578
  sheet: -0.95 (0.39), residues: 149
  loop : -1.25 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 765 
 TYR   0.013   0.001   TYR B 470 
 PHE   0.017   0.001   PHE A 734 
 TRP   0.011   0.001   TRP A 195 
 HIS   0.003   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10587)
  covalent geometry    : angle       0.49646 (14280)
  hydrogen bonds       : bond        0.04040 (  480)
  hydrogen bonds       : angle       3.93053 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  162 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8083 (mtm180)
REVERT: A  352 ASP cc_start: 0.7689 (m-30) cc_final: 0.7107 (m-30)
REVERT: A  476 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7690 (tm-30)
REVERT: A  488 ASP cc_start: 0.7329 (p0) cc_final: 0.6855 (p0)
REVERT: A  599 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8886 (mtp)
REVERT: A  697 MET cc_start: 0.9012 (ttt) cc_final: 0.8732 (mmt)
REVERT: A  723 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7092 (pttp)
REVERT: A  739 MET cc_start: 0.9069 (mtm) cc_final: 0.8860 (mtm)
REVERT: A  970 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6612 (tm-30)
REVERT: B  403 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6677 (mm-30)
  outliers start: 22
  outliers final: 11
  residues processed: 170
  average time/residue: 0.1031
  time to fit residues: 24.2211
Evaluate side-chains
  161 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  723 LYS
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0870
   chunk 89 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 111 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.9762

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 384 ASN
A 450 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.174575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.110700 restraints weight = 11783.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.68
r_work: 0.2937 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10587  Z= 0.120
  Angle     :  0.514   7.562  14280  Z= 0.262
  Chirality :  0.041   0.149   1537
  Planarity :  0.004   0.067   1835
  Dihedral  :  4.045  24.853   1388
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.43 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.24), residues: 1239
  helix:  1.31 (0.22), residues: 579
  sheet: -0.83 (0.40), residues: 149
  loop : -1.20 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 382 
 TYR   0.014   0.001   TYR B 470 
 PHE   0.015   0.002   PHE A 734 
 TRP   0.013   0.001   TRP A 383 
 HIS   0.003   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10587)
  covalent geometry    : angle       0.51378 (14280)
  hydrogen bonds       : bond        0.04045 (  480)
  hydrogen bonds       : angle       3.89602 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  162 ARG cc_start: 0.8506 (tpp80) cc_final: 0.7955 (mtm180)
REVERT: A  278 MET cc_start: 0.8578 (tpp) cc_final: 0.8360 (mmm)
REVERT: A  352 ASP cc_start: 0.7601 (m-30) cc_final: 0.7065 (m-30)
REVERT: A  476 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7511 (tm-30)
REVERT: A  488 ASP cc_start: 0.7302 (p0) cc_final: 0.6849 (p0)
REVERT: A  599 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8788 (mtp)
REVERT: A  723 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7136 (pttp)
REVERT: A  739 MET cc_start: 0.9067 (mtm) cc_final: 0.8574 (mtm)
REVERT: A  970 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6603 (tm-30)
REVERT: B  403 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6678 (mm-30)
REVERT: B  525 MET cc_start: 0.7830 (mmp) cc_final: 0.6887 (mmp)
REVERT: B  584 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6395 (tt)
  outliers start: 20
  outliers final: 12
  residues processed: 159
  average time/residue: 0.1025
  time to fit residues: 22.6137
Evaluate side-chains
  160 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  723 LYS
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 112 optimal weight:    2.9990
   chunk 119 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 384 ASN
A 643 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.172515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.113471 restraints weight = 11803.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.47
r_work: 0.2891 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10587  Z= 0.191
  Angle     :  0.559   6.706  14280  Z= 0.286
  Chirality :  0.043   0.153   1537
  Planarity :  0.004   0.067   1835
  Dihedral  :  4.214  26.435   1388
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.44 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.09 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.24), residues: 1239
  helix:  1.17 (0.21), residues: 580
  sheet: -0.90 (0.40), residues: 147
  loop : -1.24 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 765 
 TYR   0.015   0.001   TYR B 470 
 PHE   0.019   0.002   PHE A 734 
 TRP   0.012   0.001   TRP A 195 
 HIS   0.004   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (10587)
  covalent geometry    : angle       0.55949 (14280)
  hydrogen bonds       : bond        0.04501 (  480)
  hydrogen bonds       : angle       3.98931 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.7941 (m-80) cc_final: 0.7420 (m-80)
REVERT: A  162 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8029 (mtm180)
REVERT: A  278 MET cc_start: 0.8664 (tpp) cc_final: 0.8441 (mmm)
REVERT: A  352 ASP cc_start: 0.7671 (m-30) cc_final: 0.7114 (m-30)
REVERT: A  476 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.7771 (tm-30)
REVERT: A  488 ASP cc_start: 0.7305 (p0) cc_final: 0.6873 (p0)
REVERT: A  723 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7327 (pttp)
REVERT: A  739 MET cc_start: 0.9095 (mtm) cc_final: 0.8769 (mtm)
REVERT: A  970 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6492 (tm-30)
REVERT: B  403 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6693 (mm-30)
REVERT: B  525 MET cc_start: 0.7792 (mmp) cc_final: 0.6769 (mmp)
  outliers start: 21
  outliers final: 17
  residues processed: 157
  average time/residue: 0.1069
  time to fit residues: 23.2806
Evaluate side-chains
  159 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  723 LYS
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 86 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0270
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1644

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 450 HIS
A 749 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.173064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.107635 restraints weight = 11779.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.21
r_work: 0.2901 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.169  10587  Z= 0.187
  Angle     :  0.845  59.199  14280  Z= 0.482
  Chirality :  0.042   0.150   1537
  Planarity :  0.004   0.067   1835
  Dihedral  :  4.203  26.448   1388
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.26 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.24), residues: 1239
  helix:  1.18 (0.21), residues: 580
  sheet: -1.05 (0.38), residues: 159
  loop : -1.24 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 777 
 TYR   0.015   0.001   TYR B 470 
 PHE   0.018   0.002   PHE A 734 
 TRP   0.012   0.001   TRP A 479 
 HIS   0.003   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10587)
  covalent geometry    : angle       0.84544 (14280)
  hydrogen bonds       : bond        0.04421 (  480)
  hydrogen bonds       : angle       3.98675 ( 1347)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.7898 (m-80) cc_final: 0.7361 (m-80)
REVERT: A  162 ARG cc_start: 0.8559 (tpp80) cc_final: 0.7990 (mtm180)
REVERT: A  278 MET cc_start: 0.8654 (tpp) cc_final: 0.8430 (mmm)
REVERT: A  352 ASP cc_start: 0.7654 (m-30) cc_final: 0.7091 (m-30)
REVERT: A  476 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7705 (tm-30)
REVERT: A  488 ASP cc_start: 0.7265 (p0) cc_final: 0.6833 (p0)
REVERT: A  723 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7306 (pttp)
REVERT: A  739 MET cc_start: 0.9080 (mtm) cc_final: 0.8591 (mtm)
REVERT: A  970 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6468 (tm-30)
REVERT: B  403 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6661 (mm-30)
REVERT: B  525 MET cc_start: 0.7787 (mmp) cc_final: 0.6764 (mmp)
  outliers start: 19
  outliers final: 16
  residues processed: 152
  average time/residue: 0.1158
  time to fit residues: 24.6025
Evaluate side-chains
  157 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  723 LYS
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0050
   chunk 59 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    0.4980
   chunk 115 optimal weight:   20.0000
   chunk 100 optimal weight:   10.0000
   chunk 112 optimal weight:    0.9990
   chunk 107 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 450 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.173012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.114734 restraints weight = 11829.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.24
r_work: 0.2945 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.169  10587  Z= 0.187
  Angle     :  0.845  59.199  14280  Z= 0.482
  Chirality :  0.042   0.150   1537
  Planarity :  0.004   0.067   1835
  Dihedral  :  4.203  26.448   1388
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.35 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.24), residues: 1239
  helix:  1.18 (0.21), residues: 580
  sheet: -1.05 (0.38), residues: 159
  loop : -1.24 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 777 
 TYR   0.015   0.001   TYR B 470 
 PHE   0.018   0.002   PHE A 734 
 TRP   0.012   0.001   TRP A 479 
 HIS   0.003   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10587)
  covalent geometry    : angle       0.84544 (14280)
  hydrogen bonds       : bond        0.04421 (  480)
  hydrogen bonds       : angle       3.98675 ( 1347)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3410.24 seconds
wall clock time: 58 minutes 58.67 seconds (3538.67 seconds total)