Starting phenix.real_space_refine
on Fri Feb 14 14:15:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ils_35545/02_2025/8ils_35545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ils_35545/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ils_35545/02_2025/8ils_35545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ils_35545/02_2025/8ils_35545.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ils_35545/02_2025/8ils_35545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ils_35545/02_2025/8ils_35545.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.68, per 1000 atoms: 0.64
  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: 2.66
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.13
  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: 3.41

  Time building geometry restraints manager: 2.91 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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.820
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.080
-------------------------------------------------------------------------------
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= 0.377
  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 : 25.11
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.013   0.001   TRP B 597 
 HIS   0.003   0.001   HIS A 917 
 PHE   0.016   0.002   PHE A 430 
 TYR   0.011   0.001   TYR A 432 
 ARG   0.003   0.000   ARG A  87 

*********************** 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  : 1.219 
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: 0.7054 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2621
  time to fit residues: 65.0866
Evaluate side-chains
  154 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0870
   chunk 112 optimal weight:    3.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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
** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1047 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.174746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.113002 restraints weight = 11705.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.56
r_work: 0.2909 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10587  Z= 0.184
  Angle     :  0.566   6.944  14280  Z= 0.295
  Chirality :  0.042   0.175   1537
  Planarity :  0.004   0.058   1835
  Dihedral  :  4.264  31.560   1388
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.06 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.30 %
    Favored  : 91.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.24), residues: 1239
  helix:  0.82 (0.21), residues: 568
  sheet: -1.27 (0.40), residues: 159
  loop : -0.99 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 597 
 HIS   0.004   0.001   HIS A  59 
 PHE   0.021   0.002   PHE A  70 
 TYR   0.015   0.001   TYR A 904 
 ARG   0.005   0.000   ARG B 503 

*********************** 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
  171 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 162
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.6161 (mmp) cc_final: 0.5798 (mmm)
REVERT: A  100 LYS cc_start: 0.7300 (tttt) cc_final: 0.6996 (tttt)
REVERT: A  162 ARG cc_start: 0.8573 (tpp80) cc_final: 0.7765 (mtm180)
REVERT: A  352 ASP cc_start: 0.7668 (m-30) cc_final: 0.7181 (m-30)
REVERT: A  488 ASP cc_start: 0.7497 (p0) cc_final: 0.6924 (p0)
REVERT: A  733 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8084 (ptmm)
REVERT: A  976 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7609 (mm-30)
REVERT: B  525 MET cc_start: 0.8164 (mmp) cc_final: 0.7953 (mmp)
  outliers start: 9
  outliers final: 8
  residues processed: 169
  average time/residue: 0.2421
  time to fit residues: 57.4394
Evaluate side-chains
  147 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  378 CYS
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 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 73 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 106 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 809 GLN

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 = 0.173673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.111887 restraints weight = 11838.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.55
r_work: 0.2926 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10587  Z= 0.220
  Angle     :  0.533   6.489  14280  Z= 0.277
  Chirality :  0.042   0.152   1537
  Planarity :  0.004   0.065   1835
  Dihedral  :  4.236  28.069   1388
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.79 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.17 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.24), residues: 1239
  helix:  1.14 (0.22), residues: 572
  sheet: -1.17 (0.39), residues: 159
  loop : -1.09 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 479 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.016   0.002   PHE A  70 
 TYR   0.013   0.001   TYR A 904 
 ARG   0.004   0.000   ARG B 503 

*********************** 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: 13
    poor density    : 155
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.6009 (mmp) cc_final: 0.5597 (mmm)
REVERT: A   58 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5935 (mp)
REVERT: A  162 ARG cc_start: 0.8621 (tpp80) cc_final: 0.7744 (mtm180)
REVERT: A  278 MET cc_start: 0.8309 (tpp) cc_final: 0.7964 (tpp)
REVERT: A  352 ASP cc_start: 0.7688 (m-30) cc_final: 0.7156 (m-30)
REVERT: A  488 ASP cc_start: 0.7355 (p0) cc_final: 0.6827 (p0)
REVERT: A  697 MET cc_start: 0.9004 (ttt) cc_final: 0.8697 (mmt)
REVERT: A  733 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8046 (ptmm)
REVERT: A  739 MET cc_start: 0.9025 (mtm) cc_final: 0.8491 (mtm)
REVERT: A  976 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7506 (mm-30)
REVERT: B  525 MET cc_start: 0.8153 (mmp) cc_final: 0.7834 (mmp)
  outliers start: 13
  outliers final: 7
  residues processed: 162
  average time/residue: 0.2667
  time to fit residues: 59.5313
Evaluate side-chains
  150 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
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  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  599 MET
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 111 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 86 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 803 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.170493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.105013 restraints weight = 11851.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.20
r_work: 0.2856 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
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 = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1878

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= 0.452
  Angle     :  0.630   7.721  14280  Z= 0.322
  Chirality :  0.046   0.168   1537
  Planarity :  0.004   0.067   1835
  Dihedral  :  4.419  26.605   1388
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.52 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.30 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.23), residues: 1239
  helix:  0.98 (0.21), residues: 572
  sheet: -1.11 (0.40), residues: 152
  loop : -1.27 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 479 
 HIS   0.006   0.001   HIS A1047 
 PHE   0.023   0.002   PHE A  98 
 TYR   0.015   0.002   TYR B 470 
 ARG   0.004   0.001   ARG A 765 

*********************** 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
  170 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.6045 (mmp) cc_final: 0.5793 (mmm)
REVERT: A  162 ARG cc_start: 0.8629 (tpp80) cc_final: 0.7720 (mtm180)
REVERT: A  278 MET cc_start: 0.8260 (tpp) cc_final: 0.7924 (tpp)
REVERT: A  352 ASP cc_start: 0.7680 (m-30) cc_final: 0.7097 (m-30)
REVERT: A  476 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7691 (tm-30)
REVERT: A  488 ASP cc_start: 0.7403 (p0) cc_final: 0.6854 (p0)
REVERT: A  697 MET cc_start: 0.9049 (ttt) cc_final: 0.8788 (mmt)
REVERT: A  733 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8033 (ptmm)
REVERT: A  976 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7581 (mm-30)
REVERT: B  525 MET cc_start: 0.8131 (mmp) cc_final: 0.7143 (tpp)
  outliers start: 23
  outliers final: 15
  residues processed: 160
  average time/residue: 0.2604
  time to fit residues: 57.1301
Evaluate side-chains
  155 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
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  208 THR
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  330 ILE
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  717 ASP
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain B residue  339 SER
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 122 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 18 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3926 r_free = 0.3926 target = 0.174004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.113556 restraints weight = 11678.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.37
r_work: 0.2966 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2303

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= 0.158
  Angle     :  0.494   6.529  14280  Z= 0.256
  Chirality :  0.041   0.142   1537
  Planarity :  0.004   0.067   1835
  Dihedral  :  4.112  23.959   1388
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.39
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1239
  helix:  1.34 (0.22), residues: 572
  sheet: -1.13 (0.38), residues: 161
  loop : -1.20 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 479 
 HIS   0.004   0.000   HIS A  59 
 PHE   0.017   0.001   PHE A  70 
 TYR   0.014   0.001   TYR A 904 
 ARG   0.004   0.000   ARG A 777 

*********************** 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
  173 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.6041 (mmp) cc_final: 0.5729 (mmm)
REVERT: A  278 MET cc_start: 0.8344 (tpp) cc_final: 0.8049 (tpp)
REVERT: A  352 ASP cc_start: 0.7652 (m-30) cc_final: 0.7112 (m-30)
REVERT: A  488 ASP cc_start: 0.7338 (p0) cc_final: 0.6883 (p0)
REVERT: A  599 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8896 (mtp)
REVERT: A  697 MET cc_start: 0.8959 (ttt) cc_final: 0.8697 (mmt)
REVERT: A  733 LYS cc_start: 0.8523 (ptpt) cc_final: 0.8049 (ptmm)
REVERT: B  403 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6733 (mm-30)
REVERT: B  525 MET cc_start: 0.8102 (mmp) cc_final: 0.6810 (tpt)
REVERT: B  584 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6306 (tt)
  outliers start: 16
  outliers final: 9
  residues processed: 163
  average time/residue: 0.2690
  time to fit residues: 61.6034
Evaluate side-chains
  156 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
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  211 ILE
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  409 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  717 ASP
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 119 optimal weight:    9.9990
   chunk 94 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0570
   chunk 60 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.6104

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.172379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.114868 restraints weight = 11734.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.21
r_work: 0.2948 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10587  Z= 0.244
  Angle     :  0.531   7.558  14280  Z= 0.273
  Chirality :  0.042   0.147   1537
  Planarity :  0.004   0.068   1835
  Dihedral  :  4.144  27.914   1388
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.96 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.24), residues: 1239
  helix:  1.29 (0.22), residues: 580
  sheet: -1.03 (0.39), residues: 159
  loop : -1.27 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 195 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.019   0.002   PHE A 734 
 TYR   0.014   0.001   TYR B 470 
 ARG   0.005   0.000   ARG A 765 

*********************** 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
  175 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 ARG cc_start: 0.8635 (tpp80) cc_final: 0.7792 (mtm180)
REVERT: A  218 GLU cc_start: 0.8348 (pt0) cc_final: 0.8128 (pt0)
REVERT: A  223 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7546 (tp30)
REVERT: A  278 MET cc_start: 0.8330 (tpp) cc_final: 0.8024 (tpp)
REVERT: A  291 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7662 (mm-30)
REVERT: A  352 ASP cc_start: 0.7647 (m-30) cc_final: 0.7093 (m-30)
REVERT: A  476 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7715 (tm-30)
REVERT: A  488 ASP cc_start: 0.7363 (p0) cc_final: 0.6874 (p0)
REVERT: A  697 MET cc_start: 0.8980 (ttt) cc_final: 0.8744 (mmt)
REVERT: A  733 LYS cc_start: 0.8601 (ptpt) cc_final: 0.8058 (ptmm)
REVERT: A  970 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6688 (tm-30)
REVERT: B  403 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6728 (mm-30)
REVERT: B  525 MET cc_start: 0.8050 (mmp) cc_final: 0.6747 (tpt)
  outliers start: 22
  outliers final: 15
  residues processed: 167
  average time/residue: 0.2568
  time to fit residues: 59.3897
Evaluate side-chains
  165 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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  211 ILE
Chi-restraints excluded: chain A residue  330 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  881 LEU
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  370 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:   30.0000
   chunk 82 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 46 optimal weight:   20.0000
   chunk 89 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0980
   chunk 30 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    2.6188

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.171330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.105403 restraints weight = 11979.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.31
r_work: 0.2872 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  10587  Z= 0.358
  Angle     :  0.579   7.303  14280  Z= 0.297
  Chirality :  0.044   0.157   1537
  Planarity :  0.004   0.067   1835
  Dihedral  :  4.353  28.479   1388
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.60 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.57 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.24), residues: 1239
  helix:  1.19 (0.22), residues: 574
  sheet: -1.03 (0.39), residues: 152
  loop : -1.25 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 195 
 HIS   0.004   0.001   HIS A1047 
 PHE   0.026   0.002   PHE A  98 
 TYR   0.015   0.001   TYR B 470 
 ARG   0.006   0.000   ARG A 765 

*********************** 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
  177 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 1.275 
Fit side-chains
REVERT: A   23 GLU cc_start: 0.7787 (pm20) cc_final: 0.7586 (pm20)
REVERT: A  162 ARG cc_start: 0.8624 (tpp80) cc_final: 0.7762 (mtm180)
REVERT: A  218 GLU cc_start: 0.8342 (pt0) cc_final: 0.8110 (pt0)
REVERT: A  223 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7571 (tp30)
REVERT: A  278 MET cc_start: 0.8268 (tpp) cc_final: 0.7936 (tpp)
REVERT: A  291 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7651 (mm-30)
REVERT: A  352 ASP cc_start: 0.7664 (m-30) cc_final: 0.7050 (m-30)
REVERT: A  456 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8870 (mp)
REVERT: A  476 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7700 (tm-30)
REVERT: A  488 ASP cc_start: 0.7334 (p0) cc_final: 0.6794 (p0)
REVERT: A  610 MET cc_start: 0.8799 (mmm) cc_final: 0.8582 (mmm)
REVERT: A  697 MET cc_start: 0.9061 (ttt) cc_final: 0.8803 (mmt)
REVERT: A  704 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8246 (mtp180)
REVERT: A  733 LYS cc_start: 0.8580 (ptpt) cc_final: 0.8035 (ptmm)
REVERT: A  970 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6617 (tm-30)
REVERT: B  403 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6694 (mm-30)
REVERT: B  525 MET cc_start: 0.7930 (mmp) cc_final: 0.6974 (tpp)
  outliers start: 24
  outliers final: 18
  residues processed: 170
  average time/residue: 0.2706
  time to fit residues: 62.6949
Evaluate side-chains
  168 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
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  211 ILE
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  384 ASN
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  456 LEU
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  659 THR
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  746 ASP
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain B residue  339 SER
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 749 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.174516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.113187 restraints weight = 11805.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.39
r_work: 0.2923 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10587  Z= 0.173
  Angle     :  0.503   6.455  14280  Z= 0.260
  Chirality :  0.041   0.148   1537
  Planarity :  0.004   0.065   1835
  Dihedral  :  4.150  26.481   1388
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.63 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.91 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.24), residues: 1239
  helix:  1.37 (0.22), residues: 578
  sheet: -1.07 (0.38), residues: 161
  loop : -1.25 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 195 
 HIS   0.003   0.001   HIS A  59 
 PHE   0.022   0.002   PHE A  98 
 TYR   0.014   0.001   TYR B 470 
 ARG   0.005   0.000   ARG A 765 

*********************** 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
  172 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 1.217 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.7844 (m-80) cc_final: 0.7073 (m-80)
REVERT: A  162 ARG cc_start: 0.8542 (tpp80) cc_final: 0.7978 (mtm180)
REVERT: A  218 GLU cc_start: 0.8366 (pt0) cc_final: 0.8126 (pt0)
REVERT: A  223 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7634 (tp30)
REVERT: A  278 MET cc_start: 0.8285 (tpp) cc_final: 0.7983 (tpp)
REVERT: A  352 ASP cc_start: 0.7679 (m-30) cc_final: 0.7100 (m-30)
REVERT: A  476 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7659 (tm-30)
REVERT: A  488 ASP cc_start: 0.7286 (p0) cc_final: 0.6804 (p0)
REVERT: A  599 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8902 (mtp)
REVERT: A  610 MET cc_start: 0.8737 (mmm) cc_final: 0.8527 (mmm)
REVERT: A  697 MET cc_start: 0.8993 (ttt) cc_final: 0.8691 (mmt)
REVERT: A  733 LYS cc_start: 0.8516 (ptpt) cc_final: 0.8037 (ptmm)
REVERT: A  970 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6513 (tm-30)
REVERT: B  403 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6663 (mm-30)
REVERT: B  525 MET cc_start: 0.7898 (mmp) cc_final: 0.7490 (mmp)
REVERT: B  584 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6352 (tt)
  outliers start: 21
  outliers final: 14
  residues processed: 164
  average time/residue: 0.2620
  time to fit residues: 59.6572
Evaluate side-chains
  160 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
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  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  876 THR
Chi-restraints excluded: chain B residue  339 SER
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 112 optimal weight:    8.9990
   chunk 87 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 94 optimal weight:    0.6980
   chunk 70 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 296 GLN
A 384 ASN

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 = 0.174398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.113991 restraints weight = 11856.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.45
r_work: 0.2917 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    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 = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10587  Z= 0.187
  Angle     :  0.508   6.361  14280  Z= 0.262
  Chirality :  0.041   0.147   1537
  Planarity :  0.004   0.066   1835
  Dihedral  :  4.079  25.661   1388
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.79 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.91 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.24), residues: 1239
  helix:  1.43 (0.22), residues: 581
  sheet: -0.99 (0.38), residues: 161
  loop : -1.17 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 195 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.021   0.002   PHE A  98 
 TYR   0.014   0.001   TYR B 470 
 ARG   0.005   0.000   ARG A 765 

*********************** 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
  167 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 1.250 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.7819 (m-80) cc_final: 0.6997 (m-80)
REVERT: A  162 ARG cc_start: 0.8529 (tpp80) cc_final: 0.7972 (mtm180)
REVERT: A  218 GLU cc_start: 0.8336 (pt0) cc_final: 0.8084 (pt0)
REVERT: A  223 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7628 (tp30)
REVERT: A  278 MET cc_start: 0.8265 (tpp) cc_final: 0.7957 (tpp)
REVERT: A  352 ASP cc_start: 0.7663 (m-30) cc_final: 0.7073 (m-30)
REVERT: A  476 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7715 (tm-30)
REVERT: A  488 ASP cc_start: 0.7264 (p0) cc_final: 0.6777 (p0)
REVERT: A  599 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8913 (mtp)
REVERT: A  697 MET cc_start: 0.8956 (ttt) cc_final: 0.8642 (mmt)
REVERT: A  723 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7236 (pttp)
REVERT: A  733 LYS cc_start: 0.8517 (ptpt) cc_final: 0.8054 (ptmm)
REVERT: A  970 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6415 (tm-30)
REVERT: B  403 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6652 (mm-30)
REVERT: B  525 MET cc_start: 0.7908 (mmp) cc_final: 0.7515 (mmp)
REVERT: B  584 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6365 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 161
  average time/residue: 0.2506
  time to fit residues: 56.6028
Evaluate side-chains
  161 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
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  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  723 LYS
Chi-restraints excluded: chain A residue  876 THR
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain B residue  339 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 93 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 14 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 121 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 296 GLN
A 384 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.174897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.115162 restraints weight = 11816.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.48
r_work: 0.2939 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10587  Z= 0.184
  Angle     :  0.509   6.331  14280  Z= 0.262
  Chirality :  0.041   0.149   1537
  Planarity :  0.004   0.066   1835
  Dihedral  :  4.030  24.942   1388
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.24), residues: 1239
  helix:  1.48 (0.22), residues: 579
  sheet: -0.90 (0.39), residues: 161
  loop : -1.18 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 195 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.021   0.002   PHE A  98 
 TYR   0.014   0.001   TYR B 470 
 ARG   0.005   0.000   ARG A 765 

********************** 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
  167 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 1.270 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.7918 (m-80) cc_final: 0.7080 (m-80)
REVERT: A  162 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8047 (mtm180)
REVERT: A  209 LEU cc_start: 0.8140 (tp) cc_final: 0.7930 (tp)
REVERT: A  218 GLU cc_start: 0.8424 (pt0) cc_final: 0.8178 (pt0)
REVERT: A  223 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7675 (tp30)
REVERT: A  278 MET cc_start: 0.8360 (tpp) cc_final: 0.8069 (tpp)
REVERT: A  352 ASP cc_start: 0.7669 (m-30) cc_final: 0.7107 (m-30)
REVERT: A  476 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7787 (tm-30)
REVERT: A  488 ASP cc_start: 0.7327 (p0) cc_final: 0.6853 (p0)
REVERT: A  599 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8925 (mtp)
REVERT: A  697 MET cc_start: 0.8962 (ttt) cc_final: 0.8684 (mmt)
REVERT: A  723 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7239 (pttp)
REVERT: A  733 LYS cc_start: 0.8536 (ptpt) cc_final: 0.8065 (ptmm)
REVERT: A  746 ASP cc_start: 0.7883 (t0) cc_final: 0.7510 (m-30)
REVERT: A  970 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6483 (tm-30)
REVERT: B  403 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6737 (mm-30)
REVERT: B  525 MET cc_start: 0.7848 (mmp) cc_final: 0.7429 (mmp)
REVERT: B  584 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6446 (tt)
  outliers start: 22
  outliers final: 14
  residues processed: 159
  average time/residue: 0.2431
  time to fit residues: 53.7867
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  : 1.174 
-------------------------------------------------------------------------------
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  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  339 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 116 optimal weight:    0.0050
   chunk 62 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 46 optimal weight:   20.0000
   overall best weight:    0.7194

-------------------------------------------------------------------------------
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
B 406 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.176157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.115975 restraints weight = 11686.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.47
r_work: 0.2962 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10587  Z= 0.157
  Angle     :  0.495   6.952  14280  Z= 0.257
  Chirality :  0.040   0.146   1537
  Planarity :  0.004   0.066   1835
  Dihedral  :  3.932  23.884   1388
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.24), residues: 1239
  helix:  1.53 (0.22), residues: 582
  sheet: -0.87 (0.39), residues: 161
  loop : -1.13 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 195 
 HIS   0.003   0.000   HIS A  59 
 PHE   0.020   0.001   PHE A  98 
 TYR   0.014   0.001   TYR B 470 
 ARG   0.004   0.000   ARG A 765 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6745.16 seconds
wall clock time: 119 minutes 41.68 seconds (7181.68 seconds total)