Starting phenix.real_space_refine
on Tue Mar  3 22:49:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfi_31955/03_2026/7vfi_31955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfi_31955/03_2026/7vfi_31955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vfi_31955/03_2026/7vfi_31955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfi_31955/03_2026/7vfi_31955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfi_31955/03_2026/7vfi_31955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfi_31955/03_2026/7vfi_31955.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.042
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      36      5.16       5
     C    5719      2.51       5
     N    1497      2.21       5
     O    1651      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8903
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4366
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 554}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 4361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4361
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 554}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 33
    Chain: "C"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 71
          Classifications: {'peptide': 9}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 70
          Unusual residues: {'Y01': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.07, per 1000 atoms: 0.23
  Number of scatterers: 8903
  At special positions: 0
  Unit cell: (68.89, 107.07, 136.95, 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      36     16.00
     O    1651      8.00
     N    1497      7.00
     C    5719      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 325.0 milliseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 6 sheets defined
      68.1% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 177 through 179
      No H-bonds generated for 'chain 'A' and resid 177 through 179'
    Processing helix  chain 'A' and resid 180 through 214
      Proline residue:  A 202  - end of helix
    Processing helix  chain 'A' and resid 218 through 266
      removed outlier: 3.906A  pdb=" N   THR A 222 " --> pdb=" O   MET A 218 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A 230 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   LEU A 231 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 276
      removed outlier: 3.911A  pdb=" N   PHE A 273 " --> pdb=" O   GLU A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 298
      removed outlier: 3.827A  pdb=" N   LEU A 281 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 321
    Processing helix  chain 'A' and resid 321 through 370
      Proline residue:  A 333  - end of helix
      removed outlier: 4.263A  pdb=" N   ALA A 370 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 376
      removed outlier: 3.997A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 433
      removed outlier: 4.570A  pdb=" N   LYS A 400 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLU A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 480
      removed outlier: 3.615A  pdb=" N   LEU A 441 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   SER A 463 " --> pdb=" O   GLY A 459 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   GLY A 464 " --> pdb=" O   SER A 460 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLU A 473 " --> pdb=" O   VAL A 469 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   LYS A 474 " --> pdb=" O   GLY A 470 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   VAL A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   PHE A 476 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLU A 477 " --> pdb=" O   GLU A 473 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   PHE A 478 " --> pdb=" O   LYS A 474 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ASP A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 548
    Processing helix  chain 'A' and resid 570 through 578
    Processing helix  chain 'A' and resid 591 through 597
      removed outlier: 4.198A  pdb=" N   SER A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 615
      removed outlier: 3.532A  pdb=" N   VAL A 608 " --> pdb=" O   PRO A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 623
    Processing helix  chain 'A' and resid 626 through 630
      removed outlier: 3.795A  pdb=" N   SER A 629 " --> pdb=" O   ASP A 626 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   THR A 630 " --> pdb=" O   GLY A 627 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 626 through 630'
    Processing helix  chain 'A' and resid 632 through 637
    Processing helix  chain 'A' and resid 640 through 654
    Processing helix  chain 'A' and resid 672 through 679
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 737
    Processing helix  chain 'B' and resid 170 through 178
    Processing helix  chain 'B' and resid 180 through 214
      Proline residue:  B 202  - end of helix
    Processing helix  chain 'B' and resid 217 through 267
      removed outlier: 4.048A  pdb=" N   PHE B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR B 222 " --> pdb=" O   MET B 218 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   LEU B 230 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   SER B 267 " --> pdb=" O   ARG B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 276
      removed outlier: 4.062A  pdb=" N   PHE B 273 " --> pdb=" O   GLU B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 321
      removed outlier: 5.191A  pdb=" N   ASP B 288 " --> pdb=" O   ARG B 284 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   THR B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL B 296 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   ILE B 300 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   ASN B 301 " --> pdb=" O   SER B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 370
      Proline residue:  B 333  - end of helix
      removed outlier: 4.244A  pdb=" N   THR B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ALA B 364 " --> pdb=" O   ALA B 360 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA B 370 " --> pdb=" O   GLU B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 378
      removed outlier: 4.443A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 433
      removed outlier: 3.907A  pdb=" N   LEU B 397 " --> pdb=" O   GLN B 393 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LYS B 400 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 473
      removed outlier: 3.689A  pdb=" N   LEU B 441 " --> pdb=" O   SER B 437 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   SER B 463 " --> pdb=" O   GLY B 459 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   GLY B 464 " --> pdb=" O   SER B 460 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU B 473 " --> pdb=" O   VAL B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 549
    Processing helix  chain 'B' and resid 570 through 578
    Processing helix  chain 'B' and resid 591 through 597
    Processing helix  chain 'B' and resid 604 through 615
      removed outlier: 4.088A  pdb=" N   VAL B 608 " --> pdb=" O   PRO B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 624
    Processing helix  chain 'B' and resid 640 through 654
    Processing helix  chain 'B' and resid 672 through 681
      removed outlier: 3.628A  pdb=" N   LEU B 676 " --> pdb=" O   GLU B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 700
      removed outlier: 3.721A  pdb=" N   THR B 699 " --> pdb=" O   ARG B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 726
      removed outlier: 3.860A  pdb=" N   ALA B 725 " --> pdb=" O   GLN B 721 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 730 through 738
      removed outlier: 3.716A  pdb=" N   MET B 738 " --> pdb=" O   VAL B 734 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 524 through 525
      removed outlier: 3.950A  pdb=" N   VAL A 500 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASP A 501 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU A 560 " --> pdb=" O   ASP A 501 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 661 through 663
      removed outlier: 6.705A  pdb=" N   THR A 531 " --> pdb=" O   ILE A 692 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   VAL A 708 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 516 through 521
      removed outlier: 6.073A  pdb=" N   PHE B 507 " --> pdb=" O   VAL B 517 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   GLN B 519 " --> pdb=" O   VAL B 505 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL B 505 " --> pdb=" O   GLN B 519 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   VAL B 521 " --> pdb=" O   GLU B 503 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   GLU B 503 " --> pdb=" O   VAL B 521 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   ASN B 504 " --> pdb=" O   ARG B 558 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ARG B 558 " --> pdb=" O   ASN B 504 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR B 506 " --> pdb=" O   GLY B 556 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLY B 556 " --> pdb=" O   THR B 506 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 530 through 532
    Processing sheet with id=AA5, first strand: chain 'B' and resid 560 through 561
    Processing sheet with id=AA6, first strand: chain 'B' and resid 708 through 709
      removed outlier: 7.046A  pdb=" N   VAL B 708 " --> pdb=" O   VAL B 715 " (cutoff:3.500A)

    582 hydrogen bonds defined for protein.
    1725 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.30

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2708
        1.34 -     1.45: 1428
        1.45 -     1.57: 4869
        1.57 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 9069
  Sorted by residual:
  bond pdb=" CAY Y01 A 801 "
       pdb=" OAG Y01 A 801 "
    ideal  model  delta    sigma   weight residual
    1.207  1.431 -0.224 2.00e-02 2.50e+03 1.26e+02
  bond pdb=" CAY Y01 B 802 "
       pdb=" OAG Y01 B 802 "
    ideal  model  delta    sigma   weight residual
    1.207  1.430 -0.223 2.00e-02 2.50e+03 1.25e+02
  bond pdb=" CAY Y01 B 801 "
       pdb=" OAG Y01 B 801 "
    ideal  model  delta    sigma   weight residual
    1.207  1.430 -0.223 2.00e-02 2.50e+03 1.25e+02
  bond pdb=" CAI Y01 B 802 "
       pdb=" CAZ Y01 B 802 "
    ideal  model  delta    sigma   weight residual
    1.332  1.528 -0.196 2.00e-02 2.50e+03 9.64e+01
  bond pdb=" CAI Y01 A 801 "
       pdb=" CAZ Y01 A 801 "
    ideal  model  delta    sigma   weight residual
    1.332  1.526 -0.194 2.00e-02 2.50e+03 9.39e+01
  ... (remaining 9064 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.35: 12162
        3.35 -     6.70: 129
        6.70 -    10.05: 17
       10.05 -    13.41: 5
       13.41 -    16.76: 7
  Bond angle restraints: 12320
  Sorted by residual:
  angle pdb=" N   GLU B 448 "
        pdb=" CA  GLU B 448 "
        pdb=" C   GLU B 448 "
      ideal   model   delta    sigma   weight residual
     111.28  103.47    7.81 1.09e+00 8.42e-01 5.13e+01
  angle pdb=" CAK Y01 B 801 "
        pdb=" CAI Y01 B 801 "
        pdb=" CAZ Y01 B 801 "
      ideal   model   delta    sigma   weight residual
     124.96  108.20   16.76 3.00e+00 1.11e-01 3.12e+01
  angle pdb=" CAM Y01 B 801 "
        pdb=" CAY Y01 B 801 "
        pdb=" OAG Y01 B 801 "
      ideal   model   delta    sigma   weight residual
     125.42  108.67   16.75 3.00e+00 1.11e-01 3.12e+01
  angle pdb=" CAM Y01 B 802 "
        pdb=" CAY Y01 B 802 "
        pdb=" OAG Y01 B 802 "
      ideal   model   delta    sigma   weight residual
     125.42  108.75   16.67 3.00e+00 1.11e-01 3.09e+01
  angle pdb=" CAK Y01 A 801 "
        pdb=" CAI Y01 A 801 "
        pdb=" CAZ Y01 A 801 "
      ideal   model   delta    sigma   weight residual
     124.96  109.89   15.07 3.00e+00 1.11e-01 2.52e+01
  ... (remaining 12315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 4881
       17.13 -    34.26: 484
       34.26 -    51.39: 131
       51.39 -    68.52: 31
       68.52 -    85.65: 13
  Dihedral angle restraints: 5540
    sinusoidal: 2226
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CA  PHE B 200 "
           pdb=" C   PHE B 200 "
           pdb=" N   LEU B 201 "
           pdb=" CA  LEU B 201 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.40  -28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  VAL A 228 "
           pdb=" C   VAL A 228 "
           pdb=" N   CYS A 229 "
           pdb=" CA  CYS A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.98  -25.02     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  MET A 218 "
           pdb=" C   MET A 218 "
           pdb=" N   ASP A 219 "
           pdb=" CA  ASP A 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.73   22.27     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 5537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1382
       0.107 -    0.214: 78
       0.214 -    0.321: 3
       0.321 -    0.428: 0
       0.428 -    0.535: 1
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CBE Y01 B 802 "
            pdb=" CAP Y01 B 802 "
            pdb=" CBB Y01 B 802 "
            pdb=" CBI Y01 B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.03    0.53 2.00e-01 2.50e+01 7.15e+00
  chirality pdb=" CA  ARG C 116 "
            pdb=" N   ARG C 116 "
            pdb=" C   ARG C 116 "
            pdb=" CB  ARG C 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CBB Y01 B 802 "
            pdb=" CAC Y01 B 802 "
            pdb=" CAO Y01 B 802 "
            pdb=" CBE Y01 B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.35    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1553
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAM Y01 B 801 "    0.114 2.00e-02 2.50e+03   2.14e-01 4.57e+02
        pdb=" CAY Y01 B 801 "   -0.370 2.00e-02 2.50e+03
        pdb=" OAG Y01 B 801 "    0.127 2.00e-02 2.50e+03
        pdb=" OAW Y01 B 801 "    0.128 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAM Y01 B 802 "   -0.116 2.00e-02 2.50e+03   2.12e-01 4.50e+02
        pdb=" CAY Y01 B 802 "    0.367 2.00e-02 2.50e+03
        pdb=" OAG Y01 B 802 "   -0.124 2.00e-02 2.50e+03
        pdb=" OAW Y01 B 802 "   -0.127 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAM Y01 A 801 "    0.112 2.00e-02 2.50e+03   2.05e-01 4.20e+02
        pdb=" CAY Y01 A 801 "   -0.355 2.00e-02 2.50e+03
        pdb=" OAG Y01 A 801 "    0.123 2.00e-02 2.50e+03
        pdb=" OAW Y01 A 801 "    0.121 2.00e-02 2.50e+03
  ... (remaining 1550 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1533
        2.75 -     3.29: 9990
        3.29 -     3.83: 15747
        3.83 -     4.36: 17022
        4.36 -     4.90: 27092
  Nonbonded interactions: 71384
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 561 "
            pdb=" OH  TYR B 569 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   LEU A 561 "
            pdb=" OH  TYR A 569 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   THR A 373 "
            pdb=" OG  SER A 376 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER B 217 "
            pdb=" OD1 ASP B 219 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   THR B 373 "
            pdb=" OG  SER B 376 "
     model   vdw
     2.264 3.040
  ... (remaining 71379 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 169 through 268 or (resid 269 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 270 through 329 or (resid 330 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 331 through 669 or (resid  \ 
670 through 672 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 673 through 677 or (resid 678 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 679 through 683 or (resid 684 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 685 through 686 or (resid 687 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 688 through 695 or (resid 696  \ 
and (name N or name CA or name C or name O or name CB )) or resid 697 through 73 \ 
5 or (resid 736 through 737 and (name N or name CA or name C or name O or name C \ 
B )) or resid 738 through 801))
  selection = (chain 'B' and (resid 169 through 171 or (resid 172 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 173 through 276 or (resid 277 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 278 through 335 or (resid  \ 
336 through 337 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 338 through 634 or (resid 635 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 636 through 645 or (resid 646 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 647 through 665 or (resid 666 through 672 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 673 through 734 or \ 
 (resid 735 through 737 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 738 through 801))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.060
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
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      :  0.008   0.224   9069  Z= 0.408
  Angle     :  1.008  16.757  12320  Z= 0.518
  Chirality :  0.055   0.535   1464
  Planarity :  0.011   0.214   1553
  Dihedral  : 15.625  85.647   3414
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 11.75 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.21), residues: 1143
  helix: -1.02 (0.17), residues: 710
  sheet: -4.19 (0.71), residues: 24
  loop : -3.04 (0.27), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 389 
 TYR   0.018   0.002   TYR B 395 
 PHE   0.019   0.002   PHE A 221 
 TRP   0.013   0.003   TRP B 410 
 HIS   0.009   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00819 ( 9069)
  covalent geometry    : angle       1.00750 (12320)
  hydrogen bonds       : bond        0.13997 (  582)
  hydrogen bonds       : angle       6.02321 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 152
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9182 (m-30) cc_final: 0.8976 (m-30)
REVERT: A  352 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8959 (mt-10)
REVERT: A  485 MET cc_start: 0.9474 (tpt) cc_final: 0.9269 (tmm)
REVERT: A  598 TYR cc_start: 0.8904 (t80) cc_final: 0.8637 (t80)
REVERT: A  610 GLU cc_start: 0.9870 (tt0) cc_final: 0.9620 (tp30)
REVERT: B  260 CYS cc_start: 0.9551 (t) cc_final: 0.9326 (t)
REVERT: B  336 MET cc_start: 0.9199 (mmt) cc_final: 0.8522 (tmm)
REVERT: B  466 MET cc_start: 0.8930 (mmm) cc_final: 0.8451 (mmm)
REVERT: B  576 ARG cc_start: 0.9452 (ttt-90) cc_final: 0.8557 (tpt90)
  outliers start: 2
  outliers final: 2
  residues processed: 153
  average time/residue: 0.0657
  time to fit residues: 15.4807
Evaluate side-chains
  121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  449 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    0.1980
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.8504

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 504 ASN
A 520 ASN
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 ASN
A 643 GLN
A 645 GLN
A 682 HIS
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 ASN
B 398 ASN
B 519 GLN
B 638 GLN
** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 722 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.052537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.039303 restraints weight = 50763.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.040854 restraints weight = 29216.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.041966 restraints weight = 20026.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.042692 restraints weight = 15215.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.043340 restraints weight = 12629.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9069  Z= 0.143
  Angle     :  0.643   9.281  12320  Z= 0.331
  Chirality :  0.041   0.315   1464
  Planarity :  0.004   0.046   1553
  Dihedral  :  8.427  59.525   1460
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.30 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.24), residues: 1143
  helix:  0.39 (0.19), residues: 748
  sheet: -2.22 (0.66), residues: 44
  loop : -2.75 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 256 
 TYR   0.017   0.001   TYR B 346 
 PHE   0.022   0.001   PHE A 190 
 TRP   0.007   0.001   TRP A 410 
 HIS   0.002   0.001   HIS B 720 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9069)
  covalent geometry    : angle       0.64343 (12320)
  hydrogen bonds       : bond        0.05801 (  582)
  hydrogen bonds       : angle       4.75040 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9150 (m-30) cc_final: 0.8890 (m-30)
REVERT: A  479 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9285 (mm)
REVERT: A  598 TYR cc_start: 0.8698 (t80) cc_final: 0.8218 (t80)
REVERT: A  649 MET cc_start: 0.9546 (tmm) cc_final: 0.9062 (ppp)
REVERT: B  336 MET cc_start: 0.9145 (mmt) cc_final: 0.8498 (tmm)
REVERT: B  466 MET cc_start: 0.8875 (mmm) cc_final: 0.8454 (mmm)
REVERT: B  576 ARG cc_start: 0.9398 (ttt-90) cc_final: 0.8611 (tpt90)
  outliers start: 21
  outliers final: 9
  residues processed: 152
  average time/residue: 0.0639
  time to fit residues: 15.2216
Evaluate side-chains
  124 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 46 optimal weight:   20.0000
   chunk 42 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 717 GLN
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 575 HIS
B 688 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.052854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.039715 restraints weight = 49289.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.041272 restraints weight = 29012.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.042392 restraints weight = 20148.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.043211 restraints weight = 15415.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.043851 restraints weight = 12655.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9069  Z= 0.130
  Angle     :  0.637  11.692  12320  Z= 0.320
  Chirality :  0.042   0.306   1464
  Planarity :  0.004   0.050   1553
  Dihedral  :  8.006  59.883   1458
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.62 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.25), residues: 1143
  helix:  0.85 (0.19), residues: 746
  sheet: -1.86 (0.69), residues: 44
  loop : -2.57 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 277 
 TYR   0.015   0.001   TYR B 346 
 PHE   0.017   0.001   PHE A 190 
 TRP   0.006   0.001   TRP A 322 
 HIS   0.003   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9069)
  covalent geometry    : angle       0.63748 (12320)
  hydrogen bonds       : bond        0.05320 (  582)
  hydrogen bonds       : angle       4.50396 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9095 (m-30) cc_final: 0.8825 (m-30)
REVERT: A  296 VAL cc_start: 0.8945 (t) cc_final: 0.8733 (p)
REVERT: A  479 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9279 (mm)
REVERT: A  598 TYR cc_start: 0.8712 (t80) cc_final: 0.8222 (t80)
REVERT: A  610 GLU cc_start: 0.9855 (tt0) cc_final: 0.9629 (tp30)
REVERT: B  291 MET cc_start: 0.9474 (ttt) cc_final: 0.8823 (tmm)
REVERT: B  336 MET cc_start: 0.9146 (mmt) cc_final: 0.8474 (tmm)
REVERT: B  416 LEU cc_start: 0.9655 (tp) cc_final: 0.9442 (pp)
REVERT: B  466 MET cc_start: 0.8860 (mmm) cc_final: 0.8526 (mmm)
REVERT: B  576 ARG cc_start: 0.9419 (ttt-90) cc_final: 0.8585 (tpt90)
  outliers start: 31
  outliers final: 18
  residues processed: 156
  average time/residue: 0.0599
  time to fit residues: 14.7613
Evaluate side-chains
  144 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  632 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0470
   chunk 108 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7682

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.053161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.039952 restraints weight = 50102.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.041540 restraints weight = 29329.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.042703 restraints weight = 20290.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.043466 restraints weight = 15422.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.044160 restraints weight = 12779.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9069  Z= 0.125
  Angle     :  0.632  10.366  12320  Z= 0.312
  Chirality :  0.041   0.301   1464
  Planarity :  0.003   0.042   1553
  Dihedral  :  7.673  59.954   1458
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.38 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 1143
  helix:  1.14 (0.19), residues: 746
  sheet: -1.57 (0.73), residues: 44
  loop : -2.44 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 277 
 TYR   0.017   0.001   TYR A 346 
 PHE   0.014   0.001   PHE A 620 
 TRP   0.007   0.001   TRP B 322 
 HIS   0.002   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9069)
  covalent geometry    : angle       0.63203 (12320)
  hydrogen bonds       : bond        0.04975 (  582)
  hydrogen bonds       : angle       4.35836 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 144
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9052 (m-30) cc_final: 0.8851 (m-30)
REVERT: A  479 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9226 (mm)
REVERT: A  653 LEU cc_start: 0.9560 (tp) cc_final: 0.9157 (mm)
REVERT: B  291 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.8819 (tmm)
REVERT: B  336 MET cc_start: 0.9136 (mmt) cc_final: 0.8475 (tmm)
REVERT: B  382 GLU cc_start: 0.9481 (mp0) cc_final: 0.9037 (pm20)
REVERT: B  416 LEU cc_start: 0.9642 (tp) cc_final: 0.9431 (pp)
REVERT: B  465 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9331 (pp)
REVERT: B  466 MET cc_start: 0.8854 (mmm) cc_final: 0.8407 (mmm)
REVERT: B  548 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9340 (mm)
REVERT: B  576 ARG cc_start: 0.9427 (ttt-90) cc_final: 0.8571 (tpt90)
  outliers start: 32
  outliers final: 18
  residues processed: 161
  average time/residue: 0.0573
  time to fit residues: 14.7706
Evaluate side-chains
  150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  454 CYS
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  632 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    0.4980
   chunk 101 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    1.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 638 GLN
B 583 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.053230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.039925 restraints weight = 50404.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.041480 restraints weight = 29582.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.042632 restraints weight = 20652.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.043491 restraints weight = 15735.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.044135 restraints weight = 12835.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9069  Z= 0.127
  Angle     :  0.632  10.896  12320  Z= 0.313
  Chirality :  0.041   0.294   1464
  Planarity :  0.003   0.043   1553
  Dihedral  :  7.369  59.990   1456
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.96 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.25), residues: 1143
  helix:  1.35 (0.19), residues: 748
  sheet: -1.37 (0.77), residues: 44
  loop : -2.31 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 258 
 TYR   0.014   0.001   TYR A 346 
 PHE   0.014   0.001   PHE A 273 
 TRP   0.007   0.001   TRP A 322 
 HIS   0.003   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9069)
  covalent geometry    : angle       0.63198 (12320)
  hydrogen bonds       : bond        0.04798 (  582)
  hydrogen bonds       : angle       4.32182 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  607 MET cc_start: 0.9657 (ttt) cc_final: 0.9238 (tpt)
REVERT: A  610 GLU cc_start: 0.9858 (tt0) cc_final: 0.9628 (tp30)
REVERT: A  653 LEU cc_start: 0.9542 (tp) cc_final: 0.9171 (mm)
REVERT: B  291 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.8866 (tmm)
REVERT: B  336 MET cc_start: 0.9139 (mmt) cc_final: 0.8499 (tmm)
REVERT: B  371 MET cc_start: 0.8723 (ppp) cc_final: 0.8433 (ppp)
REVERT: B  382 GLU cc_start: 0.9480 (mp0) cc_final: 0.9120 (pm20)
REVERT: B  416 LEU cc_start: 0.9648 (tp) cc_final: 0.9430 (pp)
REVERT: B  466 MET cc_start: 0.8832 (mmm) cc_final: 0.8494 (mmm)
REVERT: B  485 MET cc_start: 0.9023 (mmt) cc_final: 0.8361 (mmm)
  outliers start: 33
  outliers final: 25
  residues processed: 146
  average time/residue: 0.0546
  time to fit residues: 13.0387
Evaluate side-chains
  148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  632 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 71 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 110 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 583 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.051289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.038295 restraints weight = 51732.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.039799 restraints weight = 30291.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.040885 restraints weight = 21048.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.041684 restraints weight = 16127.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.042269 restraints weight = 13179.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9069  Z= 0.203
  Angle     :  0.678  10.415  12320  Z= 0.347
  Chirality :  0.042   0.290   1464
  Planarity :  0.004   0.045   1553
  Dihedral  :  7.302  56.357   1456
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 23.81 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.25), residues: 1143
  helix:  1.21 (0.19), residues: 758
  sheet: -1.40 (0.76), residues: 44
  loop : -2.26 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 348 
 TYR   0.016   0.001   TYR A 346 
 PHE   0.013   0.002   PHE B 273 
 TRP   0.004   0.001   TRP A 322 
 HIS   0.007   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 9069)
  covalent geometry    : angle       0.67830 (12320)
  hydrogen bonds       : bond        0.05046 (  582)
  hydrogen bonds       : angle       4.60262 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 121
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9025 (m-30) cc_final: 0.8812 (m-30)
REVERT: A  607 MET cc_start: 0.9656 (ttt) cc_final: 0.9244 (tpt)
REVERT: A  610 GLU cc_start: 0.9847 (tt0) cc_final: 0.9624 (tp30)
REVERT: A  649 MET cc_start: 0.9655 (tmm) cc_final: 0.9021 (ppp)
REVERT: B  291 MET cc_start: 0.9511 (OUTLIER) cc_final: 0.8857 (tmm)
REVERT: B  336 MET cc_start: 0.9155 (mmt) cc_final: 0.8510 (tmm)
REVERT: B  382 GLU cc_start: 0.9513 (mp0) cc_final: 0.9172 (pm20)
REVERT: B  416 LEU cc_start: 0.9665 (tp) cc_final: 0.9438 (pp)
REVERT: B  465 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9179 (pp)
REVERT: B  466 MET cc_start: 0.8848 (mmm) cc_final: 0.8313 (mmm)
REVERT: B  548 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9409 (mm)
REVERT: B  576 ARG cc_start: 0.9457 (ttt-90) cc_final: 0.8644 (tpt90)
  outliers start: 41
  outliers final: 29
  residues processed: 144
  average time/residue: 0.0571
  time to fit residues: 13.1508
Evaluate side-chains
  147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  297 SER
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  679 GLN
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  317 MET
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  454 CYS
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  632 THR
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 94 optimal weight:    8.9990
   chunk 104 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.052179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.039273 restraints weight = 50906.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.040819 restraints weight = 29438.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.041949 restraints weight = 20261.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.042767 restraints weight = 15359.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.043394 restraints weight = 12481.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9069  Z= 0.154
  Angle     :  0.663  10.431  12320  Z= 0.330
  Chirality :  0.042   0.287   1464
  Planarity :  0.003   0.046   1553
  Dihedral  :  7.239  57.445   1456
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 24.34 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.25), residues: 1143
  helix:  1.30 (0.19), residues: 760
  sheet: -1.12 (0.79), residues: 44
  loop : -2.14 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 242 
 TYR   0.016   0.001   TYR A 598 
 PHE   0.013   0.001   PHE A 190 
 TRP   0.004   0.001   TRP B 322 
 HIS   0.004   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9069)
  covalent geometry    : angle       0.66295 (12320)
  hydrogen bonds       : bond        0.05011 (  582)
  hydrogen bonds       : angle       4.49315 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 123
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9000 (m-30) cc_final: 0.8765 (m-30)
REVERT: A  607 MET cc_start: 0.9656 (ttt) cc_final: 0.9246 (tpt)
REVERT: A  610 GLU cc_start: 0.9853 (tt0) cc_final: 0.9626 (tp30)
REVERT: B  288 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8264 (t70)
REVERT: B  291 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.8850 (tmm)
REVERT: B  336 MET cc_start: 0.9156 (mmt) cc_final: 0.8516 (tmm)
REVERT: B  382 GLU cc_start: 0.9499 (mp0) cc_final: 0.9137 (pm20)
REVERT: B  416 LEU cc_start: 0.9659 (tp) cc_final: 0.9450 (pp)
REVERT: B  466 MET cc_start: 0.8837 (mmm) cc_final: 0.8403 (mmm)
REVERT: B  485 MET cc_start: 0.8926 (mmt) cc_final: 0.8237 (mmm)
REVERT: B  548 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9372 (mm)
  outliers start: 38
  outliers final: 27
  residues processed: 145
  average time/residue: 0.0587
  time to fit residues: 13.9239
Evaluate side-chains
  148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  297 SER
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  679 GLN
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  545 VAL
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  632 THR
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 112 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0570
   chunk 100 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0170
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   chunk 60 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 688 HIS
B 268 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.053683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.040668 restraints weight = 50136.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.042272 restraints weight = 29120.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.043437 restraints weight = 20098.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.044304 restraints weight = 15251.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.044940 restraints weight = 12328.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9069  Z= 0.126
  Angle     :  0.687  13.056  12320  Z= 0.326
  Chirality :  0.043   0.308   1464
  Planarity :  0.003   0.047   1553
  Dihedral  :  7.141  59.139   1456
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 25.50 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1143
  helix:  1.49 (0.19), residues: 760
  sheet: -0.81 (0.81), residues: 44
  loop : -2.11 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 242 
 TYR   0.019   0.001   TYR A 598 
 PHE   0.014   0.001   PHE A 190 
 TRP   0.008   0.001   TRP B 322 
 HIS   0.003   0.001   HIS B 571 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9069)
  covalent geometry    : angle       0.68650 (12320)
  hydrogen bonds       : bond        0.04744 (  582)
  hydrogen bonds       : angle       4.26583 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.8992 (m-30) cc_final: 0.8750 (m-30)
REVERT: A  607 MET cc_start: 0.9652 (ttt) cc_final: 0.9242 (tpt)
REVERT: A  610 GLU cc_start: 0.9852 (tt0) cc_final: 0.9623 (tp30)
REVERT: A  653 LEU cc_start: 0.9461 (tp) cc_final: 0.9070 (mm)
REVERT: B  288 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8397 (t70)
REVERT: B  291 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.8873 (tmm)
REVERT: B  336 MET cc_start: 0.9150 (mmt) cc_final: 0.8507 (tmm)
REVERT: B  382 GLU cc_start: 0.9462 (mp0) cc_final: 0.9110 (pm20)
REVERT: B  416 LEU cc_start: 0.9632 (tp) cc_final: 0.9428 (pp)
REVERT: B  465 LEU cc_start: 0.9546 (tt) cc_final: 0.9342 (pp)
REVERT: B  466 MET cc_start: 0.8837 (mmm) cc_final: 0.8369 (mmm)
REVERT: B  485 MET cc_start: 0.8894 (mmt) cc_final: 0.8146 (mmm)
REVERT: B  548 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9364 (mm)
  outliers start: 32
  outliers final: 26
  residues processed: 150
  average time/residue: 0.0554
  time to fit residues: 13.5071
Evaluate side-chains
  155 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  679 GLN
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  454 CYS
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  632 THR
Chi-restraints excluded: chain B residue  700 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 95 optimal weight:    9.9990
   chunk 112 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9980
   chunk 43 optimal weight:   10.0000
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.053310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.040158 restraints weight = 51324.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.041728 restraints weight = 30454.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.042875 restraints weight = 21193.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.043692 restraints weight = 16185.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.044340 restraints weight = 13285.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9069  Z= 0.138
  Angle     :  0.703  11.723  12320  Z= 0.340
  Chirality :  0.044   0.291   1464
  Planarity :  0.003   0.045   1553
  Dihedral  :  7.102  57.116   1456
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 26.24 %
    Favored  : 69.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1143
  helix:  1.45 (0.19), residues: 760
  sheet: -0.64 (0.83), residues: 44
  loop : -2.03 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 242 
 TYR   0.020   0.001   TYR A 346 
 PHE   0.013   0.001   PHE A 318 
 TRP   0.006   0.001   TRP B 322 
 HIS   0.004   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9069)
  covalent geometry    : angle       0.70308 (12320)
  hydrogen bonds       : bond        0.04748 (  582)
  hydrogen bonds       : angle       4.38994 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9002 (m-30) cc_final: 0.8740 (m-30)
REVERT: A  607 MET cc_start: 0.9650 (ttt) cc_final: 0.9245 (tpt)
REVERT: A  610 GLU cc_start: 0.9847 (tt0) cc_final: 0.9622 (tp30)
REVERT: A  653 LEU cc_start: 0.9480 (tp) cc_final: 0.9110 (mm)
REVERT: B  288 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8447 (t70)
REVERT: B  291 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.8861 (tmm)
REVERT: B  336 MET cc_start: 0.9148 (mmt) cc_final: 0.8498 (tmm)
REVERT: B  382 GLU cc_start: 0.9479 (mp0) cc_final: 0.9120 (pm20)
REVERT: B  416 LEU cc_start: 0.9663 (tp) cc_final: 0.9453 (pp)
REVERT: B  466 MET cc_start: 0.8816 (mmm) cc_final: 0.8416 (mmm)
REVERT: B  548 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9427 (mm)
REVERT: B  738 MET cc_start: 0.9144 (pmm) cc_final: 0.8827 (pmm)
  outliers start: 36
  outliers final: 28
  residues processed: 145
  average time/residue: 0.0578
  time to fit residues: 13.6804
Evaluate side-chains
  157 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  679 GLN
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  545 VAL
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  632 THR
Chi-restraints excluded: chain B residue  700 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 67 optimal weight:    0.1980
   chunk 61 optimal weight:    0.4980
   chunk 102 optimal weight:    2.9990
   chunk 35 optimal weight:   20.0000
   chunk 83 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 91 optimal weight:    8.9990
   chunk 104 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.053091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.040181 restraints weight = 50119.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.041728 restraints weight = 29575.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.042877 restraints weight = 20624.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.043747 restraints weight = 15675.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.044313 restraints weight = 12697.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9069  Z= 0.131
  Angle     :  0.692  11.780  12320  Z= 0.334
  Chirality :  0.043   0.304   1464
  Planarity :  0.003   0.045   1553
  Dihedral  :  7.068  57.358   1456
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 26.88 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.25), residues: 1143
  helix:  1.47 (0.19), residues: 760
  sheet: -0.49 (0.84), residues: 44
  loop : -2.02 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 242 
 TYR   0.019   0.001   TYR A 346 
 PHE   0.013   0.001   PHE B 605 
 TRP   0.006   0.001   TRP B 322 
 HIS   0.003   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9069)
  covalent geometry    : angle       0.69172 (12320)
  hydrogen bonds       : bond        0.04699 (  582)
  hydrogen bonds       : angle       4.36109 ( 1725)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9012 (m-30) cc_final: 0.8778 (m-30)
REVERT: A  607 MET cc_start: 0.9653 (ttt) cc_final: 0.9246 (tpt)
REVERT: A  610 GLU cc_start: 0.9850 (tt0) cc_final: 0.9625 (tp30)
REVERT: A  653 LEU cc_start: 0.9489 (tp) cc_final: 0.9120 (mm)
REVERT: B  288 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8459 (t70)
REVERT: B  291 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.8849 (tmm)
REVERT: B  336 MET cc_start: 0.9139 (mmt) cc_final: 0.8494 (tmm)
REVERT: B  466 MET cc_start: 0.8794 (mmm) cc_final: 0.8385 (mmm)
REVERT: B  485 MET cc_start: 0.8891 (mmt) cc_final: 0.8107 (mmm)
REVERT: B  548 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9418 (mm)
REVERT: B  738 MET cc_start: 0.9146 (pmm) cc_final: 0.8793 (pmm)
  outliers start: 33
  outliers final: 29
  residues processed: 143
  average time/residue: 0.0578
  time to fit residues: 13.4952
Evaluate side-chains
  157 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  679 GLN
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  200 PHE
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  545 VAL
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  632 THR
Chi-restraints excluded: chain B residue  700 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 39 optimal weight:   30.0000
   chunk 100 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.053701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.040602 restraints weight = 49591.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.042178 restraints weight = 29130.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.043328 restraints weight = 20166.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.044178 restraints weight = 15351.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.044819 restraints weight = 12482.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9069  Z= 0.141
  Angle     :  0.702  12.875  12320  Z= 0.339
  Chirality :  0.043   0.304   1464
  Planarity :  0.003   0.047   1553
  Dihedral  :  7.068  57.886   1456
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 27.09 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.25), residues: 1143
  helix:  1.54 (0.19), residues: 748
  sheet: -0.46 (0.84), residues: 44
  loop : -1.93 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 242 
 TYR   0.019   0.001   TYR A 346 
 PHE   0.013   0.001   PHE B 605 
 TRP   0.005   0.001   TRP B 322 
 HIS   0.004   0.001   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9069)
  covalent geometry    : angle       0.70211 (12320)
  hydrogen bonds       : bond        0.04701 (  582)
  hydrogen bonds       : angle       4.40087 ( 1725)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1350.69 seconds
wall clock time: 24 minutes 6.12 seconds (1446.12 seconds total)