Starting phenix.real_space_refine
on Thu Feb 13 15:13:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfi_31955/02_2025/7vfi_31955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfi_31955/02_2025/7vfi_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_31955/02_2025/7vfi_31955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfi_31955/02_2025/7vfi_31955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfi_31955/02_2025/7vfi_31955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfi_31955/02_2025/7vfi_31955.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          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: 5.69, per 1000 atoms: 0.64
  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.87
  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: 2.72

  Time building geometry restraints manager: 2.83 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 or resid 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 or resid 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:             1.250
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.410
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.390
-------------------------------------------------------------------------------
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= 0.552
  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 : 10.24
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.013   0.003   TRP B 410 
 HIS   0.009   0.001   HIS B 487 
 PHE   0.019   0.002   PHE A 221 
 TYR   0.018   0.002   TYR B 395 
 ARG   0.008   0.001   ARG B 389 

*********************** 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  : 1.023 
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: 0.8450 (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: 0.1698
  time to fit residues: 39.0085
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  : 1.020 
-------------------------------------------------------------------------------
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 96 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:   20.0000
   chunk 89 optimal weight:   20.0000
   chunk 34 optimal weight:    0.0470
   chunk 54 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    4.0086

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 435 GLN
A 504 ASN
A 520 ASN
** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 ASN
A 638 GLN
A 643 GLN
A 645 GLN
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 ASN
B 519 GLN
B 638 GLN
B 722 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.051264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.038285 restraints weight = 50973.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.039734 restraints weight = 29490.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.040804 restraints weight = 20438.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9069  Z= 0.258
  Angle     :  0.674   8.728  12320  Z= 0.356
  Chirality :  0.041   0.310   1464
  Planarity :  0.004   0.047   1553
  Dihedral  :  8.581  59.412   1460
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.93 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.24), residues: 1143
  helix:  0.27 (0.18), residues: 744
  sheet: -2.36 (0.65), residues: 44
  loop : -2.78 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 410 
 HIS   0.004   0.001   HIS B 487 
 PHE   0.020   0.002   PHE A 190 
 TYR   0.016   0.001   TYR A 395 
 ARG   0.004   0.001   ARG A 256 

*********************** 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
  160 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9128 (m-30) cc_final: 0.8853 (m-30)
REVERT: A  479 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9294 (mm)
REVERT: A  598 TYR cc_start: 0.8836 (t80) cc_final: 0.8604 (t80)
REVERT: B  260 CYS cc_start: 0.9536 (t) cc_final: 0.9318 (t)
REVERT: B  291 MET cc_start: 0.9572 (tpt) cc_final: 0.8992 (tmm)
REVERT: B  336 MET cc_start: 0.9158 (mmt) cc_final: 0.8542 (tmm)
REVERT: B  466 MET cc_start: 0.8880 (mmm) cc_final: 0.8456 (mmm)
REVERT: B  576 ARG cc_start: 0.9416 (ttt-90) cc_final: 0.8629 (tpt90)
  outliers start: 26
  outliers final: 17
  residues processed: 144
  average time/residue: 0.1551
  time to fit residues: 34.0540
Evaluate side-chains
  133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  260 CYS
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  451 LEU
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  315 VAL
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  449 PHE
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 110 optimal weight:   30.0000
   chunk 84 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   chunk 111 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 94 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 682 HIS
A 717 GLN
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.052274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.039227 restraints weight = 51030.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.040747 restraints weight = 29695.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.041863 restraints weight = 20488.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9069  Z= 0.193
  Angle     :  0.644  10.805  12320  Z= 0.329
  Chirality :  0.042   0.306   1464
  Planarity :  0.004   0.051   1553
  Dihedral  :  8.191  59.774   1460
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.68 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 1143
  helix:  0.82 (0.19), residues: 746
  sheet: -2.07 (0.68), residues: 44
  loop : -2.53 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 322 
 HIS   0.003   0.001   HIS B 487 
 PHE   0.014   0.001   PHE A 444 
 TYR   0.024   0.001   TYR A 552 
 ARG   0.003   0.000   ARG B 242 

*********************** 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
  160 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
REVERT: A  288 ASP cc_start: 0.9068 (m-30) cc_final: 0.8776 (m-30)
REVERT: A  479 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9282 (mm)
REVERT: A  598 TYR cc_start: 0.8723 (t80) cc_final: 0.8503 (t80)
REVERT: A  610 GLU cc_start: 0.9860 (tt0) cc_final: 0.9631 (pt0)
REVERT: A  649 MET cc_start: 0.9619 (tmm) cc_final: 0.9099 (ppp)
REVERT: B  260 CYS cc_start: 0.9527 (t) cc_final: 0.9241 (t)
REVERT: B  291 MET cc_start: 0.9564 (tpt) cc_final: 0.8865 (tmm)
REVERT: B  336 MET cc_start: 0.9163 (mmt) cc_final: 0.8543 (tmm)
REVERT: B  466 MET cc_start: 0.8871 (mmm) cc_final: 0.8460 (mmm)
REVERT: B  576 ARG cc_start: 0.9420 (ttt-90) cc_final: 0.8609 (tpt90)
  outliers start: 30
  outliers final: 18
  residues processed: 146
  average time/residue: 0.2052
  time to fit residues: 45.8828
Evaluate side-chains
  133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  451 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  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  289 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 109 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 575 HIS
** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.052758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.039611 restraints weight = 50431.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.041166 restraints weight = 29316.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.042314 restraints weight = 20228.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2140

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= 0.167
  Angle     :  0.619  10.274  12320  Z= 0.313
  Chirality :  0.041   0.303   1464
  Planarity :  0.003   0.045   1553
  Dihedral  :  7.811  59.789   1458
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.38 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1143
  helix:  1.15 (0.19), residues: 744
  sheet: -1.78 (0.72), residues: 44
  loop : -2.42 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 322 
 HIS   0.002   0.001   HIS A 618 
 PHE   0.014   0.001   PHE A 190 
 TYR   0.016   0.001   TYR A 552 
 ARG   0.003   0.000   ARG B 242 

*********************** 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
  170 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8803 (m-30) cc_final: 0.8575 (m-30)
REVERT: A  288 ASP cc_start: 0.9040 (m-30) cc_final: 0.8746 (m-30)
REVERT: A  296 VAL cc_start: 0.8965 (t) cc_final: 0.8751 (p)
REVERT: A  451 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9241 (tp)
REVERT: A  454 CYS cc_start: 0.9622 (m) cc_final: 0.9419 (p)
REVERT: A  598 TYR cc_start: 0.8732 (t80) cc_final: 0.8482 (t80)
REVERT: A  653 LEU cc_start: 0.9576 (tp) cc_final: 0.9165 (mm)
REVERT: B  260 CYS cc_start: 0.9524 (t) cc_final: 0.9258 (t)
REVERT: B  291 MET cc_start: 0.9558 (tpt) cc_final: 0.8942 (tmm)
REVERT: B  336 MET cc_start: 0.9150 (mmt) cc_final: 0.8508 (tmm)
REVERT: B  382 GLU cc_start: 0.9492 (mp0) cc_final: 0.9082 (pm20)
REVERT: B  416 LEU cc_start: 0.9593 (tt) cc_final: 0.9369 (pp)
REVERT: B  466 MET cc_start: 0.8848 (mmm) cc_final: 0.8433 (mmm)
REVERT: B  479 ILE cc_start: 0.9461 (tt) cc_final: 0.9216 (tt)
REVERT: B  549 GLU cc_start: 0.9210 (pt0) cc_final: 0.8976 (pt0)
REVERT: B  576 ARG cc_start: 0.9426 (ttt-90) cc_final: 0.8600 (tpt90)
  outliers start: 33
  outliers final: 21
  residues processed: 155
  average time/residue: 0.1501
  time to fit residues: 35.7831
Evaluate side-chains
  146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  451 LEU
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  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  289 THR
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  632 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 40 optimal weight:   20.0000
   chunk 109 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.8986

-------------------------------------------------------------------------------
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
B 583 GLN
B 688 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.053414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.040342 restraints weight = 49364.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.041928 restraints weight = 29060.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.043081 restraints weight = 20083.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9069  Z= 0.160
  Angle     :  0.642  11.764  12320  Z= 0.316
  Chirality :  0.041   0.298   1464
  Planarity :  0.003   0.050   1553
  Dihedral  :  7.541  59.281   1458
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.22 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.25), residues: 1143
  helix:  1.36 (0.19), residues: 744
  sheet: -1.53 (0.75), residues: 44
  loop : -2.37 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 322 
 HIS   0.002   0.001   HIS A 618 
 PHE   0.014   0.001   PHE A 620 
 TYR   0.018   0.001   TYR A 346 
 ARG   0.003   0.000   ARG B 242 

*********************** 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
  173 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A  274 ASP cc_start: 0.8878 (m-30) cc_final: 0.8558 (m-30)
REVERT: A  288 ASP cc_start: 0.9011 (m-30) cc_final: 0.8721 (m-30)
REVERT: A  451 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9292 (tp)
REVERT: A  598 TYR cc_start: 0.8676 (t80) cc_final: 0.8217 (t80)
REVERT: A  653 LEU cc_start: 0.9543 (tp) cc_final: 0.9160 (mm)
REVERT: B  260 CYS cc_start: 0.9491 (t) cc_final: 0.9220 (t)
REVERT: B  291 MET cc_start: 0.9554 (tpt) cc_final: 0.8950 (tmm)
REVERT: B  336 MET cc_start: 0.9152 (mmt) cc_final: 0.8521 (tmm)
REVERT: B  382 GLU cc_start: 0.9483 (mp0) cc_final: 0.9134 (pm20)
REVERT: B  416 LEU cc_start: 0.9578 (tt) cc_final: 0.9339 (pp)
REVERT: B  465 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9239 (pp)
REVERT: B  466 MET cc_start: 0.8867 (mmm) cc_final: 0.8328 (mmm)
REVERT: B  479 ILE cc_start: 0.9434 (tt) cc_final: 0.9179 (tt)
REVERT: B  485 MET cc_start: 0.9051 (mmt) cc_final: 0.8375 (mmm)
REVERT: B  548 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9378 (mm)
  outliers start: 37
  outliers final: 20
  residues processed: 156
  average time/residue: 0.1629
  time to fit residues: 40.0460
Evaluate side-chains
  151 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  451 LEU
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  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  289 THR
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  451 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0670
   chunk 58 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1324

-------------------------------------------------------------------------------
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 = 0.3107 r_free = 0.3107 target = 0.053946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.040766 restraints weight = 49784.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.042371 restraints weight = 29279.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.043531 restraints weight = 20272.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9069  Z= 0.162
  Angle     :  0.652  10.141  12320  Z= 0.316
  Chirality :  0.041   0.290   1464
  Planarity :  0.003   0.045   1553
  Dihedral  :  7.381  59.420   1458
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 25.40 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.25), residues: 1143
  helix:  1.43 (0.19), residues: 746
  sheet: -1.09 (0.79), residues: 44
  loop : -2.29 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 322 
 HIS   0.003   0.001   HIS A 575 
 PHE   0.015   0.001   PHE A 190 
 TYR   0.018   0.001   TYR A 346 
 ARG   0.003   0.000   ARG B 242 

*********************** 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
  163 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  274 ASP cc_start: 0.8880 (m-30) cc_final: 0.8551 (m-30)
REVERT: A  288 ASP cc_start: 0.9034 (m-30) cc_final: 0.8823 (m-30)
REVERT: A  436 MET cc_start: 0.8164 (pmm) cc_final: 0.7919 (pmm)
REVERT: A  598 TYR cc_start: 0.8755 (t80) cc_final: 0.8250 (t80)
REVERT: A  607 MET cc_start: 0.9551 (mmm) cc_final: 0.9249 (mmm)
REVERT: A  653 LEU cc_start: 0.9536 (tp) cc_final: 0.9163 (mm)
REVERT: B  260 CYS cc_start: 0.9528 (t) cc_final: 0.9260 (t)
REVERT: B  291 MET cc_start: 0.9539 (tpt) cc_final: 0.8925 (tmm)
REVERT: B  336 MET cc_start: 0.9144 (mmt) cc_final: 0.8518 (tmm)
REVERT: B  382 GLU cc_start: 0.9484 (mp0) cc_final: 0.9133 (pm20)
REVERT: B  416 LEU cc_start: 0.9573 (tt) cc_final: 0.9323 (pp)
REVERT: B  465 LEU cc_start: 0.9537 (tt) cc_final: 0.9227 (pp)
REVERT: B  466 MET cc_start: 0.8860 (mmm) cc_final: 0.8342 (mmm)
REVERT: B  479 ILE cc_start: 0.9420 (tt) cc_final: 0.9170 (tt)
REVERT: B  548 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9370 (mm)
REVERT: B  549 GLU cc_start: 0.9197 (pt0) cc_final: 0.8986 (pt0)
  outliers start: 27
  outliers final: 18
  residues processed: 152
  average time/residue: 0.1421
  time to fit residues: 34.1508
Evaluate side-chains
  145 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  326 LEU
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  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  289 THR
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  714 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 106 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 70 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3103 r_free = 0.3103 target = 0.053834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.040755 restraints weight = 50001.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.042348 restraints weight = 29335.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.043518 restraints weight = 20300.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2885

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= 0.164
  Angle     :  0.654  12.569  12320  Z= 0.318
  Chirality :  0.041   0.283   1464
  Planarity :  0.003   0.047   1553
  Dihedral  :  7.143  58.137   1456
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 26.46 %
    Favored  : 70.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.25), residues: 1143
  helix:  1.46 (0.19), residues: 748
  sheet: -0.91 (0.80), residues: 44
  loop : -2.16 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 322 
 HIS   0.002   0.001   HIS B 487 
 PHE   0.014   0.001   PHE A 190 
 TYR   0.015   0.001   TYR A 346 
 ARG   0.003   0.000   ARG B 242 

*********************** 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
  159 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8904 (m-30) cc_final: 0.8589 (m-30)
REVERT: A  288 ASP cc_start: 0.9049 (m-30) cc_final: 0.8835 (m-30)
REVERT: A  317 MET cc_start: 0.9492 (mmm) cc_final: 0.9257 (mpp)
REVERT: A  598 TYR cc_start: 0.8785 (t80) cc_final: 0.8516 (t80)
REVERT: A  607 MET cc_start: 0.9559 (mmm) cc_final: 0.9243 (mmm)
REVERT: A  653 LEU cc_start: 0.9527 (tp) cc_final: 0.9197 (mm)
REVERT: B  260 CYS cc_start: 0.9537 (t) cc_final: 0.9244 (t)
REVERT: B  291 MET cc_start: 0.9530 (tpt) cc_final: 0.8904 (tmm)
REVERT: B  336 MET cc_start: 0.9152 (mmt) cc_final: 0.8528 (tmm)
REVERT: B  382 GLU cc_start: 0.9487 (mp0) cc_final: 0.9127 (pm20)
REVERT: B  416 LEU cc_start: 0.9575 (tt) cc_final: 0.9323 (pp)
REVERT: B  465 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9227 (pp)
REVERT: B  466 MET cc_start: 0.8858 (mmm) cc_final: 0.8352 (mmm)
REVERT: B  548 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9377 (mm)
  outliers start: 28
  outliers final: 22
  residues processed: 148
  average time/residue: 0.1448
  time to fit residues: 33.8566
Evaluate side-chains
  147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  295 LEU
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  441 LEU
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  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  289 THR
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  395 TYR
Chi-restraints excluded: chain B residue  451 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 48 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.3586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.054066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.041091 restraints weight = 50030.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.042720 restraints weight = 29261.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.043905 restraints weight = 20112.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9069  Z= 0.159
  Angle     :  0.656  11.555  12320  Z= 0.317
  Chirality :  0.041   0.272   1464
  Planarity :  0.003   0.046   1553
  Dihedral  :  7.046  57.779   1456
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 26.77 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1143
  helix:  1.57 (0.19), residues: 748
  sheet: -0.54 (0.84), residues: 44
  loop : -2.09 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 322 
 HIS   0.003   0.001   HIS A 575 
 PHE   0.014   0.001   PHE A 190 
 TYR   0.016   0.001   TYR A 346 
 ARG   0.003   0.000   ARG B 242 

*********************** 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
  159 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8910 (m-30) cc_final: 0.8592 (m-30)
REVERT: A  288 ASP cc_start: 0.9040 (m-30) cc_final: 0.8793 (m-30)
REVERT: A  291 MET cc_start: 0.9244 (mmm) cc_final: 0.8934 (mtp)
REVERT: A  436 MET cc_start: 0.8210 (pmm) cc_final: 0.7983 (pmm)
REVERT: A  598 TYR cc_start: 0.8758 (t80) cc_final: 0.8463 (t80)
REVERT: A  607 MET cc_start: 0.9560 (mmm) cc_final: 0.9227 (mmm)
REVERT: A  653 LEU cc_start: 0.9525 (tp) cc_final: 0.9145 (mm)
REVERT: B  260 CYS cc_start: 0.9528 (t) cc_final: 0.9237 (t)
REVERT: B  291 MET cc_start: 0.9532 (tpt) cc_final: 0.8901 (tmm)
REVERT: B  336 MET cc_start: 0.9156 (mmt) cc_final: 0.8527 (tmm)
REVERT: B  382 GLU cc_start: 0.9479 (mp0) cc_final: 0.9101 (pm20)
REVERT: B  416 LEU cc_start: 0.9592 (tt) cc_final: 0.9321 (pp)
REVERT: B  465 LEU cc_start: 0.9545 (tt) cc_final: 0.9238 (pp)
REVERT: B  466 MET cc_start: 0.8868 (mmm) cc_final: 0.8358 (mmm)
REVERT: B  548 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9402 (mm)
  outliers start: 29
  outliers final: 22
  residues processed: 150
  average time/residue: 0.1491
  time to fit residues: 35.4144
Evaluate side-chains
  149 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  295 LEU
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  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  289 THR
Chi-restraints excluded: chain B residue  301 ASN
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  714 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 77 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 113 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0050
   chunk 4 optimal weight:    2.9990
   chunk 109 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   overall best weight:    2.3600

-------------------------------------------------------------------------------
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 = 0.3096 r_free = 0.3096 target = 0.053043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.040174 restraints weight = 49604.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.041759 restraints weight = 29356.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.042912 restraints weight = 20395.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9069  Z= 0.188
  Angle     :  0.673  10.923  12320  Z= 0.329
  Chirality :  0.042   0.266   1464
  Planarity :  0.003   0.045   1553
  Dihedral  :  7.031  57.092   1456
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 27.09 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1143
  helix:  1.56 (0.19), residues: 748
  sheet: -0.50 (0.84), residues: 44
  loop : -2.02 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 322 
 HIS   0.004   0.001   HIS B 487 
 PHE   0.013   0.001   PHE A 190 
 TYR   0.014   0.001   TYR A 346 
 ARG   0.003   0.000   ARG B 242 

*********************** 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
  156 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8929 (m-30) cc_final: 0.8632 (m-30)
REVERT: A  288 ASP cc_start: 0.9062 (m-30) cc_final: 0.8829 (m-30)
REVERT: A  465 LEU cc_start: 0.9764 (tt) cc_final: 0.9545 (pp)
REVERT: A  598 TYR cc_start: 0.8788 (t80) cc_final: 0.8566 (t80)
REVERT: A  607 MET cc_start: 0.9565 (mmm) cc_final: 0.9221 (mmm)
REVERT: A  653 LEU cc_start: 0.9513 (tp) cc_final: 0.9139 (mm)
REVERT: B  260 CYS cc_start: 0.9513 (t) cc_final: 0.9221 (t)
REVERT: B  336 MET cc_start: 0.9163 (mmt) cc_final: 0.8524 (tmm)
REVERT: B  382 GLU cc_start: 0.9491 (mp0) cc_final: 0.9134 (pm20)
REVERT: B  416 LEU cc_start: 0.9566 (tt) cc_final: 0.9315 (pp)
REVERT: B  465 LEU cc_start: 0.9560 (tt) cc_final: 0.9237 (pp)
REVERT: B  466 MET cc_start: 0.8858 (mmm) cc_final: 0.8358 (mmm)
  outliers start: 28
  outliers final: 24
  residues processed: 146
  average time/residue: 0.1403
  time to fit residues: 32.2884
Evaluate side-chains
  148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 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  441 LEU
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  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  289 THR
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  395 TYR
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 96 optimal weight:    0.0270
   chunk 50 optimal weight:    9.9990
   chunk 90 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 111 optimal weight:   20.0000
   overall best weight:    2.1644

-------------------------------------------------------------------------------
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 = 0.3097 r_free = 0.3097 target = 0.053812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.040569 restraints weight = 49718.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.042153 restraints weight = 29620.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.043314 restraints weight = 20653.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9069  Z= 0.184
  Angle     :  0.695  12.660  12320  Z= 0.338
  Chirality :  0.043   0.261   1464
  Planarity :  0.003   0.045   1553
  Dihedral  :  7.035  57.563   1456
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 27.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.25), residues: 1143
  helix:  1.54 (0.19), residues: 748
  sheet: -0.47 (0.83), residues: 44
  loop : -2.01 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 322 
 HIS   0.003   0.001   HIS B 487 
 PHE   0.036   0.001   PHE B 551 
 TYR   0.015   0.001   TYR A 346 
 ARG   0.003   0.000   ARG B 242 

********************** 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
  152 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8918 (m-30) cc_final: 0.8632 (m-30)
REVERT: A  288 ASP cc_start: 0.9052 (m-30) cc_final: 0.8793 (m-30)
REVERT: A  291 MET cc_start: 0.9236 (mmm) cc_final: 0.8915 (mtp)
REVERT: A  465 LEU cc_start: 0.9761 (tt) cc_final: 0.9546 (pp)
REVERT: A  598 TYR cc_start: 0.8776 (t80) cc_final: 0.8552 (t80)
REVERT: A  607 MET cc_start: 0.9567 (mmm) cc_final: 0.9222 (mmm)
REVERT: A  653 LEU cc_start: 0.9486 (tp) cc_final: 0.9083 (mm)
REVERT: B  260 CYS cc_start: 0.9509 (t) cc_final: 0.9215 (t)
REVERT: B  291 MET cc_start: 0.9402 (ttt) cc_final: 0.8736 (tmm)
REVERT: B  336 MET cc_start: 0.9165 (mmt) cc_final: 0.8531 (tmm)
REVERT: B  382 GLU cc_start: 0.9484 (mp0) cc_final: 0.9122 (pm20)
REVERT: B  416 LEU cc_start: 0.9573 (tt) cc_final: 0.9318 (pp)
REVERT: B  465 LEU cc_start: 0.9563 (tt) cc_final: 0.9204 (pp)
REVERT: B  466 MET cc_start: 0.8818 (mmm) cc_final: 0.8317 (mmm)
  outliers start: 25
  outliers final: 25
  residues processed: 144
  average time/residue: 0.1496
  time to fit residues: 34.1814
Evaluate side-chains
  149 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 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  326 LEU
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  441 LEU
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  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  289 THR
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  395 TYR
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 26 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 107 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0970
   chunk 59 optimal weight:    5.9990
   chunk 100 optimal weight:    0.3980
   overall best weight:    1.4582

-------------------------------------------------------------------------------
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 ** 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 = 0.3122 r_free = 0.3122 target = 0.054730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.041243 restraints weight = 50175.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.042864 restraints weight = 29666.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.044053 restraints weight = 20687.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9069  Z= 0.167
  Angle     :  0.691  11.372  12320  Z= 0.332
  Chirality :  0.042   0.250   1464
  Planarity :  0.003   0.042   1553
  Dihedral  :  6.993  59.170   1456
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 27.51 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.25), residues: 1143
  helix:  1.58 (0.19), residues: 748
  sheet: -0.31 (0.84), residues: 44
  loop : -2.04 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 322 
 HIS   0.003   0.001   HIS A 575 
 PHE   0.022   0.001   PHE B 551 
 TYR   0.015   0.001   TYR A 346 
 ARG   0.006   0.000   ARG A 252 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2444.99 seconds
wall clock time: 45 minutes 4.00 seconds (2704.00 seconds total)