Starting phenix.real_space_refine
on Sat Oct 11 02:02:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x2n_38018/10_2025/8x2n_38018.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x2n_38018/10_2025/8x2n_38018.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x2n_38018/10_2025/8x2n_38018.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x2n_38018/10_2025/8x2n_38018.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x2n_38018/10_2025/8x2n_38018.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x2n_38018/10_2025/8x2n_38018.map"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.029
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      35      5.16       5
     C    7085      2.51       5
     N    1769      2.21       5
     O    1886      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10775
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5398
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 705, 5387
          Classifications: {'peptide': 705}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 673}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 54
      Conformer: "B"
        Number of residues, atoms: 705, 5387
          Classifications: {'peptide': 705}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 673}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 6, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 54
          bond proxies already assigned to first conformer: 5492
    Chain: "B"
      Number of atoms: 5377
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 701, 5366
          Classifications: {'peptide': 701}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 669}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 63
      Conformer: "B"
        Number of residues, atoms: 701, 5366
          Classifications: {'peptide': 701}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 669}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 63
          bond proxies already assigned to first conformer: 5470
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  APHE A  58 " occ=0.39
      ... (20 atoms not shown)
      pdb=" CZ BPHE A  58 " occ=0.61
    residue:
      pdb=" N  APHE B  58 " occ=0.39
      ... (20 atoms not shown)
      pdb=" CZ BPHE B  58 " occ=0.61
  Time building chain proxies: 4.69, per 1000 atoms: 0.44
  Number of scatterers: 10775
  At special positions: 0
  Unit cell: (105.664, 112.32, 104, 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      35     16.00
     O    1886      8.00
     N    1769      7.00
     C    7085      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2636

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 4 sheets defined
      68.5% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 25
    Processing helix  chain 'A' and resid 34 through 43
    Processing helix  chain 'A' and resid 46 through 58
    Processing helix  chain 'A' and resid 58 through 64
      removed outlier: 3.918A  pdb=" N   SER A  62 " --> pdb=" O  APHE A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 98
      removed outlier: 3.857A  pdb=" N   LEU A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   LEU A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   SER A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 120
      removed outlier: 4.010A  pdb=" N   GLY A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      Proline residue:  A 112  - end of helix
      removed outlier: 4.450A  pdb=" N   PHE A 118 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE A 119 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 148
    Processing helix  chain 'A' and resid 169 through 196
    Processing helix  chain 'A' and resid 199 through 205
      removed outlier: 4.099A  pdb=" N   VAL A 202 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 231
      removed outlier: 4.008A  pdb=" N   LYS A 227 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   PHE A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
      removed outlier: 3.542A  pdb=" N   GLN A 253 " --> pdb=" O   SER A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 257
    Processing helix  chain 'A' and resid 258 through 282
    Processing helix  chain 'A' and resid 291 through 308
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 332 through 366
      removed outlier: 5.688A  pdb=" N   GLY A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   ASP A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS A 364 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 396 through 407
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 3.601A  pdb=" N   ALA A 427 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 453
      removed outlier: 3.684A  pdb=" N   LEU A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   GLY A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   MET A 451 " --> pdb=" O   ASN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 465
    Processing helix  chain 'A' and resid 465 through 482
    Processing helix  chain 'A' and resid 483 through 503
      removed outlier: 3.536A  pdb=" N   LEU A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ALA A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A 503 " --> pdb=" O   ILE A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 547
      No H-bonds generated for 'chain 'A' and resid 545 through 547'
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'A' and resid 563 through 585
    Processing helix  chain 'A' and resid 612 through 618
    Processing helix  chain 'A' and resid 660 through 677
      removed outlier: 3.696A  pdb=" N   GLY A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE A 677 " --> pdb=" O   GLU A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 697
      removed outlier: 3.509A  pdb=" N   ILE A 691 " --> pdb=" O   ASP A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 707
      No H-bonds generated for 'chain 'A' and resid 705 through 707'
    Processing helix  chain 'A' and resid 712 through 728
    Processing helix  chain 'B' and resid 17 through 25
    Processing helix  chain 'B' and resid 34 through 43
    Processing helix  chain 'B' and resid 46 through 58
    Processing helix  chain 'B' and resid 58 through 64
      removed outlier: 3.927A  pdb=" N   SER B  62 " --> pdb=" O  APHE B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 99
      removed outlier: 4.329A  pdb=" N   SER B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL B  86 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 120
      removed outlier: 4.116A  pdb=" N   TYR B 107 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA B 108 " --> pdb=" O   TYR B 104 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER B 109 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
      removed outlier: 3.696A  pdb=" N   PHE B 118 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 148
    Processing helix  chain 'B' and resid 170 through 196
    Processing helix  chain 'B' and resid 199 through 205
      removed outlier: 4.082A  pdb=" N   VAL B 202 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 230
      removed outlier: 3.757A  pdb=" N   LYS B 227 " --> pdb=" O   VAL B 223 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   PHE B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
      removed outlier: 3.697A  pdb=" N   LYS B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL B 246 " --> pdb=" O   SER B 242 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLN B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 282
    Processing helix  chain 'B' and resid 291 through 308
    Processing helix  chain 'B' and resid 308 through 314
    Processing helix  chain 'B' and resid 332 through 339
    Processing helix  chain 'B' and resid 339 through 366
      removed outlier: 3.520A  pdb=" N   LYS B 364 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 388
      removed outlier: 3.501A  pdb=" N   PHE B 388 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 407
    Processing helix  chain 'B' and resid 411 through 427
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 436 through 448
      removed outlier: 3.535A  pdb=" N   LEU B 440 " --> pdb=" O   GLN B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 453
    Processing helix  chain 'B' and resid 455 through 465
      removed outlier: 4.449A  pdb=" N   GLY B 459 " --> pdb=" O   PHE B 455 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG B 463 " --> pdb=" O   GLY B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 482
    Processing helix  chain 'B' and resid 483 through 503
      removed outlier: 3.538A  pdb=" N   ALA B 489 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   THR B 503 " --> pdb=" O   ILE B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 561
      removed outlier: 4.807A  pdb=" N   GLY B 550 " --> pdb=" O   PHE B 546 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   PHE B 551 " --> pdb=" O   ALA B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 585
    Processing helix  chain 'B' and resid 610 through 618
      removed outlier: 3.584A  pdb=" N   ILE B 613 " --> pdb=" O   ASN B 610 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLU B 614 " --> pdb=" O   ASN B 611 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLN B 618 " --> pdb=" O   VAL B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 677
    Processing helix  chain 'B' and resid 687 through 697
    Processing helix  chain 'B' and resid 705 through 707
      No H-bonds generated for 'chain 'B' and resid 705 through 707'
    Processing helix  chain 'B' and resid 712 through 725
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14
    Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522
      removed outlier: 4.502A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.277A  pdb=" N   ASN A 513 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 12.051A  pdb=" N   VAL A 535 " --> pdb=" O   ASN A 513 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   PHE A 710 " --> pdb=" O   VAL A 681 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ILE A 683 " --> pdb=" O   PHE A 710 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522
      removed outlier: 4.359A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   ASN B 513 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
      removed outlier: 12.160A  pdb=" N   VAL B 535 " --> pdb=" O   ASN B 513 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 650 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   ASP B 652 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 652 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   PHE B 710 " --> pdb=" O   VAL B 681 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE B 683 " --> pdb=" O   PHE B 710 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 587 through 588

    696 hydrogen bonds defined for protein.
    2025 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 1.48 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: 3370
        1.34 -     1.46: 2383
        1.46 -     1.58: 5209
        1.58 -     1.70: 0
        1.70 -     1.82: 52
  Bond restraints: 11014
  Sorted by residual:
  bond pdb=" CB  PRO B  47 "
       pdb=" CG  PRO B  47 "
    ideal  model  delta    sigma   weight residual
    1.492  1.577 -0.085 5.00e-02 4.00e+02 2.87e+00
  bond pdb=" C   LEU B  64 "
       pdb=" N   PRO B  65 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.019 1.19e-02 7.06e+03 2.44e+00
  bond pdb=" CG  PRO B  47 "
       pdb=" CD  PRO B  47 "
    ideal  model  delta    sigma   weight residual
    1.503  1.456  0.047 3.40e-02 8.65e+02 1.92e+00
  bond pdb=" C   PHE A 111 "
       pdb=" N   PRO A 112 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.36e-02 5.41e+03 1.76e+00
  bond pdb=" C   PHE B 130 "
       pdb=" N   PRO B 131 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.016 1.36e-02 5.41e+03 1.42e+00
  ... (remaining 11009 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 14632
        1.73 -     3.47: 304
        3.47 -     5.20: 29
        5.20 -     6.93: 15
        6.93 -     8.67: 5
  Bond angle restraints: 14985
  Sorted by residual:
  angle pdb=" N   ASP B 525 "
        pdb=" CA  ASP B 525 "
        pdb=" C   ASP B 525 "
      ideal   model   delta    sigma   weight residual
     111.82  119.49   -7.67 1.16e+00 7.43e-01 4.38e+01
  angle pdb=" C   GLN B 618 "
        pdb=" N   PRO B 619 "
        pdb=" CA  PRO B 619 "
      ideal   model   delta    sigma   weight residual
     119.84  126.28   -6.44 1.25e+00 6.40e-01 2.65e+01
  angle pdb=" N   ASN A 548 "
        pdb=" CA  ASN A 548 "
        pdb=" C   ASN A 548 "
      ideal   model   delta    sigma   weight residual
     111.87  118.31   -6.44 1.41e+00 5.03e-01 2.09e+01
  angle pdb=" CA  PRO B  47 "
        pdb=" N   PRO B  47 "
        pdb=" CD  PRO B  47 "
      ideal   model   delta    sigma   weight residual
     112.00  105.87    6.13 1.40e+00 5.10e-01 1.91e+01
  angle pdb=" N   ILE A 544 "
        pdb=" CA  ILE A 544 "
        pdb=" C   ILE A 544 "
      ideal   model   delta    sigma   weight residual
     107.51  113.44   -5.93 1.49e+00 4.50e-01 1.58e+01
  ... (remaining 14980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5977
       17.97 -    35.93: 458
       35.93 -    53.90: 78
       53.90 -    71.86: 13
       71.86 -    89.83: 3
  Dihedral angle restraints: 6529
    sinusoidal: 2447
      harmonic: 4082
  Sorted by residual:
  dihedral pdb=" CA  MET A 296 "
           pdb=" C   MET A 296 "
           pdb=" N   THR A 297 "
           pdb=" CA  THR A 297 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.11   17.89     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  TYR A  16 "
           pdb=" C   TYR A  16 "
           pdb=" N   SER A  17 "
           pdb=" CA  SER A  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.20   17.80     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  PHE A 110 "
           pdb=" C   PHE A 110 "
           pdb=" N   PHE A 111 "
           pdb=" CA  PHE A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.15  -16.85     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6526 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1515
       0.057 -    0.114: 248
       0.114 -    0.171: 29
       0.171 -    0.228: 3
       0.228 -    0.285: 2
  Chirality restraints: 1797
  Sorted by residual:
  chirality pdb=" CA  ASN A 548 "
            pdb=" N   ASN A 548 "
            pdb=" C   ASN A 548 "
            pdb=" CB  ASN A 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  ASP B 525 "
            pdb=" N   ASP B 525 "
            pdb=" C   ASP B 525 "
            pdb=" CB  ASP B 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  TYR A 204 "
            pdb=" N   TYR A 204 "
            pdb=" C   TYR A 204 "
            pdb=" CB  TYR A 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1794 not shown)

  Planarity restraints: 1875
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  46 "   -0.039 5.00e-02 4.00e+02   5.70e-02 5.20e+00
        pdb=" N   PRO B  47 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B  47 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B  47 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 524 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.71e+00
        pdb=" C   LYS B 524 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LYS B 524 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASP B 525 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 590 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.55e+00
        pdb=" N   PRO B 591 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 591 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 591 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1872 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1324
        2.75 -     3.29: 11227
        3.29 -     3.82: 18052
        3.82 -     4.36: 20560
        4.36 -     4.90: 36325
  Nonbonded interactions: 87488
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 701 "
            pdb=" N   GLY B 702 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   ILE A 544 "
            pdb=" OG  SER A 663 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG1 THR B 503 "
            pdb=" OH  TYR B 545 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OE1 GLU A 207 "
            pdb=" NH1 ARG B 665 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OG  SER B  75 "
            pdb=" O   GLY B 407 "
     model   vdw
     2.275 3.040
  ... (remaining 87483 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 7 through 23 or (resid 24 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 25 through 37 or (resid 38 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 39 through 57 or resid 59 through \ 
 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or res \ 
id 72 through 168 or resid 170 through 206 or (resid 207 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 208 through 260 or (resid 261 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 262 through 295 or (r \ 
esid 296 and (name N or name CA or name C or name O or name CB )) or resid 297 t \ 
hrough 347 or (resid 348 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 349 through 393 or (resid 394 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 395 through 605 or (resid 606 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 607 through 686 or (resid 687 through \ 
 689 and (name N or name CA or name C or name O or name CB )) or resid 690 throu \ 
gh 724 or (resid 725 and (name N or name CA or name C or name O or name CB ))))
  selection = (chain 'B' and (resid 7 through 25 or (resid 26 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 27 through 50 or (resid 51 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 52 through 57 or resid 59 through \ 
 66 or (resid 67 through 68 and (name N or name CA or name C or name O or name C \ 
B )) or resid 69 through 74 or (resid 75 through 76 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 77 through 78 or (resid 79 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 80 through 280 or (resid 281  \ 
and (name N or name CA or name C or name O or name CB )) or resid 282 through 40 \ 
5 or (resid 406 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 407 through 422 or (resid 423 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 424 through 464 or (resid 465 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 466 through 586 or (resid 587 through 590 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 591 through 604 or \ 
 (resid 605 through 606 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 607 through 636 or (resid 637 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 638 through 721 or (resid 722 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 723 through 725))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.39 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.170
  Find NCS groups from input model:        0.330
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  11014  Z= 0.170
  Angle     :  0.626   8.667  14985  Z= 0.365
  Chirality :  0.043   0.285   1797
  Planarity :  0.004   0.057   1875
  Dihedral  : 13.225  89.827   3893
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 15.52 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.22), residues: 1404
  helix:  1.59 (0.17), residues: 903
  sheet:  2.19 (1.01), residues: 36
  loop : -0.16 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 579 
 TYR   0.021   0.002   TYR A 367 
 PHE   0.021   0.001   PHE A  94 
 TRP   0.011   0.002   TRP B 472 
 HIS   0.004   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (11014)
  covalent geometry    : angle       0.62571 (14985)
  hydrogen bonds       : bond        0.13762 (  696)
  hydrogen bonds       : angle       5.62289 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  397 LEU cc_start: 0.7650 (tp) cc_final: 0.7408 (tp)
REVERT: B  276 LYS cc_start: 0.7432 (tttt) cc_final: 0.7204 (ttmt)
  outliers start: 3
  outliers final: 1
  residues processed: 119
  average time/residue: 0.1019
  time to fit residues: 17.7740
Evaluate side-chains
  111 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.0170
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 513 ASN
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.152924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.121283 restraints weight = 34092.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 3.46
r_work: 0.3171 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.0700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11014  Z= 0.134
  Angle     :  0.537   6.400  14985  Z= 0.284
  Chirality :  0.041   0.165   1797
  Planarity :  0.004   0.044   1875
  Dihedral  :  3.822  20.510   1498
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.34 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.22), residues: 1404
  helix:  1.80 (0.17), residues: 907
  sheet:  2.79 (0.99), residues: 36
  loop : -0.10 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 579 
 TYR   0.015   0.001   TYR A   9 
 PHE   0.020   0.001   PHE A 430 
 TRP   0.014   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11014)
  covalent geometry    : angle       0.53717 (14985)
  hydrogen bonds       : bond        0.04747 (  696)
  hydrogen bonds       : angle       4.58804 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 LEU cc_start: 0.7500 (tp) cc_final: 0.7250 (tp)
REVERT: B  276 LYS cc_start: 0.7878 (tttt) cc_final: 0.7450 (ttmt)
REVERT: B  692 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7780 (tp30)
  outliers start: 19
  outliers final: 5
  residues processed: 140
  average time/residue: 0.0979
  time to fit residues: 20.3108
Evaluate side-chains
  120 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  692 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 136 optimal weight:    0.5980
   chunk 110 optimal weight:    0.2980
   chunk 113 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 68 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A 621 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.153683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.121995 restraints weight = 36472.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 3.68
r_work: 0.3147 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11014  Z= 0.120
  Angle     :  0.502   8.729  14985  Z= 0.264
  Chirality :  0.041   0.156   1797
  Planarity :  0.004   0.043   1875
  Dihedral  :  3.716  19.733   1496
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.78 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.22), residues: 1404
  helix:  1.84 (0.17), residues: 908
  sheet:  3.06 (0.97), residues: 36
  loop :  0.04 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 579 
 TYR   0.014   0.001   TYR B   9 
 PHE   0.018   0.001   PHE A 130 
 TRP   0.016   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (11014)
  covalent geometry    : angle       0.50156 (14985)
  hydrogen bonds       : bond        0.04270 (  696)
  hydrogen bonds       : angle       4.36110 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  337 GLN cc_start: 0.8465 (mt0) cc_final: 0.8200 (pt0)
REVERT: A  448 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7586 (mt)
REVERT: A  692 GLU cc_start: 0.8308 (tp30) cc_final: 0.7680 (tp30)
REVERT: B  116 TYR cc_start: 0.8652 (t80) cc_final: 0.8344 (t80)
REVERT: B  276 LYS cc_start: 0.7840 (tttt) cc_final: 0.7369 (ttmt)
REVERT: B  692 GLU cc_start: 0.8289 (tp30) cc_final: 0.7787 (tp30)
  outliers start: 13
  outliers final: 8
  residues processed: 121
  average time/residue: 0.0996
  time to fit residues: 17.9590
Evaluate side-chains
  122 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 126 optimal weight:    0.0870
   chunk 122 optimal weight:    0.9980
   chunk 130 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 109 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
A 621 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.152901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.121135 restraints weight = 28839.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.92
r_work: 0.3190 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11014  Z= 0.130
  Angle     :  0.497   8.452  14985  Z= 0.263
  Chirality :  0.041   0.150   1797
  Planarity :  0.004   0.042   1875
  Dihedral  :  3.703  19.520   1496
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.43 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.22), residues: 1404
  helix:  1.86 (0.17), residues: 910
  sheet:  3.11 (0.96), residues: 36
  loop :  0.08 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 579 
 TYR   0.015   0.001   TYR B   9 
 PHE   0.021   0.001   PHE A 430 
 TRP   0.017   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (11014)
  covalent geometry    : angle       0.49731 (14985)
  hydrogen bonds       : bond        0.04180 (  696)
  hydrogen bonds       : angle       4.28366 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7696 (mp0)
REVERT: A  337 GLN cc_start: 0.8487 (mt0) cc_final: 0.8235 (pt0)
REVERT: A  370 ASP cc_start: 0.7631 (t0) cc_final: 0.7159 (t70)
REVERT: A  617 ASP cc_start: 0.7404 (t0) cc_final: 0.7146 (t0)
REVERT: A  692 GLU cc_start: 0.8228 (tp30) cc_final: 0.7619 (tp30)
REVERT: A  705 LYS cc_start: 0.8560 (mttp) cc_final: 0.8357 (mtpp)
REVERT: B  116 TYR cc_start: 0.8600 (t80) cc_final: 0.8330 (t80)
REVERT: B  276 LYS cc_start: 0.7782 (tttt) cc_final: 0.7325 (ttmt)
REVERT: B  692 GLU cc_start: 0.8195 (tp30) cc_final: 0.7662 (tp30)
  outliers start: 22
  outliers final: 16
  residues processed: 134
  average time/residue: 0.0994
  time to fit residues: 19.6943
Evaluate side-chains
  131 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  665 ARG
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 90 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0270
   chunk 21 optimal weight:    0.0570
   chunk 95 optimal weight:    6.9990
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
A 124 HIS
A 582 GLN
A 621 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.156074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.123171 restraints weight = 35155.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 3.46
r_work: 0.3185 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11014  Z= 0.109
  Angle     :  0.481   8.422  14985  Z= 0.252
  Chirality :  0.040   0.144   1797
  Planarity :  0.003   0.041   1875
  Dihedral  :  3.644  19.123   1496
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 14.21 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.23), residues: 1404
  helix:  1.88 (0.17), residues: 914
  sheet:  3.14 (0.95), residues: 36
  loop :  0.16 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 579 
 TYR   0.013   0.001   TYR B   9 
 PHE   0.015   0.001   PHE A 130 
 TRP   0.016   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (11014)
  covalent geometry    : angle       0.48138 (14985)
  hydrogen bonds       : bond        0.03906 (  696)
  hydrogen bonds       : angle       4.18789 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7672 (mp0)
REVERT: A  337 GLN cc_start: 0.8467 (mt0) cc_final: 0.8244 (pt0)
REVERT: A  370 ASP cc_start: 0.7618 (t0) cc_final: 0.7119 (t70)
REVERT: A  692 GLU cc_start: 0.8291 (tp30) cc_final: 0.7681 (tp30)
REVERT: B  116 TYR cc_start: 0.8611 (t80) cc_final: 0.8333 (t80)
REVERT: B  276 LYS cc_start: 0.7843 (tttt) cc_final: 0.7367 (ttmt)
REVERT: B  692 GLU cc_start: 0.8282 (tp30) cc_final: 0.7737 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 133
  average time/residue: 0.0925
  time to fit residues: 18.5070
Evaluate side-chains
  127 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  665 ARG
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 129 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 100 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 582 GLN
A 621 ASN
** B 225 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 = 0.3705 r_free = 0.3705 target = 0.149571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.118287 restraints weight = 21582.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.38
r_work: 0.3222 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3072
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3072
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11014  Z= 0.175
  Angle     :  0.531   8.197  14985  Z= 0.280
  Chirality :  0.042   0.161   1797
  Planarity :  0.004   0.040   1875
  Dihedral  :  3.777  19.701   1496
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.60 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.23), residues: 1404
  helix:  1.82 (0.17), residues: 905
  sheet:  3.23 (0.94), residues: 36
  loop : -0.04 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 579 
 TYR   0.018   0.002   TYR B   9 
 PHE   0.022   0.002   PHE A 430 
 TRP   0.018   0.002   TRP B  63 
 HIS   0.004   0.001   HIS A 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (11014)
  covalent geometry    : angle       0.53064 (14985)
  hydrogen bonds       : bond        0.04524 (  696)
  hydrogen bonds       : angle       4.34466 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7765 (mp0)
REVERT: B  116 TYR cc_start: 0.8735 (t80) cc_final: 0.8450 (t80)
REVERT: B  276 LYS cc_start: 0.8066 (tttt) cc_final: 0.7566 (ttmt)
REVERT: B  692 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8011 (tp30)
REVERT: B  701 ASP cc_start: 0.7510 (t0) cc_final: 0.7301 (t0)
  outliers start: 29
  outliers final: 21
  residues processed: 134
  average time/residue: 0.0943
  time to fit residues: 19.0795
Evaluate side-chains
  137 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  582 GLN
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  645 SER
Chi-restraints excluded: chain B residue  665 ARG
Chi-restraints excluded: chain B residue  692 GLU
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0770
   chunk 116 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
A 582 GLN
A 621 ASN
** B 225 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 = 0.3731 r_free = 0.3731 target = 0.151978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.118511 restraints weight = 27680.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 3.03
r_work: 0.3199 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11014  Z= 0.123
  Angle     :  0.501   8.414  14985  Z= 0.260
  Chirality :  0.041   0.149   1797
  Planarity :  0.003   0.040   1875
  Dihedral  :  3.704  19.705   1496
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.30 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.23), residues: 1404
  helix:  1.85 (0.17), residues: 904
  sheet:  3.31 (0.93), residues: 36
  loop : -0.00 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 579 
 TYR   0.014   0.001   TYR B   9 
 PHE   0.016   0.001   PHE A 130 
 TRP   0.016   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (11014)
  covalent geometry    : angle       0.50101 (14985)
  hydrogen bonds       : bond        0.04108 (  696)
  hydrogen bonds       : angle       4.23202 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7584 (mp0)
REVERT: A  370 ASP cc_start: 0.7701 (t0) cc_final: 0.7318 (t0)
REVERT: B  116 TYR cc_start: 0.8625 (t80) cc_final: 0.8341 (t80)
REVERT: B  276 LYS cc_start: 0.7894 (tttt) cc_final: 0.7420 (ttmt)
REVERT: B  692 GLU cc_start: 0.8242 (tp30) cc_final: 0.7735 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 124
  average time/residue: 0.0953
  time to fit residues: 17.5943
Evaluate side-chains
  125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  582 GLN
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  665 ARG
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 115 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 582 GLN
** B 225 GLN ** 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 = 0.3686 r_free = 0.3686 target = 0.147819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.115845 restraints weight = 23630.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.62
r_work: 0.3159 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11014  Z= 0.210
  Angle     :  0.566   9.088  14985  Z= 0.297
  Chirality :  0.043   0.159   1797
  Planarity :  0.004   0.041   1875
  Dihedral  :  3.869  20.112   1496
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.39 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.23), residues: 1404
  helix:  1.71 (0.17), residues: 904
  sheet:  3.36 (0.92), residues: 36
  loop : -0.15 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 516 
 TYR   0.022   0.002   TYR B   9 
 PHE   0.022   0.002   PHE A 430 
 TRP   0.018   0.002   TRP B  63 
 HIS   0.004   0.001   HIS A 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (11014)
  covalent geometry    : angle       0.56559 (14985)
  hydrogen bonds       : bond        0.04731 (  696)
  hydrogen bonds       : angle       4.37744 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7802 (mp0)
REVERT: A  617 ASP cc_start: 0.7621 (t0) cc_final: 0.7358 (t0)
REVERT: B  276 LYS cc_start: 0.7952 (tttt) cc_final: 0.7439 (ttmt)
REVERT: B  692 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7906 (tp30)
  outliers start: 28
  outliers final: 22
  residues processed: 123
  average time/residue: 0.0915
  time to fit residues: 17.0592
Evaluate side-chains
  129 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  582 GLN
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  665 ARG
Chi-restraints excluded: chain B residue  692 GLU
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 111 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 582 GLN
** B 225 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.151128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.120186 restraints weight = 31654.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 3.26
r_work: 0.3169 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11014  Z= 0.122
  Angle     :  0.505   8.895  14985  Z= 0.263
  Chirality :  0.041   0.149   1797
  Planarity :  0.004   0.040   1875
  Dihedral  :  3.761  20.031   1496
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.17 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.23), residues: 1404
  helix:  1.81 (0.17), residues: 905
  sheet:  3.37 (0.93), residues: 36
  loop : -0.04 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 516 
 TYR   0.013   0.001   TYR B   9 
 PHE   0.016   0.001   PHE A 130 
 TRP   0.016   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (11014)
  covalent geometry    : angle       0.50532 (14985)
  hydrogen bonds       : bond        0.04124 (  696)
  hydrogen bonds       : angle       4.21610 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7648 (mp0)
REVERT: B  116 TYR cc_start: 0.8611 (t80) cc_final: 0.8286 (t80)
REVERT: B  276 LYS cc_start: 0.7864 (tttt) cc_final: 0.7368 (ttmt)
REVERT: B  692 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7654 (tp30)
  outliers start: 20
  outliers final: 17
  residues processed: 118
  average time/residue: 0.1004
  time to fit residues: 17.4852
Evaluate side-chains
  122 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  582 GLN
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  665 ARG
Chi-restraints excluded: chain B residue  692 GLU
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 132 optimal weight:    0.0980
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:   50.0000
   chunk 87 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0770
   chunk 109 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A 582 GLN
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 231 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.152743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.120036 restraints weight = 25727.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.90
r_work: 0.3209 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11014  Z= 0.109
  Angle     :  0.493   9.012  14985  Z= 0.256
  Chirality :  0.040   0.144   1797
  Planarity :  0.004   0.040   1875
  Dihedral  :  3.675  19.629   1496
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 15.69 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.23), residues: 1404
  helix:  1.86 (0.17), residues: 908
  sheet:  3.43 (0.93), residues: 36
  loop :  0.03 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 516 
 TYR   0.012   0.001   TYR B   9 
 PHE   0.024   0.001   PHE A 430 
 TRP   0.016   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (11014)
  covalent geometry    : angle       0.49250 (14985)
  hydrogen bonds       : bond        0.03887 (  696)
  hydrogen bonds       : angle       4.14250 ( 2025)

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

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

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2808 Ramachandran restraints generated.
    1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A   23 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7617 (mp0)
REVERT: B  116 TYR cc_start: 0.8576 (t80) cc_final: 0.8287 (t80)
REVERT: B  231 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7507 (tm-30)
REVERT: B  276 LYS cc_start: 0.7843 (tttt) cc_final: 0.7342 (ttmt)
REVERT: B  692 GLU cc_start: 0.8197 (tp30) cc_final: 0.7613 (tp30)
  outliers start: 16
  outliers final: 13
  residues processed: 121
  average time/residue: 0.0996
  time to fit residues: 17.9237
Evaluate side-chains
  121 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  582 GLN
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  231 GLN
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  665 ARG
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 9 optimal weight:    0.0070
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0000
   chunk 98 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 134 optimal weight:    0.8980
   chunk 121 optimal weight:    0.4980
   chunk 71 optimal weight:    6.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.4002

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

Flipped N/Q/H residues before XYZ refinement:
A 582 GLN
** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 231 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.153702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.122178 restraints weight = 35268.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 3.53
r_work: 0.3176 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3180
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11014  Z= 0.107
  Angle     :  0.488   8.937  14985  Z= 0.254
  Chirality :  0.040   0.146   1797
  Planarity :  0.004   0.040   1875
  Dihedral  :  3.634  19.302   1496
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 15.87 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.23), residues: 1404
  helix:  1.86 (0.17), residues: 908
  sheet:  3.47 (0.93), residues: 36
  loop :  0.05 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 516 
 TYR   0.012   0.001   TYR B   9 
 PHE   0.014   0.001   PHE A 130 
 TRP   0.016   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (11014)
  covalent geometry    : angle       0.48819 (14985)
  hydrogen bonds       : bond        0.03776 (  696)
  hydrogen bonds       : angle       4.11563 ( 2025)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2742.79 seconds
wall clock time: 47 minutes 53.11 seconds (2873.11 seconds total)