Starting phenix.real_space_refine
on Tue Mar  3 23:21:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xlm_33284/03_2026/7xlm_33284.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xlm_33284/03_2026/7xlm_33284.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xlm_33284/03_2026/7xlm_33284.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xlm_33284/03_2026/7xlm_33284.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xlm_33284/03_2026/7xlm_33284.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xlm_33284/03_2026/7xlm_33284.cif"
  }
  resolution = 3.73
  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=   0.001 sd=   0.005
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      52      5.16       5
     C    6090      2.51       5
     N    1478      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9268
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4629
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 21, 'TRANS': 573}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "B"
      Number of atoms: 4629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4629
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 21, 'TRANS': 573}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'SO4': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'SO4': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.90, per 1000 atoms: 0.21
  Number of scatterers: 9268
  At special positions: 0
  Unit cell: (105.439, 127.179, 100.004, 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      52     16.00
     O    1648      8.00
     N    1478      7.00
     C    6090      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 274.9 milliseconds
  

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2232

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 2 sheets defined
      58.2% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 86 through 93
      removed outlier: 3.902A  pdb=" N   GLY A  91 " --> pdb=" O   ASN A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 98
      removed outlier: 3.948A  pdb=" N   GLN A  97 " --> pdb=" O   PRO A  94 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TRP A  98 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 94 through 98'
    Processing helix  chain 'A' and resid 108 through 121
    Processing helix  chain 'A' and resid 122 through 133
      removed outlier: 3.888A  pdb=" N   ILE A 127 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 152
      removed outlier: 3.615A  pdb=" N   TYR A 142 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   PHE A 152 " --> pdb=" O   SER A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 184
      removed outlier: 3.550A  pdb=" N   GLY A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 239
      removed outlier: 3.626A  pdb=" N   MET A 220 " --> pdb=" O   CYS A 216 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL A 221 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   GLY A 222 " --> pdb=" O   ALA A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 4.516A  pdb=" N   THR A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 296
    Processing helix  chain 'A' and resid 305 through 324
      Proline residue:  A 317  - end of helix
      removed outlier: 4.261A  pdb=" N   HIS A 324 " --> pdb=" O   GLU A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 345
      removed outlier: 3.683A  pdb=" N   VAL A 338 " --> pdb=" O   PRO A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 379
      removed outlier: 3.604A  pdb=" N   LEU A 378 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 403
      removed outlier: 3.726A  pdb=" N   ILE A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 424
      removed outlier: 3.847A  pdb=" N   ILE A 421 " --> pdb=" O   GLU A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 426
      No H-bonds generated for 'chain 'A' and resid 425 through 426'
    Processing helix  chain 'A' and resid 427 through 431
    Processing helix  chain 'A' and resid 440 through 448
      removed outlier: 3.533A  pdb=" N   LEU A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 471
      removed outlier: 4.031A  pdb=" N   LEU A 464 " --> pdb=" O   THR A 460 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 467 " --> pdb=" O   VAL A 463 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE A 471 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 490
    Processing helix  chain 'A' and resid 492 through 497
    Processing helix  chain 'A' and resid 498 through 500
      No H-bonds generated for 'chain 'A' and resid 498 through 500'
    Processing helix  chain 'A' and resid 510 through 524
      removed outlier: 3.554A  pdb=" N   ILE A 514 " --> pdb=" O   MET A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 547
      removed outlier: 3.998A  pdb=" N   VAL A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ILE A 543 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 603
    Processing helix  chain 'A' and resid 605 through 616
      removed outlier: 3.560A  pdb=" N   ILE A 609 " --> pdb=" O   ASN A 605 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA A 616 " --> pdb=" O   ALA A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 678
      removed outlier: 3.736A  pdb=" N   ARG A 671 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ALA A 676 " --> pdb=" O   ARG A 672 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ILE A 677 " --> pdb=" O   ASP A 673 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLY A 678 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 696
      removed outlier: 3.722A  pdb=" N   THR A 695 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 721
      removed outlier: 3.734A  pdb=" N   VAL A 721 " --> pdb=" O   ALA A 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 93
      removed outlier: 3.902A  pdb=" N   GLY B  91 " --> pdb=" O   ASN B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 98
      removed outlier: 3.948A  pdb=" N   GLN B  97 " --> pdb=" O   PRO B  94 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TRP B  98 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 94 through 98'
    Processing helix  chain 'B' and resid 108 through 121
    Processing helix  chain 'B' and resid 122 through 133
      removed outlier: 3.888A  pdb=" N   ILE B 127 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA B 128 " --> pdb=" O   PRO B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 152
      removed outlier: 3.617A  pdb=" N   TYR B 142 " --> pdb=" O   VAL B 138 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   PHE B 152 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 184
      removed outlier: 3.550A  pdb=" N   GLY B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 239
      removed outlier: 3.626A  pdb=" N   MET B 220 " --> pdb=" O   CYS B 216 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL B 221 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLY B 222 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 268
      removed outlier: 4.517A  pdb=" N   THR B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 296
    Processing helix  chain 'B' and resid 305 through 324
      Proline residue:  B 317  - end of helix
      removed outlier: 4.260A  pdb=" N   HIS B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 345
      removed outlier: 3.682A  pdb=" N   VAL B 338 " --> pdb=" O   PRO B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 379
      removed outlier: 3.604A  pdb=" N   LEU B 378 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 403
      removed outlier: 3.727A  pdb=" N   ILE B 391 " --> pdb=" O   ILE B 387 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE B 392 " --> pdb=" O   ALA B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 424
      removed outlier: 3.848A  pdb=" N   ILE B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 426
      No H-bonds generated for 'chain 'B' and resid 425 through 426'
    Processing helix  chain 'B' and resid 427 through 431
    Processing helix  chain 'B' and resid 440 through 448
      removed outlier: 3.533A  pdb=" N   LEU B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 471
      removed outlier: 4.031A  pdb=" N   LEU B 464 " --> pdb=" O   THR B 460 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL B 467 " --> pdb=" O   VAL B 463 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE B 471 " --> pdb=" O   VAL B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 490
    Processing helix  chain 'B' and resid 492 through 497
    Processing helix  chain 'B' and resid 498 through 500
      No H-bonds generated for 'chain 'B' and resid 498 through 500'
    Processing helix  chain 'B' and resid 510 through 524
      removed outlier: 3.554A  pdb=" N   ILE B 514 " --> pdb=" O   MET B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 547
      removed outlier: 3.998A  pdb=" N   VAL B 542 " --> pdb=" O   SER B 538 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE B 543 " --> pdb=" O   ILE B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 603
    Processing helix  chain 'B' and resid 605 through 616
      removed outlier: 3.560A  pdb=" N   ILE B 609 " --> pdb=" O   ASN B 605 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA B 616 " --> pdb=" O   ALA B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 678
      removed outlier: 3.736A  pdb=" N   ARG B 671 " --> pdb=" O   LEU B 667 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ALA B 676 " --> pdb=" O   ARG B 672 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ILE B 677 " --> pdb=" O   ASP B 673 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY B 678 " --> pdb=" O   TYR B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 696
      removed outlier: 3.722A  pdb=" N   THR B 695 " --> pdb=" O   ARG B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 711 through 721
      removed outlier: 3.734A  pdb=" N   VAL B 721 " --> pdb=" O   ALA B 717 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552
      removed outlier: 3.719A  pdb=" N   SER A 552 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   PHE A 581 " --> pdb=" O   ASP A 652 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE A 649 " --> pdb=" O   LEU A 682 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 551 through 552
      removed outlier: 3.720A  pdb=" N   SER B 552 " --> pdb=" O   ARG B 582 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   PHE B 581 " --> pdb=" O   ASP B 652 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ILE B 649 " --> pdb=" O   LEU B 682 " (cutoff:3.500A)

    408 hydrogen bonds defined for protein.
    1206 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: 1.06

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2419
        1.33 -     1.45: 1627
        1.45 -     1.57: 5342
        1.57 -     1.69: 0
        1.69 -     1.80: 74
  Bond restraints: 9462
  Sorted by residual:
  bond pdb=" N   ILE A 364 "
       pdb=" CA  ILE A 364 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.23e-02 6.61e+03 1.04e+01
  bond pdb=" N   ILE B 364 "
       pdb=" CA  ILE B 364 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.23e-02 6.61e+03 8.22e+00
  bond pdb=" N   ILE B 360 "
       pdb=" CA  ILE B 360 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.60e+00
  bond pdb=" N   HIS A 363 "
       pdb=" CA  HIS A 363 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.48e+00
  bond pdb=" N   THR B 366 "
       pdb=" CA  THR B 366 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.031 1.16e-02 7.43e+03 7.02e+00
  ... (remaining 9457 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 12142
        2.17 -     4.34: 580
        4.34 -     6.51: 75
        6.51 -     8.68: 35
        8.68 -    10.85: 6
  Bond angle restraints: 12838
  Sorted by residual:
  angle pdb=" C   GLU A 558 "
        pdb=" N   GLU A 559 "
        pdb=" CA  GLU A 559 "
      ideal   model   delta    sigma   weight residual
     121.54  129.32   -7.78 1.91e+00 2.74e-01 1.66e+01
  angle pdb=" C   GLU B 558 "
        pdb=" N   GLU B 559 "
        pdb=" CA  GLU B 559 "
      ideal   model   delta    sigma   weight residual
     121.54  129.30   -7.76 1.91e+00 2.74e-01 1.65e+01
  angle pdb=" C   SER B 508 "
        pdb=" N   ARG B 509 "
        pdb=" CA  ARG B 509 "
      ideal   model   delta    sigma   weight residual
     121.54  129.26   -7.72 1.91e+00 2.74e-01 1.63e+01
  angle pdb=" C   SER A 508 "
        pdb=" N   ARG A 509 "
        pdb=" CA  ARG A 509 "
      ideal   model   delta    sigma   weight residual
     121.54  129.22   -7.68 1.91e+00 2.74e-01 1.62e+01
  angle pdb=" C   ALA A 361 "
        pdb=" N   GLY A 362 "
        pdb=" CA  GLY A 362 "
      ideal   model   delta    sigma   weight residual
     121.41  129.21   -7.80 1.96e+00 2.60e-01 1.58e+01
  ... (remaining 12833 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 4818
       16.94 -    33.89: 606
       33.89 -    50.83: 150
       50.83 -    67.77: 28
       67.77 -    84.72: 6
  Dihedral angle restraints: 5608
    sinusoidal: 2150
      harmonic: 3458
  Sorted by residual:
  dihedral pdb=" CA  TYR A 699 "
           pdb=" C   TYR A 699 "
           pdb=" N   CYS A 700 "
           pdb=" CA  CYS A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.39  -47.61     0      5.00e+00 4.00e-02 9.07e+01
  dihedral pdb=" CA  TYR B 699 "
           pdb=" C   TYR B 699 "
           pdb=" N   CYS B 700 "
           pdb=" CA  CYS B 700 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -132.44  -47.56     0      5.00e+00 4.00e-02 9.05e+01
  dihedral pdb=" CA  GLY A 697 "
           pdb=" C   GLY A 697 "
           pdb=" N   GLU A 698 "
           pdb=" CA  GLU A 698 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.68  -42.32     0      5.00e+00 4.00e-02 7.16e+01
  ... (remaining 5605 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 992
       0.050 -    0.100: 435
       0.100 -    0.151: 88
       0.151 -    0.201: 29
       0.201 -    0.251: 8
  Chirality restraints: 1552
  Sorted by residual:
  chirality pdb=" CB  VAL B 557 "
            pdb=" CA  VAL B 557 "
            pdb=" CG1 VAL B 557 "
            pdb=" CG2 VAL B 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL A 557 "
            pdb=" CA  VAL A 557 "
            pdb=" CG1 VAL A 557 "
            pdb=" CG2 VAL A 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CB  VAL B 382 "
            pdb=" CA  VAL B 382 "
            pdb=" CG1 VAL B 382 "
            pdb=" CG2 VAL B 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1549 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 585 "   -0.061 5.00e-02 4.00e+02   9.14e-02 1.34e+01
        pdb=" N   PRO B 586 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO B 586 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 586 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 585 "   -0.061 5.00e-02 4.00e+02   9.13e-02 1.33e+01
        pdb=" N   PRO A 586 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO A 586 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 586 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 501 "   -0.056 5.00e-02 4.00e+02   8.36e-02 1.12e+01
        pdb=" N   PRO A 502 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO A 502 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 502 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2714
        2.81 -     3.33: 8340
        3.33 -     3.85: 14387
        3.85 -     4.38: 15392
        4.38 -     4.90: 27152
  Nonbonded interactions: 67985
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 538 "
            pdb=" OH  TYR B 589 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR A 589 "
            pdb=" OG  SER B 538 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG  SER B 508 "
            pdb=" OD2 ASP B 511 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG  SER A 508 "
            pdb=" OD2 ASP A 511 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   SER B 254 "
            pdb=" OG  SER B 254 "
     model   vdw
     2.328 3.040
  ... (remaining 67980 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.580
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065   9462  Z= 0.364
  Angle     :  1.094  10.847  12838  Z= 0.580
  Chirality :  0.060   0.251   1552
  Planarity :  0.009   0.091   1556
  Dihedral  : 15.994  84.719   3376
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 12.69 %
    Favored  : 87.05 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 14.44 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.14 (0.18), residues: 1174
  helix: -2.87 (0.14), residues: 680
  sheet: -3.02 (0.83), residues: 36
  loop : -4.20 (0.23), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 509 
 TYR   0.022   0.003   TYR B 588 
 PHE   0.022   0.002   PHE A 658 
 TRP   0.022   0.003   TRP B 505 
 HIS   0.003   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00822 ( 9462)
  covalent geometry    : angle       1.09364 (12838)
  hydrogen bonds       : bond        0.15397 (  408)
  hydrogen bonds       : angle       5.88277 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   88 MET cc_start: 0.6574 (ttp) cc_final: 0.6137 (ttp)
REVERT: A  131 LEU cc_start: 0.8875 (tp) cc_final: 0.8595 (tt)
REVERT: A  384 VAL cc_start: 0.8566 (t) cc_final: 0.8250 (p)
REVERT: A  389 ILE cc_start: 0.9278 (pt) cc_final: 0.9073 (pt)
REVERT: A  431 PHE cc_start: 0.7892 (m-80) cc_final: 0.7630 (m-80)
REVERT: A  543 ILE cc_start: 0.9406 (pt) cc_final: 0.9095 (mt)
REVERT: A  544 LEU cc_start: 0.9340 (tp) cc_final: 0.8661 (tt)
REVERT: A  682 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8783 (pp)
REVERT: B   88 MET cc_start: 0.6576 (ttp) cc_final: 0.6134 (ttp)
REVERT: B  131 LEU cc_start: 0.8851 (tp) cc_final: 0.8570 (tt)
REVERT: B  384 VAL cc_start: 0.8562 (t) cc_final: 0.8245 (p)
REVERT: B  389 ILE cc_start: 0.9276 (pt) cc_final: 0.9073 (pt)
REVERT: B  431 PHE cc_start: 0.7872 (m-80) cc_final: 0.7627 (m-80)
REVERT: B  543 ILE cc_start: 0.9408 (pt) cc_final: 0.9093 (mt)
REVERT: B  544 LEU cc_start: 0.9338 (tp) cc_final: 0.8660 (tt)
REVERT: B  682 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8774 (pp)
  outliers start: 10
  outliers final: 4
  residues processed: 166
  average time/residue: 0.0779
  time to fit residues: 18.8121
Evaluate side-chains
  132 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  682 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 292 HIS
A 363 HIS
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 GLN
A 647 HIS
B 107 ASN
B 292 HIS
B 363 HIS
** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 573 GLN
B 647 HIS
B 696 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.170758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.145157 restraints weight = 14134.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.148271 restraints weight = 7987.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.150297 restraints weight = 5411.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.151560 restraints weight = 4160.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.152372 restraints weight = 3498.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   9462  Z= 0.120
  Angle     :  0.641   7.740  12838  Z= 0.328
  Chirality :  0.041   0.172   1552
  Planarity :  0.005   0.059   1556
  Dihedral  :  5.992  38.513   1261
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.90 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.23), residues: 1174
  helix: -0.98 (0.19), residues: 680
  sheet: -2.49 (0.92), residues: 36
  loop : -3.76 (0.25), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 545 
 TYR   0.009   0.001   TYR B 674 
 PHE   0.027   0.002   PHE B 152 
 TRP   0.014   0.002   TRP A 505 
 HIS   0.010   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9462)
  covalent geometry    : angle       0.64120 (12838)
  hydrogen bonds       : bond        0.03374 (  408)
  hydrogen bonds       : angle       3.99603 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.8830 (tp) cc_final: 0.8576 (tt)
REVERT: A  292 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7809 (m170)
REVERT: A  384 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8150 (p)
REVERT: A  431 PHE cc_start: 0.7873 (m-80) cc_final: 0.7642 (m-80)
REVERT: A  543 ILE cc_start: 0.9301 (pt) cc_final: 0.9064 (mt)
REVERT: A  544 LEU cc_start: 0.9346 (tp) cc_final: 0.8786 (tt)
REVERT: A  682 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8599 (pp)
REVERT: B  131 LEU cc_start: 0.8810 (tp) cc_final: 0.8566 (tt)
REVERT: B  292 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7810 (m170)
REVERT: B  384 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8145 (p)
REVERT: B  431 PHE cc_start: 0.7871 (m-80) cc_final: 0.7634 (m-80)
REVERT: B  543 ILE cc_start: 0.9300 (pt) cc_final: 0.9067 (mt)
REVERT: B  544 LEU cc_start: 0.9347 (tp) cc_final: 0.8790 (tt)
REVERT: B  682 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8594 (pp)
  outliers start: 27
  outliers final: 7
  residues processed: 169
  average time/residue: 0.0614
  time to fit residues: 16.3785
Evaluate side-chains
  147 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  292 HIS
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  692 ASP
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  292 HIS
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  682 LEU
Chi-restraints excluded: chain B residue  692 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0030
   chunk 65 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 94 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 85 optimal weight:    0.1980
   chunk 29 optimal weight:    8.9990
   overall best weight:    1.7794

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
A 363 HIS
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 292 HIS
** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 696 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.166156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.140861 restraints weight = 14198.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.143742 restraints weight = 9122.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.144825 restraints weight = 5831.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.144989 restraints weight = 4819.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.145149 restraints weight = 4549.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9462  Z= 0.158
  Angle     :  0.651   7.672  12838  Z= 0.328
  Chirality :  0.042   0.174   1552
  Planarity :  0.004   0.052   1556
  Dihedral  :  5.689  38.515   1257
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.00 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.47 (0.24), residues: 1174
  helix: -0.32 (0.20), residues: 682
  sheet: -2.45 (0.94), residues: 36
  loop : -3.73 (0.25), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 509 
 TYR   0.010   0.001   TYR A 588 
 PHE   0.032   0.002   PHE A 152 
 TRP   0.014   0.002   TRP A 505 
 HIS   0.005   0.001   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 9462)
  covalent geometry    : angle       0.65060 (12838)
  hydrogen bonds       : bond        0.03470 (  408)
  hydrogen bonds       : angle       3.82105 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.8853 (tp) cc_final: 0.8586 (tt)
REVERT: A  349 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6979 (m-80)
REVERT: A  384 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8204 (p)
REVERT: A  431 PHE cc_start: 0.7932 (m-80) cc_final: 0.7721 (m-80)
REVERT: A  543 ILE cc_start: 0.9341 (pt) cc_final: 0.9073 (mt)
REVERT: A  544 LEU cc_start: 0.9338 (tp) cc_final: 0.8763 (tt)
REVERT: A  682 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8571 (pp)
REVERT: B  131 LEU cc_start: 0.8825 (tp) cc_final: 0.8566 (tt)
REVERT: B  384 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8204 (p)
REVERT: B  431 PHE cc_start: 0.7925 (m-80) cc_final: 0.7713 (m-80)
REVERT: B  543 ILE cc_start: 0.9339 (pt) cc_final: 0.9059 (mt)
REVERT: B  544 LEU cc_start: 0.9340 (tp) cc_final: 0.8768 (tt)
REVERT: B  682 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8568 (pp)
  outliers start: 34
  outliers final: 22
  residues processed: 161
  average time/residue: 0.0663
  time to fit residues: 16.6165
Evaluate side-chains
  162 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLN
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  262 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  711 SER
Chi-restraints excluded: chain B residue   97 GLN
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  682 LEU
Chi-restraints excluded: chain B residue  711 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 23 optimal weight:    0.0970
   chunk 89 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
** B 490 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.170524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.146007 restraints weight = 14307.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.148093 restraints weight = 7891.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.150083 restraints weight = 5232.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.150464 restraints weight = 4422.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.150630 restraints weight = 3835.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9462  Z= 0.102
  Angle     :  0.584   8.411  12838  Z= 0.293
  Chirality :  0.040   0.196   1552
  Planarity :  0.003   0.044   1556
  Dihedral  :  5.187  33.433   1257
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.84 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.25), residues: 1174
  helix:  0.20 (0.20), residues: 688
  sheet: -2.14 (1.00), residues: 36
  loop : -3.72 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 545 
 TYR   0.007   0.001   TYR A 674 
 PHE   0.032   0.001   PHE A 152 
 TRP   0.014   0.001   TRP B 505 
 HIS   0.001   0.000   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 9462)
  covalent geometry    : angle       0.58368 (12838)
  hydrogen bonds       : bond        0.02614 (  408)
  hydrogen bonds       : angle       3.54732 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.8798 (tp) cc_final: 0.8538 (tt)
REVERT: A  349 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6991 (m-80)
REVERT: A  384 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8086 (p)
REVERT: A  431 PHE cc_start: 0.7884 (m-80) cc_final: 0.7622 (m-80)
REVERT: A  529 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8350 (mp)
REVERT: A  544 LEU cc_start: 0.9295 (tp) cc_final: 0.8995 (tt)
REVERT: A  682 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8450 (pp)
REVERT: B  131 LEU cc_start: 0.8764 (tp) cc_final: 0.8511 (tt)
REVERT: B  384 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8078 (p)
REVERT: B  431 PHE cc_start: 0.7872 (m-80) cc_final: 0.7611 (m-80)
REVERT: B  529 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8358 (mp)
REVERT: B  544 LEU cc_start: 0.9307 (tp) cc_final: 0.9012 (tt)
REVERT: B  682 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8595 (pp)
  outliers start: 31
  outliers final: 15
  residues processed: 166
  average time/residue: 0.0604
  time to fit residues: 15.9441
Evaluate side-chains
  156 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  262 PHE
Chi-restraints excluded: chain A residue  349 PHE
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  692 ASP
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  682 LEU
Chi-restraints excluded: chain B residue  692 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 64 optimal weight:    0.1980
   chunk 79 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 82 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 109 optimal weight:    0.0970
   chunk 83 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    0.5578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.171029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.144738 restraints weight = 14281.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.147952 restraints weight = 8133.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.150105 restraints weight = 5563.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.151338 restraints weight = 4295.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.152292 restraints weight = 3645.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9462  Z= 0.098
  Angle     :  0.580   9.878  12838  Z= 0.287
  Chirality :  0.040   0.195   1552
  Planarity :  0.003   0.040   1556
  Dihedral  :  4.965  32.485   1257
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.97 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.25), residues: 1174
  helix:  0.50 (0.21), residues: 682
  sheet: -1.94 (1.02), residues: 36
  loop : -3.70 (0.25), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 672 
 TYR   0.007   0.001   TYR B 142 
 PHE   0.034   0.001   PHE A 152 
 TRP   0.012   0.001   TRP A 505 
 HIS   0.001   0.000   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 9462)
  covalent geometry    : angle       0.57966 (12838)
  hydrogen bonds       : bond        0.02496 (  408)
  hydrogen bonds       : angle       3.47987 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 160
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.8771 (tp) cc_final: 0.8530 (tt)
REVERT: A  376 TRP cc_start: 0.6264 (m-10) cc_final: 0.5764 (t60)
REVERT: A  384 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8104 (p)
REVERT: A  431 PHE cc_start: 0.7886 (m-80) cc_final: 0.7647 (m-80)
REVERT: A  529 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8337 (mp)
REVERT: A  544 LEU cc_start: 0.9181 (tp) cc_final: 0.8911 (tt)
REVERT: A  682 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8591 (pp)
REVERT: B  131 LEU cc_start: 0.8739 (tp) cc_final: 0.8503 (tt)
REVERT: B  376 TRP cc_start: 0.6265 (m-10) cc_final: 0.5776 (t60)
REVERT: B  384 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8100 (p)
REVERT: B  431 PHE cc_start: 0.7879 (m-80) cc_final: 0.7636 (m-80)
REVERT: B  529 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8344 (mp)
REVERT: B  544 LEU cc_start: 0.9203 (tp) cc_final: 0.8946 (tt)
REVERT: B  682 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8580 (pp)
  outliers start: 40
  outliers final: 21
  residues processed: 184
  average time/residue: 0.0607
  time to fit residues: 17.8560
Evaluate side-chains
  174 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  262 PHE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  692 ASP
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  539 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  682 LEU
Chi-restraints excluded: chain B residue  692 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0030
   chunk 93 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A  97 GLN
A 685 GLN
B  97 GLN
B 685 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.171018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.146629 restraints weight = 14315.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.150391 restraints weight = 9515.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.151602 restraints weight = 5667.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.151512 restraints weight = 4843.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.151851 restraints weight = 4632.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   9462  Z= 0.095
  Angle     :  0.580   9.375  12838  Z= 0.286
  Chirality :  0.040   0.198   1552
  Planarity :  0.003   0.038   1556
  Dihedral  :  4.769  30.286   1257
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 24.61 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.25), residues: 1174
  helix:  0.75 (0.21), residues: 682
  sheet: -1.79 (1.03), residues: 36
  loop : -3.65 (0.25), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 671 
 TYR   0.008   0.001   TYR B 589 
 PHE   0.034   0.001   PHE A 152 
 TRP   0.011   0.001   TRP B 505 
 HIS   0.001   0.000   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 9462)
  covalent geometry    : angle       0.58047 (12838)
  hydrogen bonds       : bond        0.02325 (  408)
  hydrogen bonds       : angle       3.38318 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.8750 (tp) cc_final: 0.8525 (tt)
REVERT: A  376 TRP cc_start: 0.6259 (m-10) cc_final: 0.5713 (t60)
REVERT: A  384 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8095 (p)
REVERT: A  529 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8328 (mp)
REVERT: A  544 LEU cc_start: 0.9188 (tp) cc_final: 0.8920 (tt)
REVERT: A  682 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8534 (pp)
REVERT: B  131 LEU cc_start: 0.8719 (tp) cc_final: 0.8489 (tt)
REVERT: B  180 LEU cc_start: 0.7962 (tt) cc_final: 0.7644 (tp)
REVERT: B  376 TRP cc_start: 0.6267 (m-10) cc_final: 0.5736 (t60)
REVERT: B  384 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8089 (p)
REVERT: B  431 PHE cc_start: 0.7777 (m-80) cc_final: 0.7576 (m-80)
REVERT: B  529 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8323 (mp)
REVERT: B  544 LEU cc_start: 0.9192 (tp) cc_final: 0.8935 (tt)
REVERT: B  682 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8531 (pp)
  outliers start: 41
  outliers final: 23
  residues processed: 176
  average time/residue: 0.0551
  time to fit residues: 15.5661
Evaluate side-chains
  167 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  262 PHE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  539 ILE
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  682 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 51 optimal weight:    0.3980
   chunk 69 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 109 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.168840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.141874 restraints weight = 14359.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.145023 restraints weight = 8395.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.147154 restraints weight = 5817.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148545 restraints weight = 4520.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.149295 restraints weight = 3821.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   9462  Z= 0.119
  Angle     :  0.597   8.205  12838  Z= 0.295
  Chirality :  0.041   0.181   1552
  Planarity :  0.003   0.041   1556
  Dihedral  :  4.858  31.622   1257
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 26.55 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.25), residues: 1174
  helix:  0.79 (0.21), residues: 686
  sheet: -1.78 (1.02), residues: 36
  loop : -3.64 (0.25), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 509 
 TYR   0.009   0.001   TYR A 589 
 PHE   0.034   0.001   PHE B 152 
 TRP   0.010   0.001   TRP B 505 
 HIS   0.002   0.000   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9462)
  covalent geometry    : angle       0.59737 (12838)
  hydrogen bonds       : bond        0.02705 (  408)
  hydrogen bonds       : angle       3.40376 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.8744 (tp) cc_final: 0.8512 (tt)
REVERT: A  180 LEU cc_start: 0.7887 (tt) cc_final: 0.7592 (tt)
REVERT: A  384 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8150 (p)
REVERT: A  529 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8341 (mp)
REVERT: A  544 LEU cc_start: 0.9245 (tp) cc_final: 0.8988 (tt)
REVERT: A  682 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8593 (pp)
REVERT: B  131 LEU cc_start: 0.8713 (tp) cc_final: 0.8488 (tt)
REVERT: B  150 ILE cc_start: 0.8500 (tt) cc_final: 0.8298 (mt)
REVERT: B  384 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8144 (p)
REVERT: B  431 PHE cc_start: 0.7946 (m-80) cc_final: 0.7656 (m-80)
REVERT: B  529 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8340 (mp)
REVERT: B  544 LEU cc_start: 0.9236 (tp) cc_final: 0.8978 (tt)
REVERT: B  682 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8588 (pp)
  outliers start: 38
  outliers final: 27
  residues processed: 165
  average time/residue: 0.0587
  time to fit residues: 15.4387
Evaluate side-chains
  165 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  262 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  539 ILE
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  682 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 64 optimal weight:    0.1980
   chunk 102 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
** B 490 ASN ** 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 = 0.4025 r_free = 0.4025 target = 0.168694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142056 restraints weight = 14314.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.145101 restraints weight = 8449.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.147185 restraints weight = 5926.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.148367 restraints weight = 4638.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.149373 restraints weight = 3972.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9462  Z= 0.118
  Angle     :  0.602   9.641  12838  Z= 0.296
  Chirality :  0.041   0.184   1552
  Planarity :  0.003   0.040   1556
  Dihedral  :  4.850  31.759   1257
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.31 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 26.74 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.26), residues: 1174
  helix:  0.87 (0.21), residues: 688
  sheet: -1.76 (1.02), residues: 36
  loop : -3.55 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 158 
 TYR   0.009   0.001   TYR B 589 
 PHE   0.033   0.001   PHE B 152 
 TRP   0.010   0.001   TRP B 505 
 HIS   0.001   0.000   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9462)
  covalent geometry    : angle       0.60189 (12838)
  hydrogen bonds       : bond        0.02654 (  408)
  hydrogen bonds       : angle       3.37288 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.8767 (tp) cc_final: 0.8524 (tt)
REVERT: A  376 TRP cc_start: 0.6382 (m-10) cc_final: 0.5686 (t60)
REVERT: A  384 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8133 (p)
REVERT: A  529 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8369 (mp)
REVERT: A  544 LEU cc_start: 0.9221 (tp) cc_final: 0.8967 (tt)
REVERT: A  682 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8599 (pp)
REVERT: B  131 LEU cc_start: 0.8780 (tp) cc_final: 0.8560 (tt)
REVERT: B  150 ILE cc_start: 0.8525 (tt) cc_final: 0.8324 (mt)
REVERT: B  376 TRP cc_start: 0.6397 (m-10) cc_final: 0.5690 (t60)
REVERT: B  384 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8138 (p)
REVERT: B  431 PHE cc_start: 0.7884 (m-80) cc_final: 0.7571 (m-80)
REVERT: B  529 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8365 (mp)
REVERT: B  544 LEU cc_start: 0.9226 (tp) cc_final: 0.8973 (tt)
REVERT: B  682 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8595 (pp)
  outliers start: 34
  outliers final: 25
  residues processed: 163
  average time/residue: 0.0636
  time to fit residues: 16.2243
Evaluate side-chains
  164 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  262 PHE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  539 ILE
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  682 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0970
   chunk 29 optimal weight:    0.2980
   chunk 82 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 103 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.172288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.147737 restraints weight = 14311.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.151930 restraints weight = 9225.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.152506 restraints weight = 5234.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.153530 restraints weight = 4497.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.153555 restraints weight = 4230.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9462  Z= 0.096
  Angle     :  0.588  10.063  12838  Z= 0.286
  Chirality :  0.039   0.191   1552
  Planarity :  0.003   0.039   1556
  Dihedral  :  4.622  29.572   1257
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 27.13 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.26), residues: 1174
  helix:  0.97 (0.21), residues: 690
  sheet: -1.62 (1.02), residues: 36
  loop : -3.48 (0.25), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 671 
 TYR   0.007   0.001   TYR A 589 
 PHE   0.033   0.001   PHE B 152 
 TRP   0.009   0.001   TRP A 505 
 HIS   0.001   0.000   HIS A 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 9462)
  covalent geometry    : angle       0.58781 (12838)
  hydrogen bonds       : bond        0.02221 (  408)
  hydrogen bonds       : angle       3.26043 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   88 MET cc_start: 0.6114 (ttp) cc_final: 0.3708 (tpt)
REVERT: A  376 TRP cc_start: 0.6365 (m-10) cc_final: 0.5735 (t60)
REVERT: A  384 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8065 (p)
REVERT: A  529 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8322 (mp)
REVERT: A  544 LEU cc_start: 0.9226 (tp) cc_final: 0.8753 (tt)
REVERT: A  682 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8432 (pp)
REVERT: B   88 MET cc_start: 0.6091 (ttp) cc_final: 0.3647 (tpt)
REVERT: B  376 TRP cc_start: 0.6374 (m-10) cc_final: 0.5756 (t60)
REVERT: B  384 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8057 (p)
REVERT: B  529 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8323 (mp)
REVERT: B  544 LEU cc_start: 0.9233 (tp) cc_final: 0.8974 (tt)
REVERT: B  682 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8413 (pp)
  outliers start: 32
  outliers final: 21
  residues processed: 161
  average time/residue: 0.0602
  time to fit residues: 15.5435
Evaluate side-chains
  162 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  262 PHE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  682 LEU
Chi-restraints excluded: chain B residue  692 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 85 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.164839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.137190 restraints weight = 14480.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140257 restraints weight = 8644.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.142316 restraints weight = 6082.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.143731 restraints weight = 4789.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.144640 restraints weight = 4073.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9462  Z= 0.206
  Angle     :  0.686   9.542  12838  Z= 0.341
  Chirality :  0.044   0.182   1552
  Planarity :  0.004   0.044   1556
  Dihedral  :  5.171  35.488   1257
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 26.65 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.25), residues: 1174
  helix:  0.65 (0.21), residues: 704
  sheet: -1.97 (0.97), residues: 36
  loop : -3.81 (0.24), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 509 
 TYR   0.011   0.001   TYR B 589 
 PHE   0.035   0.002   PHE B 152 
 TRP   0.010   0.002   TRP B 505 
 HIS   0.003   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 9462)
  covalent geometry    : angle       0.68650 (12838)
  hydrogen bonds       : bond        0.03544 (  408)
  hydrogen bonds       : angle       3.57530 ( 1206)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 131
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  309 LEU cc_start: 0.7876 (mt) cc_final: 0.7562 (tt)
REVERT: A  376 TRP cc_start: 0.6168 (m-10) cc_final: 0.5934 (t60)
REVERT: A  384 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8167 (p)
REVERT: A  529 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (mp)
REVERT: A  544 LEU cc_start: 0.9309 (tp) cc_final: 0.9044 (tt)
REVERT: A  682 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8872 (pp)
REVERT: B  250 ASP cc_start: 0.8580 (t0) cc_final: 0.8375 (t0)
REVERT: B  309 LEU cc_start: 0.7876 (mt) cc_final: 0.7563 (tt)
REVERT: B  376 TRP cc_start: 0.6179 (m-10) cc_final: 0.5934 (t60)
REVERT: B  384 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8188 (p)
REVERT: B  529 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8441 (mp)
REVERT: B  544 LEU cc_start: 0.9314 (tp) cc_final: 0.9049 (tt)
REVERT: B  682 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8863 (pp)
REVERT: B  692 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7724 (m-30)
  outliers start: 39
  outliers final: 29
  residues processed: 160
  average time/residue: 0.0633
  time to fit residues: 15.6935
Evaluate side-chains
  166 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  262 PHE
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  711 SER
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  682 LEU
Chi-restraints excluded: chain B residue  689 THR
Chi-restraints excluded: chain B residue  692 ASP
Chi-restraints excluded: chain B residue  711 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 111 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 108 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.169513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.144677 restraints weight = 14253.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.147407 restraints weight = 10340.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.149262 restraints weight = 6719.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.149056 restraints weight = 5498.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.149411 restraints weight = 4902.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9462  Z= 0.109
  Angle     :  0.659  13.813  12838  Z= 0.309
  Chirality :  0.040   0.185   1552
  Planarity :  0.003   0.043   1556
  Dihedral  :  4.895  31.524   1257
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 28.00 %
    Favored  : 69.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.26), residues: 1174
  helix:  0.79 (0.21), residues: 708
  sheet: -1.81 (1.00), residues: 36
  loop : -3.65 (0.25), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 671 
 TYR   0.007   0.001   TYR A 588 
 PHE   0.036   0.001   PHE A 152 
 TRP   0.011   0.001   TRP B 505 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9462)
  covalent geometry    : angle       0.65886 (12838)
  hydrogen bonds       : bond        0.02611 (  408)
  hydrogen bonds       : angle       3.36862 ( 1206)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1281.89 seconds
wall clock time: 22 minutes 58.99 seconds (1378.99 seconds total)