Starting phenix.real_space_refine
on Fri Aug 22 19:37:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jzx_36754/08_2025/8jzx_36754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jzx_36754/08_2025/8jzx_36754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jzx_36754/08_2025/8jzx_36754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jzx_36754/08_2025/8jzx_36754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jzx_36754/08_2025/8jzx_36754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jzx_36754/08_2025/8jzx_36754.cif"
  }
  resolution = 2.5
  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=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4760      2.51       5
     N    1126      2.21       5
     O    1186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7108
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3452
          Classifications: {'peptide': 455}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 436}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 3452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3452
          Classifications: {'peptide': 455}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 436}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 102
          Unusual residues: {'CLR': 2, 'NAG': 1, 'Q09': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 102
          Unusual residues: {'CLR': 2, 'NAG': 1, 'Q09': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.89, per 1000 atoms: 0.27
  Number of scatterers: 7108
  At special positions: 0
  Unit cell: (80.9568, 59.031, 124.808, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1186      8.00
     N    1126      7.00
     C    4760      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 153 " distance=2.03

  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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 436 "
      " NAG B 601 " - " ASN B 436 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 357.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 2 sheets defined
      81.6% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 26
    Processing helix  chain 'A' and resid 33 through 56
      removed outlier: 3.810A  pdb=" N   VAL A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 70 through 88
      removed outlier: 3.568A  pdb=" N   TYR A  86 " --> pdb=" O   MET A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 99
      removed outlier: 3.836A  pdb=" N   ALA A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 116
    Processing helix  chain 'A' and resid 118 through 125
      removed outlier: 3.661A  pdb=" N   LEU A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 134
      removed outlier: 4.513A  pdb=" N   ALA A 130 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ALA A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 181
      removed outlier: 3.611A  pdb=" N   ALA A 159 " --> pdb=" O   PRO A 155 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLY A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   THR A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
      removed outlier: 3.790A  pdb=" N   ALA A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 212
      removed outlier: 3.649A  pdb=" N   ALA A 190 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ARG A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TRP A 197 " --> pdb=" O   ARG A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 220
      removed outlier: 3.631A  pdb=" N   GLN A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 244
      Proline residue:  A 229  - end of helix
      removed outlier: 3.857A  pdb=" N   PHE A 240 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 328
      removed outlier: 3.561A  pdb=" N   VAL A 319 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE A 321 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
      Proline residue:  A 323  - end of helix
    Processing helix  chain 'A' and resid 328 through 348
      removed outlier: 3.578A  pdb=" N   GLN A 339 " --> pdb=" O   TYR A 335 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 369
      removed outlier: 3.528A  pdb=" N   TRP A 368 " --> pdb=" O   PRO A 365 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 369 " --> pdb=" O   ALA A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 365 through 369'
    Processing helix  chain 'A' and resid 370 through 388
      removed outlier: 4.607A  pdb=" N   ALA A 374 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU A 376 " --> pdb=" O   PHE A 372 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      Proline residue:  A 382  - end of helix
    Processing helix  chain 'A' and resid 390 through 395
      removed outlier: 3.601A  pdb=" N   HIS A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 430
      removed outlier: 3.568A  pdb=" N   ARG A 404 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET A 413 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 453
      removed outlier: 3.511A  pdb=" N   TRP A 453 " --> pdb=" O   SER A 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 450 through 453'
    Processing helix  chain 'A' and resid 454 through 479
      removed outlier: 3.728A  pdb=" N   LEU A 460 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE A 470 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 510
    Processing helix  chain 'A' and resid 531 through 558
      removed outlier: 3.689A  pdb=" N   TYR A 535 " --> pdb=" O   TYR A 531 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE A 552 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 26
    Processing helix  chain 'B' and resid 33 through 56
      removed outlier: 3.810A  pdb=" N   VAL B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY B  53 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE B  54 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 70 through 88
      removed outlier: 3.568A  pdb=" N   TYR B  86 " --> pdb=" O   MET B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 99
      removed outlier: 3.836A  pdb=" N   ALA B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG B  99 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 116
    Processing helix  chain 'B' and resid 118 through 125
      removed outlier: 3.661A  pdb=" N   LEU B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 134
      removed outlier: 4.513A  pdb=" N   ALA B 130 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ALA B 131 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU B 132 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 181
      removed outlier: 3.612A  pdb=" N   ALA B 159 " --> pdb=" O   PRO B 155 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY B 160 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU B 163 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   THR B 176 " --> pdb=" O   LYS B 172 " (cutoff:3.500A)
      Proline residue:  B 177  - end of helix
      removed outlier: 3.790A  pdb=" N   ALA B 180 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 212
      removed outlier: 3.648A  pdb=" N   ALA B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   THR B 191 " --> pdb=" O   GLY B 187 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ARG B 192 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TRP B 197 " --> pdb=" O   ARG B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 220
      removed outlier: 3.631A  pdb=" N   GLN B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 244
      Proline residue:  B 229  - end of helix
      removed outlier: 3.857A  pdb=" N   PHE B 240 " --> pdb=" O   ALA B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 328
      removed outlier: 3.562A  pdb=" N   VAL B 319 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE B 321 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      Proline residue:  B 323  - end of helix
    Processing helix  chain 'B' and resid 328 through 348
      removed outlier: 3.577A  pdb=" N   GLN B 339 " --> pdb=" O   TYR B 335 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL B 343 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 369
      removed outlier: 3.528A  pdb=" N   TRP B 368 " --> pdb=" O   PRO B 365 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU B 369 " --> pdb=" O   ALA B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 369'
    Processing helix  chain 'B' and resid 370 through 388
      removed outlier: 4.607A  pdb=" N   ALA B 374 " --> pdb=" O   THR B 370 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU B 376 " --> pdb=" O   PHE B 372 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B 379 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
      Proline residue:  B 382  - end of helix
    Processing helix  chain 'B' and resid 390 through 395
      removed outlier: 3.600A  pdb=" N   HIS B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 430
      removed outlier: 3.568A  pdb=" N   ARG B 404 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET B 413 " --> pdb=" O   MET B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 453
      removed outlier: 3.511A  pdb=" N   TRP B 453 " --> pdb=" O   SER B 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 450 through 453'
    Processing helix  chain 'B' and resid 454 through 479
      removed outlier: 3.728A  pdb=" N   LEU B 460 " --> pdb=" O   PRO B 456 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ILE B 470 " --> pdb=" O   ILE B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 510
    Processing helix  chain 'B' and resid 531 through 558
      removed outlier: 3.689A  pdb=" N   TYR B 535 " --> pdb=" O   TYR B 531 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE B 552 " --> pdb=" O   LEU B 548 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439
      removed outlier: 3.834A  pdb=" N   VAL A 442 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 435 through 439
      removed outlier: 3.834A  pdb=" N   VAL B 442 " --> pdb=" O   ILE B 439 " (cutoff:3.500A)

    481 hydrogen bonds defined for protein.
    1437 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: 1.11

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1048
        1.31 -     1.43: 2025
        1.43 -     1.56: 4165
        1.56 -     1.68: 0
        1.68 -     1.81: 54
  Bond restraints: 7292
  Sorted by residual:
  bond pdb=" C25 Q09 B 604 "
       pdb=" N26 Q09 B 604 "
    ideal  model  delta    sigma   weight residual
    1.464  1.212  0.252 2.00e-02 2.50e+03 1.59e+02
  bond pdb=" C25 Q09 A 603 "
       pdb=" N26 Q09 A 603 "
    ideal  model  delta    sigma   weight residual
    1.464  1.212  0.252 2.00e-02 2.50e+03 1.58e+02
  bond pdb=" C20 Q09 A 603 "
       pdb=" N22 Q09 A 603 "
    ideal  model  delta    sigma   weight residual
    1.343  1.457 -0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" C20 Q09 B 604 "
       pdb=" N22 Q09 B 604 "
    ideal  model  delta    sigma   weight residual
    1.343  1.457 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C28 Q09 B 604 "
       pdb=" C29 Q09 B 604 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.082 2.00e-02 2.50e+03 1.69e+01
  ... (remaining 7287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 9507
        2.33 -     4.65: 327
        4.65 -     6.98: 79
        6.98 -     9.31: 21
        9.31 -    11.64: 6
  Bond angle restraints: 9940
  Sorted by residual:
  angle pdb=" C   ALA B  29 "
        pdb=" N   PHE B  30 "
        pdb=" CA  PHE B  30 "
      ideal   model   delta    sigma   weight residual
     121.54  133.18  -11.64 1.91e+00 2.74e-01 3.71e+01
  angle pdb=" C   ALA A  29 "
        pdb=" N   PHE A  30 "
        pdb=" CA  PHE A  30 "
      ideal   model   delta    sigma   weight residual
     121.54  133.17  -11.63 1.91e+00 2.74e-01 3.71e+01
  angle pdb=" C   PHE A  30 "
        pdb=" N   ALA A  31 "
        pdb=" CA  ALA A  31 "
      ideal   model   delta    sigma   weight residual
     121.54  131.27   -9.73 1.91e+00 2.74e-01 2.60e+01
  angle pdb=" C   PHE B  30 "
        pdb=" N   ALA B  31 "
        pdb=" CA  ALA B  31 "
      ideal   model   delta    sigma   weight residual
     121.54  131.24   -9.70 1.91e+00 2.74e-01 2.58e+01
  angle pdb=" C   GLN B 485 "
        pdb=" N   SER B 486 "
        pdb=" CA  SER B 486 "
      ideal   model   delta    sigma   weight residual
     121.54  130.07   -8.53 1.91e+00 2.74e-01 1.99e+01
  ... (remaining 9935 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 4177
       16.73 -    33.45: 197
       33.45 -    50.18: 30
       50.18 -    66.91: 18
       66.91 -    83.64: 6
  Dihedral angle restraints: 4428
    sinusoidal: 1832
      harmonic: 2596
  Sorted by residual:
  dihedral pdb=" CA  PHE B  30 "
           pdb=" C   PHE B  30 "
           pdb=" N   ALA B  31 "
           pdb=" CA  ALA B  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.10   27.90     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  PHE A  30 "
           pdb=" C   PHE A  30 "
           pdb=" N   ALA A  31 "
           pdb=" CA  ALA A  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.10   27.90     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  PRO B 390 "
           pdb=" C   PRO B 390 "
           pdb=" N   ILE B 391 "
           pdb=" CA  ILE B 391 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.57  -23.43     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 4425 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1058
       0.082 -    0.164: 90
       0.164 -    0.245: 18
       0.245 -    0.327: 6
       0.327 -    0.409: 4
  Chirality restraints: 1176
  Sorted by residual:
  chirality pdb=" C13 CLR A 604 "
            pdb=" C12 CLR A 604 "
            pdb=" C14 CLR A 604 "
            pdb=" C17 CLR A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.52   -0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" C13 CLR B 602 "
            pdb=" C12 CLR B 602 "
            pdb=" C14 CLR B 602 "
            pdb=" C17 CLR B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.53   -0.40 2.00e-01 2.50e+01 4.08e+00
  chirality pdb=" C14 CLR B 602 "
            pdb=" C13 CLR B 602 "
            pdb=" C15 CLR B 602 "
            pdb=" C8  CLR B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.67    0.35 2.00e-01 2.50e+01 3.04e+00
  ... (remaining 1173 not shown)

  Planarity restraints: 1190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 536 "   -0.018 2.00e-02 2.50e+03   1.79e-02 5.58e+00
        pdb=" CG  PHE B 536 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 536 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 536 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 536 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 536 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 536 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 536 "    0.017 2.00e-02 2.50e+03   1.77e-02 5.49e+00
        pdb=" CG  PHE A 536 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 536 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 536 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 536 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 536 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 536 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 120 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO A 121 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 121 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 121 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1187 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2211
        2.82 -     3.34: 6508
        3.34 -     3.86: 11688
        3.86 -     4.38: 14332
        4.38 -     4.90: 24430
  Nonbonded interactions: 59169
  Sorted by model distance:
  nonbonded pdb=" C21 CLR A 602 "
            pdb=" C23 CLR A 602 "
     model   vdw
     2.300 3.088
  nonbonded pdb=" C21 CLR B 603 "
            pdb=" C23 CLR B 603 "
     model   vdw
     2.301 3.088
  nonbonded pdb=" O   ALA A  27 "
            pdb=" NH1 ARG A 193 "
     model   vdw
     2.367 3.120
  nonbonded pdb=" O   ALA B  27 "
            pdb=" NH1 ARG B 193 "
     model   vdw
     2.368 3.120
  nonbonded pdb=" O   PHE B  30 "
            pdb=" N   GLY B  32 "
     model   vdw
     2.385 3.120
  ... (remaining 59164 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 18 through 602)
  selection = (chain 'B' and resid 18 through 602)
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.790
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  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:9.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
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      :  0.011   0.491   7297  Z= 0.709
  Angle     :  1.136  11.637   9950  Z= 0.581
  Chirality :  0.060   0.409   1176
  Planarity :  0.007   0.050   1188
  Dihedral  : 11.298  83.636   2758
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.07 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  1.14 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.11 (0.16), residues: 890
  helix: -4.21 (0.09), residues: 652
  sheet:  None (None), residues: 0
  loop : -2.69 (0.33), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 193 
 TYR   0.027   0.003   TYR B 113 
 PHE   0.040   0.003   PHE B 536 
 TRP   0.019   0.003   TRP B 368 
 HIS   0.002   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00907 ( 7292)
  covalent geometry    : angle       1.13578 ( 9940)
  SS BOND              : bond        0.00487 (    2)
  SS BOND              : angle       1.04926 (    4)
  hydrogen bonds       : bond        0.29394 (  481)
  hydrogen bonds       : angle      10.84573 ( 1437)
  Misc. bond           : bond        0.49057 (    1)
  link_NAG-ASN         : bond        0.00138 (    2)
  link_NAG-ASN         : angle       1.87559 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 PHE cc_start: 0.7655 (m-10) cc_final: 0.7366 (t80)
REVERT: B   73 GLN cc_start: 0.7785 (mt0) cc_final: 0.7231 (mt0)
REVERT: B   80 LEU cc_start: 0.8172 (mt) cc_final: 0.7948 (tm)
REVERT: B  372 PHE cc_start: 0.7597 (m-10) cc_final: 0.7373 (m-10)
REVERT: B  457 GLN cc_start: 0.8227 (mt0) cc_final: 0.7954 (mt0)
  outliers start: 2
  outliers final: 1
  residues processed: 169
  average time/residue: 0.4602
  time to fit residues: 82.3475
Evaluate side-chains
  89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 ASN
B 457 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.101124 restraints weight = 8462.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 1.94
r_work: 0.3151 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7297  Z= 0.154
  Angle     :  0.706   9.851   9950  Z= 0.360
  Chirality :  0.041   0.200   1176
  Planarity :  0.005   0.035   1188
  Dihedral  :  9.584  73.532   1314
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.61 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.97 %
    Favored  : 88.18 %
  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 aren not related in a simple way.
  whole: -2.62 (0.24), residues: 890
  helix: -1.27 (0.17), residues: 698
  sheet:  None (None), residues: 0
  loop : -2.91 (0.38), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 394 
 TYR   0.009   0.002   TYR B 226 
 PHE   0.019   0.002   PHE B 194 
 TRP   0.018   0.002   TRP A 453 
 HIS   0.003   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7292)
  covalent geometry    : angle       0.70469 ( 9940)
  SS BOND              : bond        0.00506 (    2)
  SS BOND              : angle       0.76998 (    4)
  hydrogen bonds       : bond        0.06071 (  481)
  hydrogen bonds       : angle       5.05068 ( 1437)
  Misc. bond           : bond        0.00319 (    1)
  link_NAG-ASN         : bond        0.00078 (    2)
  link_NAG-ASN         : angle       1.57644 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  453 TRP cc_start: 0.7652 (m100) cc_final: 0.7036 (m100)
REVERT: A  465 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8053 (mt-10)
REVERT: B   84 LEU cc_start: 0.8506 (tp) cc_final: 0.8219 (tp)
REVERT: B  151 ARG cc_start: 0.6930 (mtt90) cc_final: 0.6619 (mtp180)
REVERT: B  457 GLN cc_start: 0.8112 (mt0) cc_final: 0.7472 (mt0)
REVERT: B  482 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8529 (tptt)
  outliers start: 13
  outliers final: 1
  residues processed: 102
  average time/residue: 0.4740
  time to fit residues: 51.4267
Evaluate side-chains
  84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 45 optimal weight:   20.0000
   chunk 41 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0870
   chunk 78 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 457 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.130366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.101179 restraints weight = 8265.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.94
r_work: 0.3157 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7297  Z= 0.132
  Angle     :  0.630   9.949   9950  Z= 0.317
  Chirality :  0.039   0.137   1176
  Planarity :  0.004   0.033   1188
  Dihedral  :  8.005  58.767   1312
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.16 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.68 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.28), residues: 890
  helix:  0.59 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -2.53 (0.41), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 186 
 TYR   0.010   0.001   TYR A  52 
 PHE   0.014   0.001   PHE B 194 
 TRP   0.011   0.001   TRP B 197 
 HIS   0.002   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7292)
  covalent geometry    : angle       0.62897 ( 9940)
  SS BOND              : bond        0.00104 (    2)
  SS BOND              : angle       0.41953 (    4)
  hydrogen bonds       : bond        0.04967 (  481)
  hydrogen bonds       : angle       4.46584 ( 1437)
  Misc. bond           : bond        0.00157 (    1)
  link_NAG-ASN         : bond        0.00028 (    2)
  link_NAG-ASN         : angle       1.56582 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  453 TRP cc_start: 0.7932 (m100) cc_final: 0.7195 (m100)
REVERT: B   84 LEU cc_start: 0.8540 (tp) cc_final: 0.8251 (tp)
REVERT: B  151 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6437 (mtt90)
REVERT: B  184 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8141 (ttpt)
REVERT: B  457 GLN cc_start: 0.8001 (mt0) cc_final: 0.7196 (mt0)
REVERT: B  482 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8589 (tptt)
REVERT: B  513 LYS cc_start: 0.7325 (ptpp) cc_final: 0.7062 (ttpt)
  outliers start: 7
  outliers final: 2
  residues processed: 101
  average time/residue: 0.4989
  time to fit residues: 53.6208
Evaluate side-chains
  86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain B residue   79 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 86 optimal weight:    5.9990
   chunk 50 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.128166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.099396 restraints weight = 8402.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.93
r_work: 0.3129 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7297  Z= 0.139
  Angle     :  0.630   9.732   9950  Z= 0.314
  Chirality :  0.039   0.169   1176
  Planarity :  0.004   0.034   1188
  Dihedral  :  7.353  51.114   1312
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.38 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.97 %
    Favored  : 86.18 %
  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 aren not related in a simple way.
  whole:  0.87 (0.29), residues: 890
  helix:  1.36 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -2.42 (0.42), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 404 
 TYR   0.009   0.001   TYR B 335 
 PHE   0.017   0.002   PHE A  30 
 TRP   0.014   0.001   TRP B 453 
 HIS   0.003   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7292)
  covalent geometry    : angle       0.62884 ( 9940)
  SS BOND              : bond        0.00070 (    2)
  SS BOND              : angle       0.30973 (    4)
  hydrogen bonds       : bond        0.04862 (  481)
  hydrogen bonds       : angle       4.32889 ( 1437)
  Misc. bond           : bond        0.00190 (    1)
  link_NAG-ASN         : bond        0.00050 (    2)
  link_NAG-ASN         : angle       1.58373 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 ASP cc_start: 0.8058 (t0) cc_final: 0.7855 (p0)
REVERT: A  457 GLN cc_start: 0.8217 (mt0) cc_final: 0.7859 (mt0)
REVERT: B   84 LEU cc_start: 0.8518 (tp) cc_final: 0.8241 (tp)
REVERT: B  151 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6635 (mtt90)
REVERT: B  184 LYS cc_start: 0.8292 (ttpt) cc_final: 0.8059 (ttpt)
REVERT: B  371 MET cc_start: 0.8443 (mtm) cc_final: 0.8194 (mtp)
REVERT: B  457 GLN cc_start: 0.7939 (mt0) cc_final: 0.7153 (mt0)
  outliers start: 13
  outliers final: 5
  residues processed: 98
  average time/residue: 0.5148
  time to fit residues: 53.7103
Evaluate side-chains
  83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.126882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.098016 restraints weight = 8411.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.93
r_work: 0.3113 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7297  Z= 0.142
  Angle     :  0.632   9.813   9950  Z= 0.314
  Chirality :  0.040   0.134   1176
  Planarity :  0.004   0.060   1188
  Dihedral  :  7.193  50.736   1312
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.61 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.97 %
    Favored  : 85.90 %
  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 aren not related in a simple way.
  whole:  1.24 (0.29), residues: 890
  helix:  1.62 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -2.27 (0.43), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 404 
 TYR   0.010   0.001   TYR A  52 
 PHE   0.016   0.001   PHE A  30 
 TRP   0.011   0.001   TRP B 197 
 HIS   0.003   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7292)
  covalent geometry    : angle       0.63121 ( 9940)
  SS BOND              : bond        0.00090 (    2)
  SS BOND              : angle       0.27860 (    4)
  hydrogen bonds       : bond        0.04846 (  481)
  hydrogen bonds       : angle       4.28029 ( 1437)
  Misc. bond           : bond        0.00246 (    1)
  link_NAG-ASN         : bond        0.00094 (    2)
  link_NAG-ASN         : angle       1.61042 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 GLN cc_start: 0.8240 (mt0) cc_final: 0.7916 (mt0)
REVERT: B   84 LEU cc_start: 0.8524 (tp) cc_final: 0.8263 (tp)
REVERT: B  151 ARG cc_start: 0.7191 (mtt90) cc_final: 0.6559 (mtt90)
REVERT: B  371 MET cc_start: 0.8444 (mtm) cc_final: 0.8214 (mtp)
REVERT: B  457 GLN cc_start: 0.7895 (mt0) cc_final: 0.7319 (mt0)
  outliers start: 15
  outliers final: 4
  residues processed: 95
  average time/residue: 0.4187
  time to fit residues: 42.7846
Evaluate side-chains
  82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    0.0170
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0470
   chunk 74 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0970
   overall best weight:    0.3714

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.129866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.101515 restraints weight = 8368.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.91
r_work: 0.3167 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7297  Z= 0.117
  Angle     :  0.594   9.205   9950  Z= 0.296
  Chirality :  0.038   0.132   1176
  Planarity :  0.004   0.056   1188
  Dihedral  :  6.769  50.773   1312
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.61 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.96 %
    Favored  : 85.61 %
  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 aren not related in a simple way.
  whole:  1.54 (0.29), residues: 890
  helix:  1.86 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -2.29 (0.43), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 394 
 TYR   0.010   0.001   TYR B 335 
 PHE   0.016   0.001   PHE B 120 
 TRP   0.009   0.001   TRP B 197 
 HIS   0.001   0.000   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7292)
  covalent geometry    : angle       0.59258 ( 9940)
  SS BOND              : bond        0.00050 (    2)
  SS BOND              : angle       0.32814 (    4)
  hydrogen bonds       : bond        0.04200 (  481)
  hydrogen bonds       : angle       4.15778 ( 1437)
  Misc. bond           : bond        0.00150 (    1)
  link_NAG-ASN         : bond        0.00065 (    2)
  link_NAG-ASN         : angle       1.65731 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.8115 (m-80) cc_final: 0.7633 (m-80)
REVERT: A  457 GLN cc_start: 0.8068 (mt0) cc_final: 0.7781 (mt0)
REVERT: B   84 LEU cc_start: 0.8512 (tp) cc_final: 0.8236 (tp)
REVERT: B  151 ARG cc_start: 0.7261 (mtt90) cc_final: 0.6704 (mtt90)
  outliers start: 10
  outliers final: 4
  residues processed: 94
  average time/residue: 0.4326
  time to fit residues: 43.8343
Evaluate side-chains
  82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0270
   chunk 78 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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 = 0.3624 r_free = 0.3624 target = 0.128563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.100065 restraints weight = 8397.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.92
r_work: 0.3147 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7297  Z= 0.126
  Angle     :  0.612  10.039   9950  Z= 0.301
  Chirality :  0.038   0.133   1176
  Planarity :  0.004   0.053   1188
  Dihedral  :  6.810  50.628   1312
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  3.93 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.68 %
    Favored  : 84.76 %
  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 aren not related in a simple way.
  whole:  1.70 (0.29), residues: 890
  helix:  1.95 (0.20), residues: 700
  sheet:  None (None), residues: 0
  loop : -2.13 (0.43), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 404 
 TYR   0.010   0.001   TYR B 335 
 PHE   0.016   0.001   PHE B 120 
 TRP   0.010   0.001   TRP B 197 
 HIS   0.003   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7292)
  covalent geometry    : angle       0.61145 ( 9940)
  SS BOND              : bond        0.00070 (    2)
  SS BOND              : angle       0.26946 (    4)
  hydrogen bonds       : bond        0.04425 (  481)
  hydrogen bonds       : angle       4.15441 ( 1437)
  Misc. bond           : bond        0.00138 (    1)
  link_NAG-ASN         : bond        0.00079 (    2)
  link_NAG-ASN         : angle       1.58677 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.8074 (m-80) cc_final: 0.7623 (m-80)
REVERT: A  457 GLN cc_start: 0.8141 (mt0) cc_final: 0.7855 (mt0)
REVERT: A  501 PHE cc_start: 0.7511 (m-10) cc_final: 0.7309 (m-10)
REVERT: B   84 LEU cc_start: 0.8527 (tp) cc_final: 0.8241 (tp)
REVERT: B  151 ARG cc_start: 0.7222 (mtt90) cc_final: 0.6668 (mtt90)
REVERT: B  457 GLN cc_start: 0.7823 (mt0) cc_final: 0.7203 (mt0)
  outliers start: 11
  outliers final: 7
  residues processed: 87
  average time/residue: 0.4376
  time to fit residues: 40.9049
Evaluate side-chains
  82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0010
   chunk 57 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 88 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
B 203 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.129780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.101169 restraints weight = 8447.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.93
r_work: 0.3157 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7297  Z= 0.122
  Angle     :  0.602   9.270   9950  Z= 0.296
  Chirality :  0.038   0.132   1176
  Planarity :  0.004   0.049   1188
  Dihedral  :  6.630  50.640   1312
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  3.71 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.10 %
    Favored  : 84.62 %
  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 aren not related in a simple way.
  whole:  1.84 (0.29), residues: 890
  helix:  2.04 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -2.14 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 193 
 TYR   0.010   0.001   TYR B 335 
 PHE   0.015   0.001   PHE B 120 
 TRP   0.009   0.001   TRP B 197 
 HIS   0.002   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7292)
  covalent geometry    : angle       0.60078 ( 9940)
  SS BOND              : bond        0.00048 (    2)
  SS BOND              : angle       0.30067 (    4)
  hydrogen bonds       : bond        0.04263 (  481)
  hydrogen bonds       : angle       4.12810 ( 1437)
  Misc. bond           : bond        0.00126 (    1)
  link_NAG-ASN         : bond        0.00067 (    2)
  link_NAG-ASN         : angle       1.54885 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.8136 (m-80) cc_final: 0.7629 (m-80)
REVERT: A  184 LYS cc_start: 0.8228 (ttpt) cc_final: 0.8024 (ttpt)
REVERT: A  457 GLN cc_start: 0.8106 (mt0) cc_final: 0.7787 (mt0)
REVERT: A  501 PHE cc_start: 0.7547 (m-10) cc_final: 0.7341 (m-10)
REVERT: B  151 ARG cc_start: 0.7241 (mtt90) cc_final: 0.6649 (mtt90)
REVERT: B  457 GLN cc_start: 0.7828 (mt0) cc_final: 0.7252 (mt0)
  outliers start: 9
  outliers final: 6
  residues processed: 84
  average time/residue: 0.4450
  time to fit residues: 39.9980
Evaluate side-chains
  79 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3610 r_free = 0.3610 target = 0.127672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.098857 restraints weight = 8375.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.93
r_work: 0.3128 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7297  Z= 0.138
  Angle     :  0.624   9.022   9950  Z= 0.307
  Chirality :  0.039   0.145   1176
  Planarity :  0.004   0.045   1188
  Dihedral  :  6.727  50.706   1312
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.16 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.96 %
    Favored  : 83.90 %
  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 aren not related in a simple way.
  whole:  1.84 (0.29), residues: 890
  helix:  2.01 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -2.05 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 102 
 TYR   0.011   0.001   TYR A  52 
 PHE   0.017   0.001   PHE B 120 
 TRP   0.010   0.001   TRP B 197 
 HIS   0.003   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7292)
  covalent geometry    : angle       0.62300 ( 9940)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.28317 (    4)
  hydrogen bonds       : bond        0.04623 (  481)
  hydrogen bonds       : angle       4.15161 ( 1437)
  Misc. bond           : bond        0.00114 (    1)
  link_NAG-ASN         : bond        0.00100 (    2)
  link_NAG-ASN         : angle       1.53277 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.8157 (m-80) cc_final: 0.7792 (m-80)
REVERT: A  184 LYS cc_start: 0.8259 (ttpt) cc_final: 0.8045 (ttpt)
REVERT: A  457 GLN cc_start: 0.8202 (mt0) cc_final: 0.7900 (mt0)
REVERT: A  501 PHE cc_start: 0.7546 (m-10) cc_final: 0.7324 (m-10)
REVERT: B  151 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6582 (mtt90)
REVERT: B  453 TRP cc_start: 0.7903 (m100) cc_final: 0.7661 (m100)
REVERT: B  457 GLN cc_start: 0.7895 (mt0) cc_final: 0.7270 (mt0)
  outliers start: 8
  outliers final: 5
  residues processed: 81
  average time/residue: 0.4834
  time to fit residues: 41.8205
Evaluate side-chains
  79 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 70 optimal weight:    0.2980
   chunk 55 optimal weight:    0.0870
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.129749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.101234 restraints weight = 8358.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.93
r_work: 0.3160 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7297  Z= 0.122
  Angle     :  0.610   9.336   9950  Z= 0.299
  Chirality :  0.039   0.150   1176
  Planarity :  0.004   0.043   1188
  Dihedral  :  6.526  52.213   1312
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.27 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.81 %
    Favored  : 84.05 %
  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 aren not related in a simple way.
  whole:  1.92 (0.29), residues: 890
  helix:  2.06 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -2.02 (0.45), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 193 
 TYR   0.012   0.001   TYR B 335 
 PHE   0.019   0.001   PHE B 120 
 TRP   0.009   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7292)
  covalent geometry    : angle       0.60920 ( 9940)
  SS BOND              : bond        0.00034 (    2)
  SS BOND              : angle       0.31614 (    4)
  hydrogen bonds       : bond        0.04245 (  481)
  hydrogen bonds       : angle       4.10314 ( 1437)
  Misc. bond           : bond        0.00119 (    1)
  link_NAG-ASN         : bond        0.00089 (    2)
  link_NAG-ASN         : angle       1.56570 (    6)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.8176 (m-80) cc_final: 0.7672 (m-80)
REVERT: A  184 LYS cc_start: 0.8250 (ttpt) cc_final: 0.8037 (ttpt)
REVERT: A  457 GLN cc_start: 0.8112 (mt0) cc_final: 0.7834 (mt0)
REVERT: B  151 ARG cc_start: 0.7135 (mtt90) cc_final: 0.6595 (mtt90)
REVERT: B  453 TRP cc_start: 0.7897 (m100) cc_final: 0.7682 (m100)
REVERT: B  457 GLN cc_start: 0.7855 (mt0) cc_final: 0.7297 (mt0)
  outliers start: 8
  outliers final: 5
  residues processed: 83
  average time/residue: 0.4935
  time to fit residues: 43.8711
Evaluate side-chains
  78 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  438 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.125537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.096555 restraints weight = 8391.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.93
r_work: 0.3093 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7297  Z= 0.165
  Angle     :  0.664   9.168   9950  Z= 0.325
  Chirality :  0.042   0.154   1176
  Planarity :  0.004   0.038   1188
  Dihedral  :  6.913  51.458   1312
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.49 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.81 %
    Favored  : 84.05 %
  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 aren not related in a simple way.
  whole:  1.79 (0.29), residues: 890
  helix:  1.94 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -1.93 (0.46), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 193 
 TYR   0.012   0.002   TYR A  52 
 PHE   0.026   0.002   PHE B 120 
 TRP   0.011   0.001   TRP B  94 
 HIS   0.004   0.001   HIS A 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 7292)
  covalent geometry    : angle       0.66278 ( 9940)
  SS BOND              : bond        0.00108 (    2)
  SS BOND              : angle       0.32931 (    4)
  hydrogen bonds       : bond        0.05079 (  481)
  hydrogen bonds       : angle       4.24103 ( 1437)
  Misc. bond           : bond        0.00101 (    1)
  link_NAG-ASN         : bond        0.00137 (    2)
  link_NAG-ASN         : angle       1.54249 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2566.17 seconds
wall clock time: 44 minutes 30.41 seconds (2670.41 seconds total)