Starting phenix.real_space_refine
on Tue Mar  3 14:35:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6o84_0650/03_2026/6o84_0650.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6o84_0650/03_2026/6o84_0650.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6o84_0650/03_2026/6o84_0650.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6o84_0650/03_2026/6o84_0650.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6o84_0650/03_2026/6o84_0650.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6o84_0650/03_2026/6o84_0650.map"
  }
  resolution = 3.92
  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=  -0.000 sd=   0.006
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      54      5.16       5
     C    4054      2.51       5
     N    1032      2.21       5
     O    1084      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 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: 6224
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1650
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 2, 'TRANS': 206}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1462
          Classifications: {'peptide': 206}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 3, 'TRANS': 202}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 177
          Unresolved non-hydrogen dihedrals: 59
          Planarities with less than four sites: {'UNK:plan-1': 59}
          Unresolved non-hydrogen planarities: 59
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.85, per 1000 atoms: 0.30
  Number of scatterers: 6224
  At special positions: 0
  Unit cell: (86.67, 88.81, 79.18, 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      54     16.00
     O    1084      8.00
     N    1032      7.00
     C    4054      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: 0.45
  Conformation dependent library (CDL) restraints added in 321.4 milliseconds
  

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1568

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      94.5% alpha, 1.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 137
      removed outlier: 4.205A  pdb=" N   PHE A 118 " --> pdb=" O   PHE A 114 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   MET A 123 " --> pdb=" O   GLY A 119 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ALA A 134 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 166
      removed outlier: 3.861A  pdb=" N   GLN A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 209
      removed outlier: 3.543A  pdb=" N   LEU A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER A 196 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS A 206 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 239
      removed outlier: 3.524A  pdb=" N   SER A 223 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE A 224 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 234 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 271
      removed outlier: 3.530A  pdb=" N   THR A 251 " --> pdb=" O   HIS A 247 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR A 253 " --> pdb=" O   SER A 249 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   MET A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A 264 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 271 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 310
      removed outlier: 3.768A  pdb=" N   LEU A 308 " --> pdb=" O   MET A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 336
      removed outlier: 3.998A  pdb=" N   GLU A 321 " --> pdb=" O   PRO A 317 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ILE A 332 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 380
      removed outlier: 4.484A  pdb=" N   UNK A 365 " --> pdb=" O   UNK A 361 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   UNK A 366 " --> pdb=" O   UNK A 362 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   UNK A 367 " --> pdb=" O   UNK A 363 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   UNK A 369 " --> pdb=" O   UNK A 365 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   UNK A 370 " --> pdb=" O   UNK A 366 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   UNK A 376 " --> pdb=" O   UNK A 372 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   UNK A 378 " --> pdb=" O   UNK A 374 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   UNK A 379 " --> pdb=" O   UNK A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 421
      removed outlier: 3.831A  pdb=" N   UNK A 400 " --> pdb=" O   UNK A 396 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   UNK A 406 " --> pdb=" O   UNK A 402 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   UNK A 407 " --> pdb=" O   UNK A 403 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   UNK A 409 " --> pdb=" O   UNK A 405 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   UNK A 412 " --> pdb=" O   UNK A 408 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   UNK A 413 " --> pdb=" O   UNK A 409 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   UNK A 416 " --> pdb=" O   UNK A 412 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   UNK A 418 " --> pdb=" O   UNK A 414 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   UNK A 419 " --> pdb=" O   UNK A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 516
      removed outlier: 3.619A  pdb=" N   LEU A 512 " --> pdb=" O   LEU A 508 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE A 514 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER A 516 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 533
      removed outlier: 5.178A  pdb=" N   ILE A 523 " --> pdb=" O   GLY A 519 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   SER A 524 " --> pdb=" O   GLN A 520 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 526 " --> pdb=" O   GLY A 522 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   SER A 527 " --> pdb=" O   ILE A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 571
      removed outlier: 3.601A  pdb=" N   ILE A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   MET A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 574
      No H-bonds generated for 'chain 'A' and resid 572 through 574'
    Processing helix  chain 'A' and resid 607 through 631
      removed outlier: 3.624A  pdb=" N   PHE A 618 " --> pdb=" O   GLU A 614 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE A 621 " --> pdb=" O   MET A 617 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU A 629 " --> pdb=" O   MET A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 647
    Processing helix  chain 'A' and resid 648 through 683
      removed outlier: 4.581A  pdb=" N   ALA A 654 " --> pdb=" O   GLY A 650 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A 655 " --> pdb=" O   ILE A 651 " (cutoff:3.500A)
      Proline residue:  A 661  - end of helix
      removed outlier: 3.985A  pdb=" N   GLY A 672 " --> pdb=" O   MET A 668 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE A 673 " --> pdb=" O   HIS A 669 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 137
      removed outlier: 4.205A  pdb=" N   PHE B 118 " --> pdb=" O   PHE B 114 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   MET B 123 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ALA B 134 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 166
      removed outlier: 3.861A  pdb=" N   GLN B 146 " --> pdb=" O   GLU B 142 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU B 155 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 209
      removed outlier: 3.543A  pdb=" N   LEU B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL B 194 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B 196 " --> pdb=" O   PHE B 192 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS B 206 " --> pdb=" O   PHE B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 239
      removed outlier: 3.524A  pdb=" N   SER B 223 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE B 224 " --> pdb=" O   VAL B 220 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL B 234 " --> pdb=" O   SER B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 271
      removed outlier: 3.530A  pdb=" N   THR B 251 " --> pdb=" O   HIS B 247 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   MET B 256 " --> pdb=" O   ARG B 252 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU B 264 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 310
      removed outlier: 3.768A  pdb=" N   LEU B 308 " --> pdb=" O   MET B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 336
      removed outlier: 3.998A  pdb=" N   GLU B 321 " --> pdb=" O   PRO B 317 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ILE B 332 " --> pdb=" O   THR B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 380
      removed outlier: 4.484A  pdb=" N   UNK B 365 " --> pdb=" O   UNK B 361 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   UNK B 366 " --> pdb=" O   UNK B 362 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   UNK B 367 " --> pdb=" O   UNK B 363 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   UNK B 369 " --> pdb=" O   UNK B 365 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   UNK B 370 " --> pdb=" O   UNK B 366 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   UNK B 376 " --> pdb=" O   UNK B 372 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   UNK B 378 " --> pdb=" O   UNK B 374 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   UNK B 379 " --> pdb=" O   UNK B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 421
      removed outlier: 3.831A  pdb=" N   UNK B 400 " --> pdb=" O   UNK B 396 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   UNK B 406 " --> pdb=" O   UNK B 402 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   UNK B 407 " --> pdb=" O   UNK B 403 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   UNK B 409 " --> pdb=" O   UNK B 405 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   UNK B 412 " --> pdb=" O   UNK B 408 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   UNK B 413 " --> pdb=" O   UNK B 409 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   UNK B 416 " --> pdb=" O   UNK B 412 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   UNK B 418 " --> pdb=" O   UNK B 414 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   UNK B 419 " --> pdb=" O   UNK B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.619A  pdb=" N   LEU B 512 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE B 514 " --> pdb=" O   VAL B 510 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER B 516 " --> pdb=" O   LEU B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 533
      removed outlier: 5.178A  pdb=" N   ILE B 523 " --> pdb=" O   GLY B 519 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   SER B 524 " --> pdb=" O   GLN B 520 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE B 526 " --> pdb=" O   GLY B 522 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   SER B 527 " --> pdb=" O   ILE B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 571
      removed outlier: 3.601A  pdb=" N   ILE B 552 " --> pdb=" O   SER B 548 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU B 553 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   MET B 560 " --> pdb=" O   LEU B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 574
      No H-bonds generated for 'chain 'B' and resid 572 through 574'
    Processing helix  chain 'B' and resid 607 through 631
      removed outlier: 3.624A  pdb=" N   PHE B 618 " --> pdb=" O   GLU B 614 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE B 621 " --> pdb=" O   MET B 617 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU B 629 " --> pdb=" O   MET B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 647
    Processing helix  chain 'B' and resid 648 through 683
      removed outlier: 4.581A  pdb=" N   ALA B 654 " --> pdb=" O   GLY B 650 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE B 655 " --> pdb=" O   ILE B 651 " (cutoff:3.500A)
      Proline residue:  B 661  - end of helix
      removed outlier: 3.985A  pdb=" N   GLY B 672 " --> pdb=" O   MET B 668 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE B 673 " --> pdb=" O   HIS B 669 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175
    Processing sheet with id=AA2, first strand: chain 'B' and resid 173 through 175

    433 hydrogen bonds defined for protein.
    1299 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: 0.93

  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:
        1.23 -     1.34: 1954
        1.34 -     1.46: 1522
        1.46 -     1.58: 2776
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 6342
  Sorted by residual:
  bond pdb=" CA  THR A 535 "
       pdb=" C   THR A 535 "
    ideal  model  delta    sigma   weight residual
    1.521  1.537 -0.016 1.14e-02 7.69e+03 1.93e+00
  bond pdb=" CA  THR B 535 "
       pdb=" C   THR B 535 "
    ideal  model  delta    sigma   weight residual
    1.521  1.537 -0.016 1.14e-02 7.69e+03 1.93e+00
  bond pdb=" C   SER A 145 "
       pdb=" O   SER A 145 "
    ideal  model  delta    sigma   weight residual
    1.237  1.250 -0.014 1.16e-02 7.43e+03 1.36e+00
  bond pdb=" C   SER B 145 "
       pdb=" O   SER B 145 "
    ideal  model  delta    sigma   weight residual
    1.237  1.250 -0.014 1.16e-02 7.43e+03 1.36e+00
  bond pdb=" CA  SER B 145 "
       pdb=" C   SER B 145 "
    ideal  model  delta    sigma   weight residual
    1.524  1.538 -0.014 1.26e-02 6.30e+03 1.32e+00
  ... (remaining 6337 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 8106
        1.56 -     3.13: 434
        3.13 -     4.69: 44
        4.69 -     6.26: 16
        6.26 -     7.82: 10
  Bond angle restraints: 8610
  Sorted by residual:
  angle pdb=" C   ASP A 144 "
        pdb=" N   SER A 145 "
        pdb=" CA  SER A 145 "
      ideal   model   delta    sigma   weight residual
     120.44  114.21    6.23 1.36e+00 5.41e-01 2.10e+01
  angle pdb=" C   ASP B 144 "
        pdb=" N   SER B 145 "
        pdb=" CA  SER B 145 "
      ideal   model   delta    sigma   weight residual
     120.44  114.21    6.23 1.36e+00 5.41e-01 2.10e+01
  angle pdb=" N   ILE B 151 "
        pdb=" CA  ILE B 151 "
        pdb=" CB  ILE B 151 "
      ideal   model   delta    sigma   weight residual
     110.54  116.67   -6.13 1.36e+00 5.41e-01 2.03e+01
  angle pdb=" N   ILE A 151 "
        pdb=" CA  ILE A 151 "
        pdb=" CB  ILE A 151 "
      ideal   model   delta    sigma   weight residual
     110.54  116.67   -6.13 1.36e+00 5.41e-01 2.03e+01
  angle pdb=" N   GLN A 146 "
        pdb=" CA  GLN A 146 "
        pdb=" C   GLN A 146 "
      ideal   model   delta    sigma   weight residual
     111.36  116.22   -4.86 1.09e+00 8.42e-01 1.99e+01
  ... (remaining 8605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 3322
       17.33 -    34.66: 306
       34.66 -    51.99: 60
       51.99 -    69.32: 6
       69.32 -    86.65: 4
  Dihedral angle restraints: 3698
    sinusoidal: 1292
      harmonic: 2406
  Sorted by residual:
  dihedral pdb=" CA  ASP B 177 "
           pdb=" C   ASP B 177 "
           pdb=" N   HIS B 178 "
           pdb=" CA  HIS B 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.09  -22.91     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  ASP A 177 "
           pdb=" C   ASP A 177 "
           pdb=" N   HIS A 178 "
           pdb=" CA  HIS A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.09  -22.91     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  ILE B 215 "
           pdb=" C   ILE B 215 "
           pdb=" N   LEU B 216 "
           pdb=" CA  LEU B 216 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.64   20.36     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 3695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 678
       0.041 -    0.083: 310
       0.083 -    0.124: 36
       0.124 -    0.165: 12
       0.165 -    0.206: 10
  Chirality restraints: 1046
  Sorted by residual:
  chirality pdb=" CA  GLN A 146 "
            pdb=" N   GLN A 146 "
            pdb=" C   GLN A 146 "
            pdb=" CB  GLN A 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  GLN B 146 "
            pdb=" N   GLN B 146 "
            pdb=" C   GLN B 146 "
            pdb=" CB  GLN B 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ILE B 151 "
            pdb=" N   ILE B 151 "
            pdb=" C   ILE B 151 "
            pdb=" CB  ILE B 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1043 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 140 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO B 141 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 141 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 141 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 140 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A 141 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 141 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 141 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 660 "    0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO B 661 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 661 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 661 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 2188
        2.86 -     3.37: 6179
        3.37 -     3.88: 9577
        3.88 -     4.39: 10860
        4.39 -     4.90: 17928
  Nonbonded interactions: 46732
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 124 "
            pdb=" OG1 THR B 128 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   PHE A 124 "
            pdb=" OG1 THR A 128 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   LEU A 257 "
            pdb=" OG1 THR A 261 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" O   LEU B 257 "
            pdb=" OG1 THR B 261 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" OG  SER B 115 "
            pdb=" O   ARG B 252 "
     model   vdw
     2.374 3.040
  ... (remaining 46727 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'
  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:             0.520
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.860
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
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      :  0.005   0.039   6342  Z= 0.245
  Angle     :  0.838   7.820   8610  Z= 0.480
  Chirality :  0.047   0.206   1046
  Planarity :  0.004   0.041   1048
  Dihedral  : 14.014  86.651   2130
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  7.99 %
    Favored  : 91.37 %
  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: -5.68 (0.20), residues: 696
  helix: -3.51 (0.13), residues: 508
  sheet: -5.32 (0.58), residues: 20
  loop : -3.46 (0.37), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 567 
 TYR   0.010   0.002   TYR B 647 
 PHE   0.010   0.002   PHE A 665 
 TRP   0.018   0.002   TRP B 159 
 HIS   0.004   0.001   HIS B 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 6342)
  covalent geometry    : angle       0.83786 ( 8610)
  hydrogen bonds       : bond        0.30911 (  433)
  hydrogen bonds       : angle       9.03015 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 187
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8355 (mttt) cc_final: 0.7869 (pttm)
REVERT: A  150 CYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8861 (p)
REVERT: A  153 MET cc_start: 0.9200 (mtm) cc_final: 0.8968 (mtm)
REVERT: A  162 TYR cc_start: 0.8388 (t80) cc_final: 0.8187 (t80)
REVERT: A  508 LEU cc_start: 0.8490 (tp) cc_final: 0.8214 (tt)
REVERT: A  639 MET cc_start: 0.7665 (mmt) cc_final: 0.6495 (tmm)
REVERT: B  109 LYS cc_start: 0.8337 (mttt) cc_final: 0.7902 (pttm)
REVERT: B  150 CYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8864 (p)
REVERT: B  153 MET cc_start: 0.9236 (mtm) cc_final: 0.8987 (mtm)
REVERT: B  255 ILE cc_start: 0.9660 (mt) cc_final: 0.9457 (mm)
REVERT: B  617 MET cc_start: 0.8417 (tpt) cc_final: 0.7987 (tpt)
REVERT: B  639 MET cc_start: 0.7614 (mmt) cc_final: 0.6428 (tmm)
  outliers start: 4
  outliers final: 2
  residues processed: 191
  average time/residue: 0.0559
  time to fit residues: 15.1067
Evaluate side-chains
  148 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  151 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.102201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.081537 restraints weight = 15781.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.083506 restraints weight = 10285.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.084624 restraints weight = 7762.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.085663 restraints weight = 6554.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.085902 restraints weight = 5812.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6342  Z= 0.189
  Angle     :  0.638   6.046   8610  Z= 0.337
  Chirality :  0.038   0.151   1046
  Planarity :  0.004   0.032   1048
  Dihedral  :  5.407  45.029    868
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.61 %
    Favored  : 81.15 %
  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: -1.85 (0.29), residues: 696
  helix: -0.38 (0.20), residues: 528
  sheet: -5.48 (0.44), residues: 20
  loop : -3.33 (0.46), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 143 
 TYR   0.010   0.002   TYR A 666 
 PHE   0.013   0.001   PHE B 221 
 TRP   0.019   0.001   TRP A 159 
 HIS   0.003   0.001   HIS B 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 6342)
  covalent geometry    : angle       0.63792 ( 8610)
  hydrogen bonds       : bond        0.05527 (  433)
  hydrogen bonds       : angle       4.01859 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8282 (mttt) cc_final: 0.7897 (pttm)
REVERT: A  150 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8911 (p)
REVERT: A  153 MET cc_start: 0.9155 (mtm) cc_final: 0.8692 (mtp)
REVERT: A  170 GLN cc_start: 0.8264 (mp10) cc_final: 0.7808 (mp10)
REVERT: A  508 LEU cc_start: 0.8529 (tp) cc_final: 0.8021 (tt)
REVERT: A  613 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7688 (tmtt)
REVERT: A  617 MET cc_start: 0.8333 (tpt) cc_final: 0.7740 (tpp)
REVERT: A  639 MET cc_start: 0.7529 (mmt) cc_final: 0.6581 (tmm)
REVERT: B  109 LYS cc_start: 0.8255 (mttt) cc_final: 0.7914 (pttm)
REVERT: B  150 CYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8910 (p)
REVERT: B  153 MET cc_start: 0.9147 (mtm) cc_final: 0.8700 (mtp)
REVERT: B  170 GLN cc_start: 0.8215 (mp10) cc_final: 0.7769 (mp10)
REVERT: B  256 MET cc_start: 0.9025 (mmm) cc_final: 0.8794 (mmm)
REVERT: B  508 LEU cc_start: 0.8547 (tp) cc_final: 0.8271 (tt)
REVERT: B  617 MET cc_start: 0.8296 (tpt) cc_final: 0.7738 (tpp)
REVERT: B  639 MET cc_start: 0.7505 (mmt) cc_final: 0.6578 (tmm)
  outliers start: 14
  outliers final: 8
  residues processed: 168
  average time/residue: 0.0531
  time to fit residues: 12.7775
Evaluate side-chains
  144 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  323 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0050
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0020
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    1.0008

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.102628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.081973 restraints weight = 15520.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.084212 restraints weight = 9327.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.085649 restraints weight = 6747.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.086166 restraints weight = 5517.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.087040 restraints weight = 5034.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6342  Z= 0.111
  Angle     :  0.519   6.661   8610  Z= 0.269
  Chirality :  0.035   0.131   1046
  Planarity :  0.003   0.025   1048
  Dihedral  :  4.639  33.940    868
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.57 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.31), residues: 696
  helix:  0.67 (0.22), residues: 534
  sheet: -5.38 (0.38), residues: 20
  loop : -3.26 (0.47), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 644 
 TYR   0.016   0.001   TYR B 678 
 PHE   0.012   0.001   PHE A 221 
 TRP   0.025   0.002   TRP B 184 
 HIS   0.001   0.000   HIS B 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6342)
  covalent geometry    : angle       0.51855 ( 8610)
  hydrogen bonds       : bond        0.04195 (  433)
  hydrogen bonds       : angle       3.50412 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8276 (mttt) cc_final: 0.7741 (pttm)
REVERT: A  153 MET cc_start: 0.9218 (mtm) cc_final: 0.8745 (mtp)
REVERT: A  170 GLN cc_start: 0.8151 (mp10) cc_final: 0.7764 (mp10)
REVERT: A  335 LYS cc_start: 0.9273 (ttpt) cc_final: 0.8987 (ttpp)
REVERT: A  508 LEU cc_start: 0.8396 (tp) cc_final: 0.7912 (tt)
REVERT: A  617 MET cc_start: 0.8260 (tpt) cc_final: 0.7330 (tpp)
REVERT: A  639 MET cc_start: 0.7597 (mmt) cc_final: 0.6659 (tmm)
REVERT: A  676 GLU cc_start: 0.8017 (tp30) cc_final: 0.7758 (tp30)
REVERT: B  109 LYS cc_start: 0.8470 (mttt) cc_final: 0.7589 (mtmm)
REVERT: B  153 MET cc_start: 0.9218 (mtm) cc_final: 0.8736 (mtp)
REVERT: B  170 GLN cc_start: 0.8149 (mp10) cc_final: 0.7770 (mp10)
REVERT: B  256 MET cc_start: 0.9143 (mmm) cc_final: 0.8889 (mmm)
REVERT: B  335 LYS cc_start: 0.9216 (ttpt) cc_final: 0.9009 (ttpp)
REVERT: B  508 LEU cc_start: 0.8515 (tp) cc_final: 0.8196 (tt)
REVERT: B  617 MET cc_start: 0.8294 (tpt) cc_final: 0.7856 (tpp)
REVERT: B  639 MET cc_start: 0.7529 (mmt) cc_final: 0.6579 (tmm)
REVERT: B  676 GLU cc_start: 0.7986 (tp30) cc_final: 0.7723 (tp30)
  outliers start: 13
  outliers final: 4
  residues processed: 180
  average time/residue: 0.0619
  time to fit residues: 15.4452
Evaluate side-chains
  149 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 145
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.099753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.078745 restraints weight = 15915.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.080396 restraints weight = 10475.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.081849 restraints weight = 8130.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.082583 restraints weight = 6813.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.082976 restraints weight = 6126.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6342  Z= 0.240
  Angle     :  0.656   7.331   8610  Z= 0.338
  Chirality :  0.039   0.142   1046
  Planarity :  0.003   0.025   1048
  Dihedral  :  4.489  24.031    862
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.96 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.32), residues: 696
  helix:  1.08 (0.22), residues: 530
  sheet: -5.54 (0.39), residues: 20
  loop : -3.15 (0.49), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 667 
 TYR   0.020   0.002   TYR A 678 
 PHE   0.016   0.002   PHE A 545 
 TRP   0.038   0.002   TRP A 184 
 HIS   0.005   0.001   HIS B 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 6342)
  covalent geometry    : angle       0.65630 ( 8610)
  hydrogen bonds       : bond        0.04805 (  433)
  hydrogen bonds       : angle       3.80715 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8304 (mttt) cc_final: 0.7955 (pttm)
REVERT: A  150 CYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8916 (p)
REVERT: A  153 MET cc_start: 0.9127 (mtm) cc_final: 0.8611 (mtp)
REVERT: A  170 GLN cc_start: 0.8202 (mp10) cc_final: 0.7737 (mp10)
REVERT: A  508 LEU cc_start: 0.8544 (tp) cc_final: 0.8190 (tt)
REVERT: A  639 MET cc_start: 0.7503 (mmt) cc_final: 0.6550 (tmm)
REVERT: A  676 GLU cc_start: 0.7959 (tp30) cc_final: 0.7435 (tp30)
REVERT: B  109 LYS cc_start: 0.8416 (mttt) cc_final: 0.7668 (mtmm)
REVERT: B  123 MET cc_start: 0.8716 (tmm) cc_final: 0.8414 (tmm)
REVERT: B  150 CYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8877 (p)
REVERT: B  153 MET cc_start: 0.9138 (mtm) cc_final: 0.8605 (mtp)
REVERT: B  310 GLN cc_start: 0.7568 (mt0) cc_final: 0.7319 (mp10)
REVERT: B  508 LEU cc_start: 0.8702 (tp) cc_final: 0.8206 (tt)
REVERT: B  639 MET cc_start: 0.7514 (mmt) cc_final: 0.6583 (tmm)
REVERT: B  676 GLU cc_start: 0.7964 (tp30) cc_final: 0.7449 (tp30)
  outliers start: 18
  outliers final: 12
  residues processed: 159
  average time/residue: 0.0631
  time to fit residues: 13.9298
Evaluate side-chains
  149 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.101912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.082582 restraints weight = 15757.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.084805 restraints weight = 9242.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.086373 restraints weight = 6580.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.087203 restraints weight = 5273.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.088042 restraints weight = 4626.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6342  Z= 0.105
  Angle     :  0.531   8.701   8610  Z= 0.270
  Chirality :  0.035   0.144   1046
  Planarity :  0.002   0.027   1048
  Dihedral  :  4.173  23.032    862
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 26.20 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.33), residues: 696
  helix:  1.44 (0.22), residues: 534
  sheet: -5.26 (0.42), residues: 20
  loop : -3.15 (0.48), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 143 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.007   0.001   PHE A 561 
 TRP   0.039   0.002   TRP A 184 
 HIS   0.002   0.000   HIS B 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 6342)
  covalent geometry    : angle       0.53059 ( 8610)
  hydrogen bonds       : bond        0.03711 (  433)
  hydrogen bonds       : angle       3.37820 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 160
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8397 (mttt) cc_final: 0.7652 (mtmm)
REVERT: A  123 MET cc_start: 0.8666 (tmm) cc_final: 0.8436 (tmm)
REVERT: A  146 GLN cc_start: 0.8285 (mt0) cc_final: 0.8019 (mm-40)
REVERT: A  150 CYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8893 (p)
REVERT: A  153 MET cc_start: 0.9185 (mtm) cc_final: 0.8707 (mtp)
REVERT: A  170 GLN cc_start: 0.8195 (mp10) cc_final: 0.7814 (mp10)
REVERT: A  508 LEU cc_start: 0.8381 (tp) cc_final: 0.8058 (tt)
REVERT: A  617 MET cc_start: 0.8247 (tpt) cc_final: 0.7279 (tpp)
REVERT: A  639 MET cc_start: 0.7436 (mmt) cc_final: 0.6559 (tmm)
REVERT: A  676 GLU cc_start: 0.7995 (tp30) cc_final: 0.7683 (tp30)
REVERT: B  109 LYS cc_start: 0.8460 (mttt) cc_final: 0.7625 (mtmm)
REVERT: B  123 MET cc_start: 0.8788 (tmm) cc_final: 0.8412 (tmm)
REVERT: B  146 GLN cc_start: 0.8245 (mt0) cc_final: 0.8032 (mm-40)
REVERT: B  150 CYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8939 (p)
REVERT: B  153 MET cc_start: 0.9177 (mtm) cc_final: 0.8680 (mtp)
REVERT: B  256 MET cc_start: 0.9128 (mmm) cc_final: 0.8881 (mmm)
REVERT: B  310 GLN cc_start: 0.7425 (mt0) cc_final: 0.7169 (mp10)
REVERT: B  508 LEU cc_start: 0.8533 (tp) cc_final: 0.8057 (tt)
REVERT: B  617 MET cc_start: 0.8238 (tpt) cc_final: 0.7297 (tpp)
REVERT: B  639 MET cc_start: 0.7386 (mmt) cc_final: 0.6570 (tmm)
REVERT: B  645 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7950 (mp10)
REVERT: B  676 GLU cc_start: 0.8017 (tp30) cc_final: 0.7718 (tp30)
  outliers start: 13
  outliers final: 8
  residues processed: 167
  average time/residue: 0.0650
  time to fit residues: 15.0126
Evaluate side-chains
  155 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0030
   chunk 29 optimal weight:    0.9990
   chunk 26 optimal weight:   20.0000
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.103419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.083210 restraints weight = 15580.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.085476 restraints weight = 9330.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.086824 restraints weight = 6741.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.088029 restraints weight = 5505.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.088483 restraints weight = 4781.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6342  Z= 0.101
  Angle     :  0.537   9.602   8610  Z= 0.268
  Chirality :  0.035   0.142   1046
  Planarity :  0.003   0.028   1048
  Dihedral  :  3.970  21.880    862
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 27.16 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.33), residues: 696
  helix:  1.68 (0.22), residues: 532
  sheet: -5.23 (0.41), residues: 20
  loop : -3.14 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 644 
 TYR   0.009   0.001   TYR A 162 
 PHE   0.021   0.001   PHE A 545 
 TRP   0.044   0.002   TRP A 184 
 HIS   0.002   0.000   HIS A 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 6342)
  covalent geometry    : angle       0.53651 ( 8610)
  hydrogen bonds       : bond        0.03482 (  433)
  hydrogen bonds       : angle       3.25073 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8387 (mttt) cc_final: 0.7618 (mtmm)
REVERT: A  123 MET cc_start: 0.8742 (tmm) cc_final: 0.8536 (tmm)
REVERT: A  150 CYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8888 (p)
REVERT: A  153 MET cc_start: 0.9157 (mtm) cc_final: 0.8676 (mtp)
REVERT: A  170 GLN cc_start: 0.8204 (mp10) cc_final: 0.7803 (mp10)
REVERT: A  310 GLN cc_start: 0.7540 (mt0) cc_final: 0.7234 (mp10)
REVERT: A  508 LEU cc_start: 0.8453 (tp) cc_final: 0.8101 (tt)
REVERT: A  617 MET cc_start: 0.8258 (tpt) cc_final: 0.7788 (tpp)
REVERT: A  639 MET cc_start: 0.7366 (mmt) cc_final: 0.6423 (tmm)
REVERT: A  676 GLU cc_start: 0.7998 (tp30) cc_final: 0.7626 (tp30)
REVERT: B  109 LYS cc_start: 0.8282 (mttt) cc_final: 0.7488 (mtmm)
REVERT: B  123 MET cc_start: 0.8803 (tmm) cc_final: 0.8401 (tmm)
REVERT: B  150 CYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8935 (p)
REVERT: B  153 MET cc_start: 0.9181 (mtm) cc_final: 0.8703 (mtp)
REVERT: B  256 MET cc_start: 0.9126 (mmm) cc_final: 0.8883 (mmm)
REVERT: B  310 GLN cc_start: 0.7631 (mt0) cc_final: 0.7290 (mp10)
REVERT: B  617 MET cc_start: 0.8259 (tpt) cc_final: 0.7802 (tpp)
REVERT: B  639 MET cc_start: 0.7270 (mmt) cc_final: 0.6464 (tmm)
REVERT: B  645 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7908 (mp10)
REVERT: B  676 GLU cc_start: 0.7994 (tp30) cc_final: 0.7626 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 172
  average time/residue: 0.0559
  time to fit residues: 13.4484
Evaluate side-chains
  163 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  183 MET
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0570
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    2.4106

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.100499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.081410 restraints weight = 15750.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.083622 restraints weight = 9196.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.084968 restraints weight = 6498.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.086135 restraints weight = 5236.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.086696 restraints weight = 4495.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6342  Z= 0.153
  Angle     :  0.588   9.264   8610  Z= 0.297
  Chirality :  0.036   0.147   1046
  Planarity :  0.003   0.027   1048
  Dihedral  :  4.056  22.672    862
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 26.52 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.33), residues: 696
  helix:  1.61 (0.23), residues: 530
  sheet: -5.31 (0.41), residues: 20
  loop : -3.04 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 143 
 TYR   0.009   0.001   TYR B 647 
 PHE   0.019   0.001   PHE B 222 
 TRP   0.052   0.002   TRP A 184 
 HIS   0.002   0.001   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6342)
  covalent geometry    : angle       0.58814 ( 8610)
  hydrogen bonds       : bond        0.03775 (  433)
  hydrogen bonds       : angle       3.48341 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8512 (mttt) cc_final: 0.7696 (mtmm)
REVERT: A  146 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8049 (mm-40)
REVERT: A  150 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8871 (p)
REVERT: A  153 MET cc_start: 0.9178 (mtm) cc_final: 0.8710 (mtp)
REVERT: A  170 GLN cc_start: 0.8183 (mp10) cc_final: 0.7785 (mp10)
REVERT: A  310 GLN cc_start: 0.7560 (mt0) cc_final: 0.7256 (mp10)
REVERT: A  508 LEU cc_start: 0.8498 (tp) cc_final: 0.8119 (tt)
REVERT: A  617 MET cc_start: 0.8316 (tpt) cc_final: 0.7783 (tpp)
REVERT: A  639 MET cc_start: 0.7448 (mmt) cc_final: 0.6462 (tmm)
REVERT: A  676 GLU cc_start: 0.8076 (tp30) cc_final: 0.7681 (tp30)
REVERT: B  109 LYS cc_start: 0.8371 (mttt) cc_final: 0.7601 (mtmm)
REVERT: B  123 MET cc_start: 0.8884 (tmm) cc_final: 0.8516 (tmm)
REVERT: B  146 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8108 (mm-40)
REVERT: B  150 CYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8908 (p)
REVERT: B  153 MET cc_start: 0.9179 (mtm) cc_final: 0.8693 (mtp)
REVERT: B  256 MET cc_start: 0.9102 (mmm) cc_final: 0.8840 (mmm)
REVERT: B  310 GLN cc_start: 0.7588 (mt0) cc_final: 0.7265 (mp10)
REVERT: B  508 LEU cc_start: 0.8562 (tp) cc_final: 0.8079 (tt)
REVERT: B  617 MET cc_start: 0.8270 (tpt) cc_final: 0.7743 (tpp)
REVERT: B  639 MET cc_start: 0.7356 (mmt) cc_final: 0.6490 (tmm)
REVERT: B  645 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7896 (mp10)
REVERT: B  676 GLU cc_start: 0.8084 (tp30) cc_final: 0.7696 (tp30)
  outliers start: 23
  outliers final: 16
  residues processed: 167
  average time/residue: 0.0643
  time to fit residues: 14.9847
Evaluate side-chains
  167 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  206 HIS
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  206 HIS
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   chunk 10 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0570
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.103915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.084783 restraints weight = 15634.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.087146 restraints weight = 9169.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.088667 restraints weight = 6467.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.089753 restraints weight = 5164.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.090306 restraints weight = 4441.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6342  Z= 0.102
  Angle     :  0.548   8.850   8610  Z= 0.272
  Chirality :  0.035   0.139   1046
  Planarity :  0.003   0.029   1048
  Dihedral  :  3.927  20.899    862
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 27.48 %
    Favored  : 70.61 %
  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 are not related in a simple way.
  whole:  0.87 (0.33), residues: 696
  helix:  1.73 (0.22), residues: 532
  sheet: -5.28 (0.40), residues: 20
  loop : -3.06 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 609 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.022   0.001   PHE A 545 
 TRP   0.053   0.002   TRP B 184 
 HIS   0.002   0.000   HIS B 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 6342)
  covalent geometry    : angle       0.54826 ( 8610)
  hydrogen bonds       : bond        0.03251 (  433)
  hydrogen bonds       : angle       3.32733 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8474 (mttt) cc_final: 0.7672 (mtmm)
REVERT: A  150 CYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8879 (p)
REVERT: A  153 MET cc_start: 0.9164 (mtm) cc_final: 0.8690 (mtp)
REVERT: A  170 GLN cc_start: 0.8194 (mp10) cc_final: 0.7977 (mp10)
REVERT: A  310 GLN cc_start: 0.7716 (mt0) cc_final: 0.7371 (mp10)
REVERT: A  508 LEU cc_start: 0.8448 (tp) cc_final: 0.8054 (tt)
REVERT: A  617 MET cc_start: 0.8279 (tpt) cc_final: 0.7361 (tpp)
REVERT: A  639 MET cc_start: 0.7305 (mmt) cc_final: 0.6352 (tmm)
REVERT: A  666 TYR cc_start: 0.9503 (t80) cc_final: 0.9188 (t80)
REVERT: A  676 GLU cc_start: 0.8069 (tp30) cc_final: 0.7672 (tp30)
REVERT: B  109 LYS cc_start: 0.8384 (mttt) cc_final: 0.7500 (mtmm)
REVERT: B  123 MET cc_start: 0.8765 (tmm) cc_final: 0.8355 (tmm)
REVERT: B  150 CYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8957 (p)
REVERT: B  153 MET cc_start: 0.9162 (mtm) cc_final: 0.8725 (mtp)
REVERT: B  310 GLN cc_start: 0.7712 (mt0) cc_final: 0.7351 (mp10)
REVERT: B  617 MET cc_start: 0.8326 (tpt) cc_final: 0.7425 (tpp)
REVERT: B  639 MET cc_start: 0.7315 (mmt) cc_final: 0.6437 (tmm)
REVERT: B  645 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7873 (mp10)
REVERT: B  676 GLU cc_start: 0.8073 (tp30) cc_final: 0.7677 (tp30)
  outliers start: 12
  outliers final: 7
  residues processed: 174
  average time/residue: 0.0624
  time to fit residues: 14.9898
Evaluate side-chains
  159 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 6 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.104219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.083953 restraints weight = 16101.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.086455 restraints weight = 9230.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.087889 restraints weight = 6497.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.089222 restraints weight = 5231.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.089870 restraints weight = 4477.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.4611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6342  Z= 0.108
  Angle     :  0.563   8.404   8610  Z= 0.284
  Chirality :  0.036   0.210   1046
  Planarity :  0.003   0.031   1048
  Dihedral  :  3.885  21.042    862
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 27.16 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.33), residues: 696
  helix:  1.83 (0.22), residues: 532
  sheet: -5.06 (0.45), residues: 20
  loop : -3.08 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 667 
 TYR   0.013   0.001   TYR B 678 
 PHE   0.010   0.001   PHE B 222 
 TRP   0.060   0.002   TRP A 184 
 HIS   0.002   0.000   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6342)
  covalent geometry    : angle       0.56308 ( 8610)
  hydrogen bonds       : bond        0.03260 (  433)
  hydrogen bonds       : angle       3.26397 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8561 (mttt) cc_final: 0.7718 (mtmm)
REVERT: A  150 CYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8879 (p)
REVERT: A  310 GLN cc_start: 0.7747 (mt0) cc_final: 0.7318 (mp10)
REVERT: A  508 LEU cc_start: 0.8387 (tp) cc_final: 0.8028 (tt)
REVERT: A  617 MET cc_start: 0.8356 (tpt) cc_final: 0.7691 (tpp)
REVERT: A  639 MET cc_start: 0.7465 (mmt) cc_final: 0.6367 (tmm)
REVERT: A  676 GLU cc_start: 0.8185 (tp30) cc_final: 0.7781 (tp30)
REVERT: B  109 LYS cc_start: 0.8348 (mttt) cc_final: 0.7526 (mtmm)
REVERT: B  123 MET cc_start: 0.8834 (tmm) cc_final: 0.8426 (tmm)
REVERT: B  150 CYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8931 (p)
REVERT: B  153 MET cc_start: 0.9195 (mtm) cc_final: 0.8838 (mtp)
REVERT: B  310 GLN cc_start: 0.7764 (mt0) cc_final: 0.7352 (mp10)
REVERT: B  508 LEU cc_start: 0.8443 (tp) cc_final: 0.8223 (tt)
REVERT: B  617 MET cc_start: 0.8363 (tpt) cc_final: 0.7693 (tpp)
REVERT: B  639 MET cc_start: 0.7426 (mmt) cc_final: 0.6436 (tmm)
REVERT: B  645 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7924 (mp10)
REVERT: B  676 GLU cc_start: 0.8207 (tp30) cc_final: 0.7790 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 157
  average time/residue: 0.0612
  time to fit residues: 13.2614
Evaluate side-chains
  153 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0670
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   overall best weight:    0.5920

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

Flipped N/Q/H residues before XYZ refinement:
B 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.104709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.084504 restraints weight = 16008.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.086674 restraints weight = 9352.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.088408 restraints weight = 6832.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.089343 restraints weight = 5445.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.090224 restraints weight = 4742.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.4745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6342  Z= 0.108
  Angle     :  0.601  13.895   8610  Z= 0.292
  Chirality :  0.036   0.206   1046
  Planarity :  0.003   0.034   1048
  Dihedral  :  3.822  20.212    862
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 27.80 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.07 (0.33), residues: 696
  helix:  1.79 (0.22), residues: 544
  sheet: -4.73 (0.55), residues: 20
  loop : -3.11 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 667 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.022   0.001   PHE A 545 
 TRP   0.069   0.003   TRP A 184 
 HIS   0.002   0.000   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6342)
  covalent geometry    : angle       0.60063 ( 8610)
  hydrogen bonds       : bond        0.03288 (  433)
  hydrogen bonds       : angle       3.33753 ( 1299)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8532 (mttt) cc_final: 0.7691 (mtmm)
REVERT: A  150 CYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8763 (p)
REVERT: A  153 MET cc_start: 0.8836 (mtp) cc_final: 0.8571 (mtp)
REVERT: A  170 GLN cc_start: 0.8183 (mp10) cc_final: 0.7933 (mp10)
REVERT: A  186 LYS cc_start: 0.9107 (tttt) cc_final: 0.8826 (mtpt)
REVERT: A  310 GLN cc_start: 0.7805 (mt0) cc_final: 0.7432 (mp10)
REVERT: A  508 LEU cc_start: 0.8418 (tp) cc_final: 0.8079 (tt)
REVERT: A  617 MET cc_start: 0.8354 (tpt) cc_final: 0.7350 (ptm)
REVERT: A  639 MET cc_start: 0.7388 (mmt) cc_final: 0.6312 (tmm)
REVERT: A  676 GLU cc_start: 0.8223 (tp30) cc_final: 0.7785 (tp30)
REVERT: B  109 LYS cc_start: 0.8320 (mttt) cc_final: 0.7531 (mtmm)
REVERT: B  123 MET cc_start: 0.8806 (tmm) cc_final: 0.8389 (tmm)
REVERT: B  150 CYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8937 (p)
REVERT: B  153 MET cc_start: 0.9169 (mtm) cc_final: 0.8801 (mtp)
REVERT: B  310 GLN cc_start: 0.7831 (mt0) cc_final: 0.7442 (mp10)
REVERT: B  508 LEU cc_start: 0.8439 (tp) cc_final: 0.8189 (tt)
REVERT: B  617 MET cc_start: 0.8354 (tpt) cc_final: 0.7315 (ptm)
REVERT: B  639 MET cc_start: 0.7358 (mmt) cc_final: 0.6387 (tmm)
REVERT: B  645 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7960 (mp10)
REVERT: B  676 GLU cc_start: 0.8200 (tp30) cc_final: 0.7776 (tp30)
  outliers start: 13
  outliers final: 8
  residues processed: 162
  average time/residue: 0.0607
  time to fit residues: 13.7234
Evaluate side-chains
  156 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  206 HIS
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  150 CYS
Chi-restraints excluded: chain B residue  206 HIS
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.100309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.079360 restraints weight = 15844.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.081532 restraints weight = 9795.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.082766 restraints weight = 7192.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.083947 restraints weight = 5975.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.084217 restraints weight = 5224.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6342  Z= 0.237
  Angle     :  0.713  12.936   8610  Z= 0.357
  Chirality :  0.040   0.184   1046
  Planarity :  0.003   0.031   1048
  Dihedral  :  4.211  21.740    862
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 27.00 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.33), residues: 696
  helix:  1.48 (0.22), residues: 542
  sheet: -5.18 (0.49), residues: 20
  loop : -2.88 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 610 
 TYR   0.021   0.002   TYR A 678 
 PHE   0.021   0.002   PHE A 545 
 TRP   0.070   0.003   TRP B 184 
 HIS   0.005   0.001   HIS B 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 6342)
  covalent geometry    : angle       0.71334 ( 8610)
  hydrogen bonds       : bond        0.04459 (  433)
  hydrogen bonds       : angle       3.81215 ( 1299)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 934.28 seconds
wall clock time: 16 minutes 52.59 seconds (1012.59 seconds total)