Starting phenix.real_space_refine
on Tue Feb 11 15:43:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6o84_0650/02_2025/6o84_0650.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6o84_0650/02_2025/6o84_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6o84_0650/02_2025/6o84_0650.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6o84_0650/02_2025/6o84_0650.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6o84_0650/02_2025/6o84_0650.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6o84_0650/02_2025/6o84_0650.cif"
  }
  resolution = 3.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.15, per 1000 atoms: 0.83
  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: 1.30
  Conformation dependent library (CDL) restraints added in 741.4 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: 0.53
  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: 1.63

  Time building geometry restraints manager: 1.54 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: 0.03
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:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.080
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.170
-------------------------------------------------------------------------------
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= 0.316
  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 : 2.97
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.002   TRP B 159 
 HIS   0.004   0.001   HIS B 635 
 PHE   0.010   0.002   PHE A 665 
 TYR   0.010   0.002   TYR B 647 
 ARG   0.001   0.000   ARG A 567 

*********************** 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  : 0.634 
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: 0.8387 (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: 0.9171 (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: 0.1448
  time to fit residues: 37.8742
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  : 0.671 
-------------------------------------------------------------------------------
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 33 optimal weight:    7.9990
   chunk 30 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 20 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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 = 0.3510 r_free = 0.3510 target = 0.102578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.081630 restraints weight = 15609.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.083577 restraints weight = 10189.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.084711 restraints weight = 7824.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6342  Z= 0.251
  Angle     :  0.632   6.185   8610  Z= 0.334
  Chirality :  0.038   0.155   1046
  Planarity :  0.004   0.031   1048
  Dihedral  :  5.401  45.116    868
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.93 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.29), residues: 696
  helix: -0.41 (0.20), residues: 528
  sheet: -5.44 (0.45), residues: 20
  loop : -3.32 (0.45), residues: 148

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

*********************** 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
  179 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8218 (mttt) cc_final: 0.7814 (pttm)
REVERT: A  150 CYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8940 (p)
REVERT: A  153 MET cc_start: 0.9150 (mtm) cc_final: 0.8698 (mtp)
REVERT: A  508 LEU cc_start: 0.8549 (tp) cc_final: 0.8040 (tt)
REVERT: A  613 LYS cc_start: 0.8162 (tmtt) cc_final: 0.7740 (tmtt)
REVERT: A  617 MET cc_start: 0.8363 (tpt) cc_final: 0.7770 (tpp)
REVERT: A  639 MET cc_start: 0.7566 (mmt) cc_final: 0.6600 (tmm)
REVERT: B  109 LYS cc_start: 0.8257 (mttt) cc_final: 0.7908 (pttm)
REVERT: B  150 CYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8935 (p)
REVERT: B  153 MET cc_start: 0.9149 (mtm) cc_final: 0.8701 (mtp)
REVERT: B  256 MET cc_start: 0.9027 (mmm) cc_final: 0.8794 (mmm)
REVERT: B  508 LEU cc_start: 0.8563 (tp) cc_final: 0.8285 (tt)
REVERT: B  613 LYS cc_start: 0.8142 (tmtt) cc_final: 0.7717 (tmtt)
REVERT: B  617 MET cc_start: 0.8315 (tpt) cc_final: 0.7737 (tpp)
REVERT: B  639 MET cc_start: 0.7539 (mmt) cc_final: 0.6612 (tmm)
REVERT: B  645 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7855 (mp10)
  outliers start: 14
  outliers final: 8
  residues processed: 171
  average time/residue: 0.1405
  time to fit residues: 33.2489
Evaluate side-chains
  149 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0050
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   overall best weight:    0.9798

-------------------------------------------------------------------------------
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 = 0.3495 r_free = 0.3495 target = 0.102354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.082592 restraints weight = 15713.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.084769 restraints weight = 9507.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.085980 restraints weight = 6868.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3239

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= 0.149
  Angle     :  0.518   6.768   8610  Z= 0.269
  Chirality :  0.035   0.136   1046
  Planarity :  0.003   0.025   1048
  Dihedral  :  4.629  33.343    868
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 22.20 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.31), residues: 696
  helix:  0.65 (0.22), residues: 534
  sheet: -5.38 (0.39), residues: 20
  loop : -3.24 (0.47), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 184 
 HIS   0.002   0.000   HIS B 178 
 PHE   0.012   0.001   PHE A 221 
 TYR   0.010   0.001   TYR A 162 
 ARG   0.001   0.000   ARG A 252 

*********************** 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
  183 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 172
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8271 (mttt) cc_final: 0.7754 (pttm)
REVERT: A  153 MET cc_start: 0.9201 (mtm) cc_final: 0.8716 (mtp)
REVERT: A  170 GLN cc_start: 0.8128 (mp10) cc_final: 0.7755 (mp10)
REVERT: A  335 LYS cc_start: 0.9251 (ttpt) cc_final: 0.8971 (ttpp)
REVERT: A  508 LEU cc_start: 0.8400 (tp) cc_final: 0.7934 (tt)
REVERT: A  617 MET cc_start: 0.8359 (tpt) cc_final: 0.7383 (tpp)
REVERT: A  639 MET cc_start: 0.7525 (mmt) cc_final: 0.6666 (tmm)
REVERT: A  676 GLU cc_start: 0.7987 (tp30) cc_final: 0.7473 (tp30)
REVERT: B  109 LYS cc_start: 0.8486 (mttt) cc_final: 0.7620 (mtmm)
REVERT: B  153 MET cc_start: 0.9213 (mtm) cc_final: 0.8742 (mtp)
REVERT: B  170 GLN cc_start: 0.8129 (mp10) cc_final: 0.7743 (mp10)
REVERT: B  256 MET cc_start: 0.9121 (mmm) cc_final: 0.8911 (mmm)
REVERT: B  335 LYS cc_start: 0.9224 (ttpt) cc_final: 0.8977 (ttpp)
REVERT: B  508 LEU cc_start: 0.8497 (tp) cc_final: 0.8132 (tt)
REVERT: B  617 MET cc_start: 0.8303 (tpt) cc_final: 0.7714 (tpp)
REVERT: B  639 MET cc_start: 0.7521 (mmt) cc_final: 0.6603 (tmm)
REVERT: B  645 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7863 (mp10)
REVERT: B  676 GLU cc_start: 0.7984 (tp30) cc_final: 0.7477 (tp30)
  outliers start: 11
  outliers final: 3
  residues processed: 179
  average time/residue: 0.1706
  time to fit residues: 41.4488
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  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0000
   chunk 36 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    2.3992

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.099916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.079910 restraints weight = 15867.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.082045 restraints weight = 9391.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.083590 restraints weight = 6751.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6342  Z= 0.213
  Angle     :  0.562   8.023   8610  Z= 0.291
  Chirality :  0.036   0.124   1046
  Planarity :  0.003   0.025   1048
  Dihedral  :  4.234  23.148    862
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 23.48 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.32), residues: 696
  helix:  1.16 (0.22), residues: 534
  sheet: -5.32 (0.42), residues: 20
  loop : -3.14 (0.48), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 184 
 HIS   0.003   0.001   HIS A 206 
 PHE   0.019   0.001   PHE A 545 
 TYR   0.019   0.002   TYR B 678 
 ARG   0.001   0.000   ARG A 252 

*********************** 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
  169 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8310 (mttt) cc_final: 0.7878 (pttm)
REVERT: A  123 MET cc_start: 0.8837 (tmm) cc_final: 0.8409 (tmm)
REVERT: A  150 CYS cc_start: 0.9213 (p) cc_final: 0.8953 (p)
REVERT: A  153 MET cc_start: 0.9218 (mtm) cc_final: 0.8747 (mtp)
REVERT: A  170 GLN cc_start: 0.8140 (mp10) cc_final: 0.7771 (mp10)
REVERT: A  310 GLN cc_start: 0.7559 (mt0) cc_final: 0.7288 (mp10)
REVERT: A  335 LYS cc_start: 0.9390 (ttpt) cc_final: 0.9136 (ttpp)
REVERT: A  508 LEU cc_start: 0.8430 (tp) cc_final: 0.7913 (tt)
REVERT: A  617 MET cc_start: 0.8329 (tpt) cc_final: 0.7403 (tpp)
REVERT: A  639 MET cc_start: 0.7605 (mmt) cc_final: 0.6699 (tmm)
REVERT: A  676 GLU cc_start: 0.8081 (tp30) cc_final: 0.7760 (tp30)
REVERT: B  109 LYS cc_start: 0.8558 (mttt) cc_final: 0.7736 (mtmm)
REVERT: B  150 CYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8983 (p)
REVERT: B  153 MET cc_start: 0.9216 (mtm) cc_final: 0.8764 (mtp)
REVERT: B  170 GLN cc_start: 0.8142 (mp10) cc_final: 0.7771 (mp10)
REVERT: B  256 MET cc_start: 0.9126 (mmm) cc_final: 0.8878 (mmm)
REVERT: B  310 GLN cc_start: 0.7549 (mt0) cc_final: 0.7292 (mp10)
REVERT: B  508 LEU cc_start: 0.8599 (tp) cc_final: 0.8122 (tt)
REVERT: B  617 MET cc_start: 0.8347 (tpt) cc_final: 0.7807 (tpp)
REVERT: B  639 MET cc_start: 0.7661 (mmt) cc_final: 0.6637 (tmm)
REVERT: B  645 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7860 (mp10)
REVERT: B  676 GLU cc_start: 0.8088 (tp30) cc_final: 0.7540 (tp30)
  outliers start: 16
  outliers final: 10
  residues processed: 163
  average time/residue: 0.1531
  time to fit residues: 33.6087
Evaluate side-chains
  155 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
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  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  208 LEU
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  645 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 206 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.101489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.082321 restraints weight = 15649.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.084479 restraints weight = 9340.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.085790 restraints weight = 6689.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3862

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= 0.157
  Angle     :  0.511   7.150   8610  Z= 0.265
  Chirality :  0.035   0.125   1046
  Planarity :  0.002   0.026   1048
  Dihedral  :  4.052  22.097    862
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 24.76 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.32), residues: 696
  helix:  1.48 (0.22), residues: 532
  sheet: -5.29 (0.41), residues: 20
  loop : -3.12 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 184 
 HIS   0.002   0.000   HIS A 206 
 PHE   0.010   0.001   PHE A 222 
 TYR   0.010   0.001   TYR A 162 
 ARG   0.001   0.000   ARG B 506 

*********************** 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
  176 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8453 (mttt) cc_final: 0.7897 (pttm)
REVERT: A  123 MET cc_start: 0.8805 (tmm) cc_final: 0.8390 (tmm)
REVERT: A  150 CYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8876 (p)
REVERT: A  153 MET cc_start: 0.9187 (mtm) cc_final: 0.8705 (mtp)
REVERT: A  170 GLN cc_start: 0.8194 (mp10) cc_final: 0.7829 (mp10)
REVERT: A  310 GLN cc_start: 0.7559 (mt0) cc_final: 0.7208 (mp10)
REVERT: A  335 LYS cc_start: 0.9333 (ttpt) cc_final: 0.9129 (ttpp)
REVERT: A  508 LEU cc_start: 0.8438 (tp) cc_final: 0.8107 (tt)
REVERT: A  617 MET cc_start: 0.8343 (tpt) cc_final: 0.7500 (ptm)
REVERT: A  639 MET cc_start: 0.7426 (mmt) cc_final: 0.6530 (tmm)
REVERT: A  676 GLU cc_start: 0.8063 (tp30) cc_final: 0.7500 (tp30)
REVERT: B  109 LYS cc_start: 0.8286 (mttt) cc_final: 0.7532 (mtmm)
REVERT: B  123 MET cc_start: 0.8846 (tmm) cc_final: 0.8439 (tmm)
REVERT: B  150 CYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8906 (p)
REVERT: B  153 MET cc_start: 0.9198 (mtm) cc_final: 0.8698 (mtp)
REVERT: B  170 GLN cc_start: 0.8194 (mp10) cc_final: 0.7831 (mp10)
REVERT: B  256 MET cc_start: 0.9144 (mmm) cc_final: 0.8881 (mmm)
REVERT: B  310 GLN cc_start: 0.7635 (mt0) cc_final: 0.7301 (mp10)
REVERT: B  335 LYS cc_start: 0.9293 (ttpt) cc_final: 0.9071 (ttpp)
REVERT: B  508 LEU cc_start: 0.8551 (tp) cc_final: 0.8105 (tt)
REVERT: B  617 MET cc_start: 0.8427 (tpt) cc_final: 0.7886 (tpp)
REVERT: B  639 MET cc_start: 0.7443 (mmt) cc_final: 0.6472 (tmm)
REVERT: B  645 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7797 (mp10)
REVERT: B  676 GLU cc_start: 0.8039 (tp30) cc_final: 0.7691 (tp30)
  outliers start: 13
  outliers final: 10
  residues processed: 170
  average time/residue: 0.1523
  time to fit residues: 35.0038
Evaluate side-chains
  161 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
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  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  315 MET
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 35 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 206 HIS
B 206 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.102895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.083267 restraints weight = 15618.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.085472 restraints weight = 9460.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.086898 restraints weight = 6853.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4047

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= 0.139
  Angle     :  0.511   8.309   8610  Z= 0.266
  Chirality :  0.034   0.141   1046
  Planarity :  0.003   0.028   1048
  Dihedral  :  3.978  22.229    862
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 25.72 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.33), residues: 696
  helix:  1.67 (0.22), residues: 532
  sheet: -5.28 (0.38), residues: 20
  loop : -3.11 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP B 184 
 HIS   0.003   0.001   HIS A 206 
 PHE   0.036   0.001   PHE A 222 
 TYR   0.008   0.001   TYR A 162 
 ARG   0.000   0.000   ARG A 506 

*********************** 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
  179 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8411 (mttt) cc_final: 0.7591 (mtmm)
REVERT: A  123 MET cc_start: 0.8781 (tmm) cc_final: 0.8359 (tmm)
REVERT: A  150 CYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8892 (p)
REVERT: A  153 MET cc_start: 0.9145 (mtm) cc_final: 0.8614 (mtp)
REVERT: A  170 GLN cc_start: 0.8198 (mp10) cc_final: 0.7874 (mp10)
REVERT: A  310 GLN cc_start: 0.7577 (mt0) cc_final: 0.7216 (mp10)
REVERT: A  508 LEU cc_start: 0.8469 (tp) cc_final: 0.8128 (tt)
REVERT: A  617 MET cc_start: 0.8388 (tpt) cc_final: 0.7955 (tpp)
REVERT: A  639 MET cc_start: 0.7390 (mmt) cc_final: 0.6478 (tmm)
REVERT: A  676 GLU cc_start: 0.8022 (tp30) cc_final: 0.7695 (tp30)
REVERT: B  109 LYS cc_start: 0.8338 (mttt) cc_final: 0.7518 (mtmm)
REVERT: B  123 MET cc_start: 0.8850 (tmm) cc_final: 0.8498 (tmm)
REVERT: B  150 CYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8886 (p)
REVERT: B  153 MET cc_start: 0.9141 (mtm) cc_final: 0.8592 (mtp)
REVERT: B  170 GLN cc_start: 0.8179 (mp10) cc_final: 0.7868 (mp10)
REVERT: B  256 MET cc_start: 0.9132 (mmm) cc_final: 0.8874 (mmm)
REVERT: B  310 GLN cc_start: 0.7484 (mt0) cc_final: 0.7200 (mp10)
REVERT: B  335 LYS cc_start: 0.9253 (ttpt) cc_final: 0.9044 (ttpp)
REVERT: B  508 LEU cc_start: 0.8535 (tp) cc_final: 0.8066 (tt)
REVERT: B  617 MET cc_start: 0.8378 (tpt) cc_final: 0.7773 (tpp)
REVERT: B  639 MET cc_start: 0.7360 (mmt) cc_final: 0.6469 (tmm)
REVERT: B  645 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7803 (mp10)
REVERT: B  676 GLU cc_start: 0.7989 (tp30) cc_final: 0.7614 (tp30)
  outliers start: 17
  outliers final: 10
  residues processed: 171
  average time/residue: 0.1527
  time to fit residues: 35.6240
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  : 0.717 
-------------------------------------------------------------------------------
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  183 MET
Chi-restraints excluded: chain B residue  206 HIS
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 34 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 36 optimal weight:    0.0030
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    2.5194

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

Flipped N/Q/H residues before XYZ refinement:
B 206 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.100280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.080877 restraints weight = 15771.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.083043 restraints weight = 9476.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.084303 restraints weight = 6838.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6342  Z= 0.215
  Angle     :  0.553   7.155   8610  Z= 0.288
  Chirality :  0.036   0.144   1046
  Planarity :  0.003   0.027   1048
  Dihedral  :  4.023  22.695    862
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 25.24 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.33), residues: 696
  helix:  1.71 (0.23), residues: 528
  sheet: -5.42 (0.37), residues: 20
  loop : -2.92 (0.47), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 184 
 HIS   0.007   0.001   HIS B 206 
 PHE   0.019   0.001   PHE A 222 
 TYR   0.009   0.001   TYR A 647 
 ARG   0.001   0.000   ARG A 667 

*********************** 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
  167 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8492 (mttt) cc_final: 0.7680 (mtmm)
REVERT: A  123 MET cc_start: 0.8872 (tmm) cc_final: 0.8507 (tmm)
REVERT: A  150 CYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8894 (p)
REVERT: A  153 MET cc_start: 0.9142 (mtm) cc_final: 0.8641 (mtp)
REVERT: A  310 GLN cc_start: 0.7626 (mt0) cc_final: 0.7279 (mp10)
REVERT: A  508 LEU cc_start: 0.8472 (tp) cc_final: 0.8094 (tt)
REVERT: A  617 MET cc_start: 0.8326 (tpt) cc_final: 0.7859 (tpp)
REVERT: A  639 MET cc_start: 0.7499 (mmt) cc_final: 0.6514 (tmm)
REVERT: A  676 GLU cc_start: 0.8056 (tp30) cc_final: 0.7662 (tp30)
REVERT: B  109 LYS cc_start: 0.8325 (mttt) cc_final: 0.7586 (mtmm)
REVERT: B  123 MET cc_start: 0.8926 (tmm) cc_final: 0.8622 (tmm)
REVERT: B  150 CYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8890 (p)
REVERT: B  153 MET cc_start: 0.9129 (mtm) cc_final: 0.8596 (mtp)
REVERT: B  256 MET cc_start: 0.9125 (mmm) cc_final: 0.8855 (mmm)
REVERT: B  310 GLN cc_start: 0.7623 (mt0) cc_final: 0.7322 (mp10)
REVERT: B  617 MET cc_start: 0.8352 (tpt) cc_final: 0.7756 (tpp)
REVERT: B  639 MET cc_start: 0.7444 (mmt) cc_final: 0.6480 (tmm)
REVERT: B  645 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7807 (mp10)
REVERT: B  676 GLU cc_start: 0.8016 (tp30) cc_final: 0.7407 (tp30)
  outliers start: 21
  outliers final: 14
  residues processed: 159
  average time/residue: 0.1607
  time to fit residues: 35.1789
Evaluate side-chains
  163 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
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  183 MET
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  511 THR
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 6 optimal weight:   20.0000
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0570
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.5702

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.101471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.080414 restraints weight = 16030.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.082433 restraints weight = 9633.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.084134 restraints weight = 7238.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6342  Z= 0.165
  Angle     :  0.536   9.388   8610  Z= 0.274
  Chirality :  0.036   0.136   1046
  Planarity :  0.003   0.028   1048
  Dihedral  :  3.945  22.471    862
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 27.64 %
    Favored  : 69.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.33), residues: 696
  helix:  1.81 (0.22), residues: 532
  sheet: -5.49 (0.36), residues: 20
  loop : -2.92 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP B 184 
 HIS   0.002   0.001   HIS B 176 
 PHE   0.022   0.001   PHE B 545 
 TYR   0.008   0.001   TYR A 162 
 ARG   0.001   0.000   ARG A 667 

*********************** 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
  177 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8548 (mttt) cc_final: 0.7659 (mtmm)
REVERT: A  123 MET cc_start: 0.8897 (tmm) cc_final: 0.8498 (tmm)
REVERT: A  150 CYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8905 (p)
REVERT: A  153 MET cc_start: 0.9191 (mtm) cc_final: 0.8740 (mtp)
REVERT: A  170 GLN cc_start: 0.8206 (mp10) cc_final: 0.7774 (mp10)
REVERT: A  310 GLN cc_start: 0.7767 (mt0) cc_final: 0.7346 (mp10)
REVERT: A  508 LEU cc_start: 0.8498 (tp) cc_final: 0.8112 (tt)
REVERT: A  617 MET cc_start: 0.8392 (tpt) cc_final: 0.7945 (tpp)
REVERT: A  639 MET cc_start: 0.7547 (mmt) cc_final: 0.6465 (tmm)
REVERT: A  676 GLU cc_start: 0.8178 (tp30) cc_final: 0.7779 (tp30)
REVERT: B  109 LYS cc_start: 0.8368 (mttt) cc_final: 0.7569 (mtmm)
REVERT: B  123 MET cc_start: 0.8969 (tmm) cc_final: 0.8692 (tmm)
REVERT: B  150 CYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8905 (p)
REVERT: B  153 MET cc_start: 0.9187 (mtm) cc_final: 0.8705 (mtp)
REVERT: B  170 GLN cc_start: 0.8203 (mp10) cc_final: 0.7769 (mp10)
REVERT: B  256 MET cc_start: 0.9162 (mmm) cc_final: 0.8893 (mmm)
REVERT: B  310 GLN cc_start: 0.7701 (mt0) cc_final: 0.7339 (mp10)
REVERT: B  508 LEU cc_start: 0.8577 (tp) cc_final: 0.8151 (tt)
REVERT: B  617 MET cc_start: 0.8418 (tpt) cc_final: 0.7856 (tpp)
REVERT: B  639 MET cc_start: 0.7516 (mmt) cc_final: 0.6492 (tmm)
REVERT: B  645 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7804 (mp10)
REVERT: B  676 GLU cc_start: 0.8173 (tp30) cc_final: 0.7803 (tp30)
  outliers start: 19
  outliers final: 14
  residues processed: 168
  average time/residue: 0.1556
  time to fit residues: 35.3247
Evaluate side-chains
  167 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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  183 MET
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain B residue  323 SER
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 22 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.103458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.083515 restraints weight = 15671.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.085763 restraints weight = 9573.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.087132 restraints weight = 6976.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6342  Z= 0.146
  Angle     :  0.539  10.783   8610  Z= 0.274
  Chirality :  0.035   0.146   1046
  Planarity :  0.003   0.028   1048
  Dihedral  :  3.869  21.345    862
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 28.12 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.33), residues: 696
  helix:  1.97 (0.22), residues: 532
  sheet: -5.32 (0.39), residues: 20
  loop : -2.97 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 184 
 HIS   0.001   0.000   HIS B 635 
 PHE   0.012   0.001   PHE A 222 
 TYR   0.010   0.001   TYR A 162 
 ARG   0.001   0.000   ARG A 252 

*********************** 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
  180 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8508 (mttt) cc_final: 0.7705 (mtmm)
REVERT: A  123 MET cc_start: 0.8790 (tmm) cc_final: 0.8426 (tmm)
REVERT: A  150 CYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8904 (p)
REVERT: A  153 MET cc_start: 0.9057 (mtm) cc_final: 0.8787 (mtp)
REVERT: A  170 GLN cc_start: 0.8210 (mp10) cc_final: 0.7898 (mp10)
REVERT: A  256 MET cc_start: 0.9059 (mmm) cc_final: 0.8774 (mmm)
REVERT: A  310 GLN cc_start: 0.7761 (mt0) cc_final: 0.7415 (mp10)
REVERT: A  508 LEU cc_start: 0.8494 (tp) cc_final: 0.8097 (tt)
REVERT: A  617 MET cc_start: 0.8343 (tpt) cc_final: 0.7607 (tpp)
REVERT: A  639 MET cc_start: 0.7325 (mmt) cc_final: 0.6335 (tmm)
REVERT: A  676 GLU cc_start: 0.8076 (tp30) cc_final: 0.7680 (tp30)
REVERT: B  109 LYS cc_start: 0.8395 (mttt) cc_final: 0.7530 (mtmm)
REVERT: B  123 MET cc_start: 0.8863 (tmm) cc_final: 0.8581 (tmm)
REVERT: B  150 CYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8906 (p)
REVERT: B  152 LEU cc_start: 0.9559 (mt) cc_final: 0.9346 (mt)
REVERT: B  153 MET cc_start: 0.9104 (mtm) cc_final: 0.8760 (mtp)
REVERT: B  170 GLN cc_start: 0.8224 (mp10) cc_final: 0.7873 (mp10)
REVERT: B  310 GLN cc_start: 0.7739 (mt0) cc_final: 0.7353 (mp10)
REVERT: B  335 LYS cc_start: 0.9257 (ttpt) cc_final: 0.8972 (ttpp)
REVERT: B  617 MET cc_start: 0.8398 (tpt) cc_final: 0.7728 (tpp)
REVERT: B  639 MET cc_start: 0.7265 (mmt) cc_final: 0.6347 (tmm)
REVERT: B  645 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7790 (mp10)
REVERT: B  676 GLU cc_start: 0.8048 (tp30) cc_final: 0.7643 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 173
  average time/residue: 0.1489
  time to fit residues: 34.9758
Evaluate side-chains
  163 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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  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  323 SER
Chi-restraints excluded: chain B residue  511 THR
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 2 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 17 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.102680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.082219 restraints weight = 15964.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.084416 restraints weight = 9725.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.085818 restraints weight = 7144.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6342  Z= 0.158
  Angle     :  0.567  11.402   8610  Z= 0.281
  Chirality :  0.035   0.127   1046
  Planarity :  0.003   0.030   1048
  Dihedral  :  3.830  21.209    862
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 28.59 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.33), residues: 696
  helix:  2.04 (0.22), residues: 532
  sheet: -5.17 (0.44), residues: 20
  loop : -3.11 (0.43), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP B 184 
 HIS   0.001   0.000   HIS A 175 
 PHE   0.024   0.001   PHE B 545 
 TYR   0.009   0.001   TYR A 162 
 ARG   0.001   0.000   ARG B 667 

********************** 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
  172 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8543 (mttt) cc_final: 0.7718 (mtmm)
REVERT: A  123 MET cc_start: 0.8847 (tmm) cc_final: 0.8459 (tmm)
REVERT: A  150 CYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8943 (p)
REVERT: A  153 MET cc_start: 0.9126 (mtm) cc_final: 0.8867 (mtp)
REVERT: A  170 GLN cc_start: 0.8183 (mp10) cc_final: 0.7860 (mp10)
REVERT: A  256 MET cc_start: 0.9074 (mmm) cc_final: 0.8761 (mmm)
REVERT: A  310 GLN cc_start: 0.7834 (mt0) cc_final: 0.7409 (mp10)
REVERT: A  508 LEU cc_start: 0.8485 (tp) cc_final: 0.8102 (tt)
REVERT: A  617 MET cc_start: 0.8359 (tpt) cc_final: 0.7626 (tpp)
REVERT: A  639 MET cc_start: 0.7383 (mmt) cc_final: 0.6336 (tmm)
REVERT: A  666 TYR cc_start: 0.9485 (t80) cc_final: 0.9275 (t80)
REVERT: A  676 GLU cc_start: 0.8112 (tp30) cc_final: 0.7714 (tp30)
REVERT: B  109 LYS cc_start: 0.8459 (mttt) cc_final: 0.7633 (mtmm)
REVERT: B  123 MET cc_start: 0.8881 (tmm) cc_final: 0.8583 (tmm)
REVERT: B  150 CYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8925 (p)
REVERT: B  153 MET cc_start: 0.9145 (mtm) cc_final: 0.8860 (mtp)
REVERT: B  170 GLN cc_start: 0.8190 (mp10) cc_final: 0.7846 (mp10)
REVERT: B  310 GLN cc_start: 0.7824 (mt0) cc_final: 0.7393 (mp10)
REVERT: B  617 MET cc_start: 0.8439 (tpt) cc_final: 0.7805 (tpp)
REVERT: B  639 MET cc_start: 0.7346 (mmt) cc_final: 0.6352 (tmm)
REVERT: B  676 GLU cc_start: 0.8105 (tp30) cc_final: 0.7707 (tp30)
  outliers start: 17
  outliers final: 12
  residues processed: 166
  average time/residue: 0.1553
  time to fit residues: 34.9938
Evaluate side-chains
  163 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
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  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  206 HIS
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  511 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.0870
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0970
   overall best weight:    0.5556

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

Flipped N/Q/H residues before XYZ refinement:
B 176 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.103718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.084074 restraints weight = 15956.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.086438 restraints weight = 9166.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.087819 restraints weight = 6462.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6342  Z= 0.144
  Angle     :  0.570  11.354   8610  Z= 0.281
  Chirality :  0.035   0.127   1046
  Planarity :  0.003   0.032   1048
  Dihedral  :  3.757  20.762    862
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 28.27 %
    Favored  : 69.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.33), residues: 696
  helix:  2.04 (0.22), residues: 544
  sheet: -4.99 (0.50), residues: 20
  loop : -3.11 (0.46), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP B 184 
 HIS   0.002   0.000   HIS B 176 
 PHE   0.009   0.001   PHE A 222 
 TYR   0.009   0.001   TYR B 647 
 ARG   0.002   0.000   ARG B 644 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1783.83 seconds
wall clock time: 32 minutes 45.26 seconds (1965.26 seconds total)