Starting phenix.real_space_refine
on Sun Apr 27 16:18:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6o84_0650/04_2025/6o84_0650.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6o84_0650/04_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_0650/04_2025/6o84_0650.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6o84_0650/04_2025/6o84_0650.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6o84_0650/04_2025/6o84_0650.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6o84_0650/04_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-5669/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: 5.24, per 1000 atoms: 0.84
  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: 1.61
  Conformation dependent library (CDL) restraints added in 934.2 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: 0.57
  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: 2.24

  Time building geometry restraints manager: 1.85 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:             46.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.560
  Find NCS groups from input model:        0.140
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   69.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6342  Z= 0.245
  Angle     :  0.838   7.820   8610  Z= 0.480
  Chirality :  0.047   0.206   1046
  Planarity :  0.004   0.041   1048
  Dihedral  : 14.014  86.651   2130
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 2.97
  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 

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

*********************** 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  : 0.685 
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: 0.1653
  time to fit residues: 43.4453
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  : 0.721 
-------------------------------------------------------------------------------
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 = 41)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.081627 restraints weight = 15609.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.083529 restraints weight = 10203.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.084922 restraints weight = 7842.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
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= 0.181
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05666 (  433)
  hydrogen bonds       : angle       4.02852 ( 1299)
  covalent geometry    : bond        0.00395 ( 6342)
  covalent geometry    : angle       0.63221 ( 8610)

*********************** 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  : 0.577 
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: 0.8225 (mttt) cc_final: 0.7814 (pttm)
REVERT: A  150 CYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8945 (p)
REVERT: A  153 MET cc_start: 0.9162 (mtm) cc_final: 0.8716 (mtp)
REVERT: A  508 LEU cc_start: 0.8548 (tp) cc_final: 0.8038 (tt)
REVERT: A  613 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7745 (tmtt)
REVERT: A  617 MET cc_start: 0.8367 (tpt) cc_final: 0.7779 (tpp)
REVERT: A  639 MET cc_start: 0.7567 (mmt) cc_final: 0.6601 (tmm)
REVERT: B  109 LYS cc_start: 0.8258 (mttt) cc_final: 0.7905 (pttm)
REVERT: B  150 CYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8933 (p)
REVERT: B  153 MET cc_start: 0.9160 (mtm) cc_final: 0.8720 (mtp)
REVERT: B  256 MET cc_start: 0.9040 (mmm) cc_final: 0.8804 (mmm)
REVERT: B  508 LEU cc_start: 0.8559 (tp) cc_final: 0.8280 (tt)
REVERT: B  613 LYS cc_start: 0.8157 (tmtt) cc_final: 0.7735 (tmtt)
REVERT: B  617 MET cc_start: 0.8331 (tpt) cc_final: 0.7748 (tpp)
REVERT: B  639 MET cc_start: 0.7541 (mmt) cc_final: 0.6615 (tmm)
REVERT: B  645 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7854 (mp10)
  outliers start: 14
  outliers final: 8
  residues processed: 171
  average time/residue: 0.1348
  time to fit residues: 32.3471
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  : 0.871 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    9.9990
   overall best weight:    0.7722

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.102776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.082993 restraints weight = 15697.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.085241 restraints weight = 9402.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.086663 restraints weight = 6740.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3263

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= 0.108
  Angle     :  0.516   6.724   8610  Z= 0.267
  Chirality :  0.035   0.135   1046
  Planarity :  0.003   0.025   1048
  Dihedral  :  4.624  33.379    868
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 22.04 %
    Favored  : 76.20 %
  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: -0.52 (0.31), residues: 696
  helix:  0.66 (0.22), residues: 532
  sheet: -5.37 (0.39), residues: 20
  loop : -3.24 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 184 
 HIS   0.002   0.001   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 644 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04220 (  433)
  hydrogen bonds       : angle       3.48074 ( 1299)
  covalent geometry    : bond        0.00223 ( 6342)
  covalent geometry    : angle       0.51640 ( 8610)

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

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8292 (mttt) cc_final: 0.7738 (pttm)
REVERT: A  153 MET cc_start: 0.9209 (mtm) cc_final: 0.8727 (mtp)
REVERT: A  170 GLN cc_start: 0.8132 (mp10) cc_final: 0.7817 (mp10)
REVERT: A  335 LYS cc_start: 0.9248 (ttpt) cc_final: 0.8955 (ttpp)
REVERT: A  508 LEU cc_start: 0.8385 (tp) cc_final: 0.7912 (tt)
REVERT: A  617 MET cc_start: 0.8352 (tpt) cc_final: 0.7890 (tpp)
REVERT: A  639 MET cc_start: 0.7513 (mmt) cc_final: 0.6663 (tmm)
REVERT: A  676 GLU cc_start: 0.8003 (tp30) cc_final: 0.7494 (tp30)
REVERT: B  109 LYS cc_start: 0.8459 (mttt) cc_final: 0.7584 (mtmm)
REVERT: B  153 MET cc_start: 0.9220 (mtm) cc_final: 0.8755 (mtp)
REVERT: B  170 GLN cc_start: 0.8133 (mp10) cc_final: 0.7805 (mp10)
REVERT: B  256 MET cc_start: 0.9127 (mmm) cc_final: 0.8916 (mmm)
REVERT: B  335 LYS cc_start: 0.9197 (ttpt) cc_final: 0.8973 (ttpp)
REVERT: B  508 LEU cc_start: 0.8481 (tp) cc_final: 0.8114 (tt)
REVERT: B  617 MET cc_start: 0.8342 (tpt) cc_final: 0.7496 (tpp)
REVERT: B  639 MET cc_start: 0.7560 (mmt) cc_final: 0.6649 (tmm)
REVERT: B  645 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7866 (mp10)
REVERT: B  676 GLU cc_start: 0.8003 (tp30) cc_final: 0.7494 (tp30)
  outliers start: 11
  outliers final: 2
  residues processed: 180
  average time/residue: 0.1518
  time to fit residues: 37.2535
Evaluate side-chains
  147 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    7.9990
   chunk 3 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0010
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.0590

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.102371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.082949 restraints weight = 15796.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.085161 restraints weight = 9381.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.086665 restraints weight = 6666.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6342  Z= 0.110
  Angle     :  0.518   8.293   8610  Z= 0.268
  Chirality :  0.035   0.128   1046
  Planarity :  0.003   0.026   1048
  Dihedral  :  4.086  22.355    862
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 24.76 %
    Favored  : 73.80 %
  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:  0.19 (0.32), residues: 696
  helix:  1.22 (0.22), residues: 532
  sheet: -5.30 (0.40), residues: 20
  loop : -3.25 (0.46), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 184 
 HIS   0.001   0.000   HIS B 206 
 PHE   0.020   0.001   PHE A 545 
 TYR   0.016   0.001   TYR B 678 
 ARG   0.001   0.000   ARG B 644 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  433)
  hydrogen bonds       : angle       3.29606 ( 1299)
  covalent geometry    : bond        0.00226 ( 6342)
  covalent geometry    : angle       0.51765 ( 8610)

*********************** 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
  172 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8400 (mttt) cc_final: 0.7811 (pttm)
REVERT: A  123 MET cc_start: 0.8691 (tmm) cc_final: 0.8112 (tmm)
REVERT: A  150 CYS cc_start: 0.9223 (p) cc_final: 0.8951 (p)
REVERT: A  153 MET cc_start: 0.9180 (mtm) cc_final: 0.8820 (mtp)
REVERT: A  170 GLN cc_start: 0.8162 (mp10) cc_final: 0.7869 (mp10)
REVERT: A  310 GLN cc_start: 0.7526 (mt0) cc_final: 0.7220 (mp10)
REVERT: A  335 LYS cc_start: 0.9243 (ttpt) cc_final: 0.9042 (ttpp)
REVERT: A  508 LEU cc_start: 0.8420 (tp) cc_final: 0.7900 (tt)
REVERT: A  617 MET cc_start: 0.8381 (tpt) cc_final: 0.7965 (tpp)
REVERT: A  639 MET cc_start: 0.7397 (mmt) cc_final: 0.6644 (tmm)
REVERT: A  666 TYR cc_start: 0.9517 (t80) cc_final: 0.9304 (t80)
REVERT: A  676 GLU cc_start: 0.8080 (tp30) cc_final: 0.7539 (tp30)
REVERT: B  109 LYS cc_start: 0.8443 (mttt) cc_final: 0.7497 (mtmm)
REVERT: B  150 CYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8977 (p)
REVERT: B  153 MET cc_start: 0.9201 (mtm) cc_final: 0.8782 (mtp)
REVERT: B  170 GLN cc_start: 0.8174 (mp10) cc_final: 0.7886 (mp10)
REVERT: B  256 MET cc_start: 0.9174 (mmm) cc_final: 0.8934 (mmm)
REVERT: B  310 GLN cc_start: 0.7475 (mt0) cc_final: 0.7201 (mp10)
REVERT: B  508 LEU cc_start: 0.8534 (tp) cc_final: 0.8086 (tt)
REVERT: B  617 MET cc_start: 0.8299 (tpt) cc_final: 0.7388 (tpp)
REVERT: B  639 MET cc_start: 0.7448 (mmt) cc_final: 0.6558 (tmm)
REVERT: B  645 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7826 (mp10)
REVERT: B  676 GLU cc_start: 0.8033 (tp30) cc_final: 0.7502 (tp30)
  outliers start: 9
  outliers final: 6
  residues processed: 168
  average time/residue: 0.1546
  time to fit residues: 35.1190
Evaluate side-chains
  154 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
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  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  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:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0870
   chunk 31 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.8360

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

Flipped N/Q/H residues before XYZ refinement:
A 176 HIS
** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.103998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.084160 restraints weight = 15580.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.086350 restraints weight = 9437.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.087668 restraints weight = 6850.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4008

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= 0.100
  Angle     :  0.496   7.168   8610  Z= 0.258
  Chirality :  0.034   0.125   1046
  Planarity :  0.002   0.027   1048
  Dihedral  :  3.956  21.769    862
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.96 %
    Favored  : 73.80 %
  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:  0.57 (0.32), residues: 696
  helix:  1.52 (0.22), residues: 532
  sheet: -5.16 (0.42), residues: 20
  loop : -3.22 (0.46), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 184 
 HIS   0.002   0.000   HIS A 206 
 PHE   0.008   0.001   PHE B 221 
 TYR   0.011   0.001   TYR A 162 
 ARG   0.000   0.000   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03482 (  433)
  hydrogen bonds       : angle       3.28991 ( 1299)
  covalent geometry    : bond        0.00206 ( 6342)
  covalent geometry    : angle       0.49561 ( 8610)

*********************** 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
  181 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 167
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8404 (mttt) cc_final: 0.7816 (pttm)
REVERT: A  123 MET cc_start: 0.8720 (tmm) cc_final: 0.8219 (tmm)
REVERT: A  150 CYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8895 (p)
REVERT: A  153 MET cc_start: 0.9127 (mtm) cc_final: 0.8673 (mtp)
REVERT: A  170 GLN cc_start: 0.8166 (mp10) cc_final: 0.7886 (mp10)
REVERT: A  310 GLN cc_start: 0.7565 (mt0) cc_final: 0.7272 (mp10)
REVERT: A  508 LEU cc_start: 0.8423 (tp) cc_final: 0.8108 (tt)
REVERT: A  617 MET cc_start: 0.8397 (tpt) cc_final: 0.7932 (tpp)
REVERT: A  639 MET cc_start: 0.7297 (mmt) cc_final: 0.6495 (tmm)
REVERT: A  676 GLU cc_start: 0.8016 (tp30) cc_final: 0.7481 (tp30)
REVERT: B  109 LYS cc_start: 0.8240 (mttt) cc_final: 0.7410 (mtmm)
REVERT: B  150 CYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8910 (p)
REVERT: B  153 MET cc_start: 0.9158 (mtm) cc_final: 0.8671 (mtp)
REVERT: B  170 GLN cc_start: 0.8147 (mp10) cc_final: 0.7853 (mp10)
REVERT: B  256 MET cc_start: 0.9142 (mmm) cc_final: 0.8904 (mmm)
REVERT: B  310 GLN cc_start: 0.7591 (mt0) cc_final: 0.7284 (mp10)
REVERT: B  508 LEU cc_start: 0.8558 (tp) cc_final: 0.8095 (tt)
REVERT: B  617 MET cc_start: 0.8387 (tpt) cc_final: 0.7798 (tpp)
REVERT: B  639 MET cc_start: 0.7359 (mmt) cc_final: 0.6494 (tmm)
REVERT: B  645 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7798 (mp10)
REVERT: B  676 GLU cc_start: 0.7981 (tp30) cc_final: 0.7626 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 173
  average time/residue: 0.1484
  time to fit residues: 35.1327
Evaluate side-chains
  162 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  183 MET
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  183 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:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 206 HIS
B 176 HIS
B 206 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.103686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.083891 restraints weight = 15585.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.086090 restraints weight = 9446.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.087414 restraints weight = 6892.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6342  Z= 0.100
  Angle     :  0.498   7.963   8610  Z= 0.260
  Chirality :  0.034   0.136   1046
  Planarity :  0.002   0.027   1048
  Dihedral  :  3.836  21.424    862
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 25.40 %
    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:  0.90 (0.33), residues: 696
  helix:  1.76 (0.22), residues: 532
  sheet: -5.21 (0.40), residues: 20
  loop : -3.11 (0.46), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP B 184 
 HIS   0.001   0.000   HIS B 176 
 PHE   0.022   0.001   PHE A 545 
 TYR   0.016   0.001   TYR B 678 
 ARG   0.000   0.000   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03377 (  433)
  hydrogen bonds       : angle       3.18621 ( 1299)
  covalent geometry    : bond        0.00211 ( 6342)
  covalent geometry    : angle       0.49827 ( 8610)

*********************** 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
  187 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8419 (mttt) cc_final: 0.7565 (mtmm)
REVERT: A  123 MET cc_start: 0.8725 (tmm) cc_final: 0.8245 (tmm)
REVERT: A  150 CYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8895 (p)
REVERT: A  153 MET cc_start: 0.9138 (mtm) cc_final: 0.8633 (mtp)
REVERT: A  170 GLN cc_start: 0.8182 (mp10) cc_final: 0.7903 (mp10)
REVERT: A  310 GLN cc_start: 0.7625 (mt0) cc_final: 0.7266 (mp10)
REVERT: A  333 MET cc_start: 0.8901 (tpp) cc_final: 0.8458 (ttm)
REVERT: A  508 LEU cc_start: 0.8369 (tp) cc_final: 0.8042 (tt)
REVERT: A  617 MET cc_start: 0.8339 (tpt) cc_final: 0.7846 (tpp)
REVERT: A  639 MET cc_start: 0.7243 (mmt) cc_final: 0.6456 (tmm)
REVERT: A  676 GLU cc_start: 0.8037 (tp30) cc_final: 0.7598 (tp30)
REVERT: B  109 LYS cc_start: 0.8334 (mttt) cc_final: 0.7454 (mtmm)
REVERT: B  123 MET cc_start: 0.8801 (tmm) cc_final: 0.8430 (tmm)
REVERT: B  150 CYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8915 (p)
REVERT: B  153 MET cc_start: 0.9077 (mtm) cc_final: 0.8812 (mtp)
REVERT: B  170 GLN cc_start: 0.8183 (mp10) cc_final: 0.7891 (mp10)
REVERT: B  256 MET cc_start: 0.9141 (mmm) cc_final: 0.8910 (mmm)
REVERT: B  310 GLN cc_start: 0.7559 (mt0) cc_final: 0.7267 (mp10)
REVERT: B  508 LEU cc_start: 0.8513 (tp) cc_final: 0.8042 (tt)
REVERT: B  617 MET cc_start: 0.8395 (tpt) cc_final: 0.7820 (tpp)
REVERT: B  639 MET cc_start: 0.7216 (mmt) cc_final: 0.6363 (tmm)
REVERT: B  645 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7772 (mp10)
REVERT: B  676 GLU cc_start: 0.8005 (tp30) cc_final: 0.7639 (tp30)
  outliers start: 20
  outliers final: 14
  residues processed: 178
  average time/residue: 0.1557
  time to fit residues: 37.5345
Evaluate side-chains
  166 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  183 MET
Chi-restraints excluded: chain A residue  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  183 MET
Chi-restraints excluded: chain B residue  206 HIS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 30 optimal weight:    0.2980
   chunk 36 optimal weight:    0.0170
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.0420

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.103411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.082163 restraints weight = 15999.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.084530 restraints weight = 9375.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.086138 restraints weight = 6727.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6342  Z= 0.108
  Angle     :  0.515   7.359   8610  Z= 0.265
  Chirality :  0.035   0.144   1046
  Planarity :  0.002   0.027   1048
  Dihedral  :  3.807  21.774    862
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.92 %
    Favored  : 72.20 %
  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:  1.02 (0.33), residues: 696
  helix:  1.84 (0.22), residues: 532
  sheet: -5.25 (0.38), residues: 20
  loop : -3.03 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 184 
 HIS   0.002   0.000   HIS B 206 
 PHE   0.012   0.001   PHE B 222 
 TYR   0.009   0.001   TYR B 555 
 ARG   0.000   0.000   ARG A 667 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03355 (  433)
  hydrogen bonds       : angle       3.26505 ( 1299)
  covalent geometry    : bond        0.00233 ( 6342)
  covalent geometry    : angle       0.51466 ( 8610)

*********************** 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
  177 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8458 (mttt) cc_final: 0.7570 (mtmm)
REVERT: A  123 MET cc_start: 0.8804 (tmm) cc_final: 0.8299 (tmm)
REVERT: A  150 CYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8845 (p)
REVERT: A  153 MET cc_start: 0.9179 (mtm) cc_final: 0.8706 (mtp)
REVERT: A  170 GLN cc_start: 0.8208 (mp10) cc_final: 0.7870 (mp10)
REVERT: A  217 MET cc_start: 0.8818 (tpp) cc_final: 0.8608 (tpt)
REVERT: A  222 PHE cc_start: 0.8324 (m-80) cc_final: 0.8015 (m-80)
REVERT: A  310 GLN cc_start: 0.7759 (mt0) cc_final: 0.7307 (mp10)
REVERT: A  333 MET cc_start: 0.8994 (tpp) cc_final: 0.8599 (ttm)
REVERT: A  508 LEU cc_start: 0.8479 (tp) cc_final: 0.8104 (tt)
REVERT: A  617 MET cc_start: 0.8322 (tpt) cc_final: 0.7656 (tpp)
REVERT: A  639 MET cc_start: 0.7414 (mmt) cc_final: 0.6535 (tmm)
REVERT: A  676 GLU cc_start: 0.8125 (tp30) cc_final: 0.7502 (tp30)
REVERT: B  109 LYS cc_start: 0.8423 (mttt) cc_final: 0.7513 (mtmm)
REVERT: B  123 MET cc_start: 0.8891 (tmm) cc_final: 0.8514 (tmm)
REVERT: B  150 CYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8931 (p)
REVERT: B  170 GLN cc_start: 0.8196 (mp10) cc_final: 0.7862 (mp10)
REVERT: B  256 MET cc_start: 0.9179 (mmm) cc_final: 0.8932 (mmm)
REVERT: B  310 GLN cc_start: 0.7751 (mt0) cc_final: 0.7389 (mp10)
REVERT: B  617 MET cc_start: 0.8448 (tpt) cc_final: 0.7830 (tpp)
REVERT: B  639 MET cc_start: 0.7405 (mmt) cc_final: 0.6451 (tmm)
REVERT: B  645 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7768 (mp10)
REVERT: B  676 GLU cc_start: 0.8135 (tp30) cc_final: 0.7752 (tp30)
  outliers start: 18
  outliers final: 12
  residues processed: 169
  average time/residue: 0.1442
  time to fit residues: 33.5145
Evaluate side-chains
  163 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  183 MET
Chi-restraints excluded: chain A residue  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  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:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   chunk 38 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 206 HIS
** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.104833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.084893 restraints weight = 15539.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.087095 restraints weight = 9420.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.088467 restraints weight = 6871.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6342  Z= 0.099
  Angle     :  0.506   6.636   8610  Z= 0.260
  Chirality :  0.035   0.138   1046
  Planarity :  0.002   0.027   1048
  Dihedral  :  3.771  20.626    862
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 25.56 %
    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:  1.25 (0.33), residues: 696
  helix:  1.90 (0.22), residues: 546
  sheet: -5.15 (0.41), residues: 20
  loop : -2.94 (0.51), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP A 184 
 HIS   0.002   0.000   HIS B 206 
 PHE   0.023   0.001   PHE A 545 
 TYR   0.016   0.001   TYR A 678 
 ARG   0.001   0.000   ARG B 667 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03190 (  433)
  hydrogen bonds       : angle       3.12571 ( 1299)
  covalent geometry    : bond        0.00205 ( 6342)
  covalent geometry    : angle       0.50594 ( 8610)

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

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.8743 (tmm) cc_final: 0.8296 (tmm)
REVERT: A  150 CYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8871 (p)
REVERT: A  153 MET cc_start: 0.9102 (mtm) cc_final: 0.8894 (mtp)
REVERT: A  170 GLN cc_start: 0.8164 (mp10) cc_final: 0.7956 (mp10)
REVERT: A  310 GLN cc_start: 0.7682 (mt0) cc_final: 0.7358 (mp10)
REVERT: A  333 MET cc_start: 0.8890 (tpp) cc_final: 0.8431 (ttm)
REVERT: A  508 LEU cc_start: 0.8494 (tp) cc_final: 0.8160 (tt)
REVERT: A  617 MET cc_start: 0.8270 (tpt) cc_final: 0.7991 (tpp)
REVERT: A  639 MET cc_start: 0.7133 (mmt) cc_final: 0.6322 (tmm)
REVERT: A  676 GLU cc_start: 0.8021 (tp30) cc_final: 0.7670 (tp30)
REVERT: B  109 LYS cc_start: 0.8381 (mttt) cc_final: 0.7544 (mtmm)
REVERT: B  123 MET cc_start: 0.8815 (tmm) cc_final: 0.8443 (tmm)
REVERT: B  150 CYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8841 (p)
REVERT: B  153 MET cc_start: 0.8676 (mtp) cc_final: 0.8300 (mtp)
REVERT: B  310 GLN cc_start: 0.7671 (mt0) cc_final: 0.7324 (mp10)
REVERT: B  508 LEU cc_start: 0.8607 (tp) cc_final: 0.8207 (tt)
REVERT: B  617 MET cc_start: 0.8285 (tpt) cc_final: 0.7947 (tpp)
REVERT: B  639 MET cc_start: 0.7143 (mmt) cc_final: 0.6278 (tmm)
REVERT: B  676 GLU cc_start: 0.8025 (tp30) cc_final: 0.7642 (tp30)
  outliers start: 19
  outliers final: 13
  residues processed: 171
  average time/residue: 0.1442
  time to fit residues: 34.0245
Evaluate side-chains
  168 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 153
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  183 MET
Chi-restraints excluded: chain A residue  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  183 MET
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  511 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0370
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.105502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.086878 restraints weight = 15416.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.089121 restraints weight = 9061.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.090528 restraints weight = 6404.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6342  Z= 0.102
  Angle     :  0.567  11.147   8610  Z= 0.277
  Chirality :  0.035   0.141   1046
  Planarity :  0.003   0.030   1048
  Dihedral  :  3.735  19.593    862
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 26.84 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.33 (0.33), residues: 696
  helix:  1.96 (0.22), residues: 546
  sheet: -4.78 (0.50), residues: 20
  loop : -3.01 (0.51), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP B 184 
 HIS   0.004   0.000   HIS A 206 
 PHE   0.009   0.001   PHE B 222 
 TYR   0.015   0.001   TYR A 678 
 ARG   0.001   0.000   ARG A 667 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03089 (  433)
  hydrogen bonds       : angle       3.15980 ( 1299)
  covalent geometry    : bond        0.00214 ( 6342)
  covalent geometry    : angle       0.56681 ( 8610)

*********************** 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
  176 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.8767 (tmm) cc_final: 0.8318 (tmm)
REVERT: A  150 CYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8860 (p)
REVERT: A  153 MET cc_start: 0.9117 (mtm) cc_final: 0.8900 (mtp)
REVERT: A  218 ASP cc_start: 0.8842 (m-30) cc_final: 0.8441 (m-30)
REVERT: A  310 GLN cc_start: 0.7573 (mt0) cc_final: 0.7235 (mp10)
REVERT: A  333 MET cc_start: 0.8900 (tpp) cc_final: 0.8454 (ttm)
REVERT: A  508 LEU cc_start: 0.8473 (tp) cc_final: 0.8155 (tt)
REVERT: A  617 MET cc_start: 0.8155 (tpt) cc_final: 0.7661 (tpp)
REVERT: A  639 MET cc_start: 0.7067 (mmt) cc_final: 0.6271 (tmm)
REVERT: A  676 GLU cc_start: 0.8032 (tp30) cc_final: 0.7422 (tp30)
REVERT: B  109 LYS cc_start: 0.8209 (mttt) cc_final: 0.7453 (mtmm)
REVERT: B  123 MET cc_start: 0.8790 (tmm) cc_final: 0.8422 (tmm)
REVERT: B  150 CYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8816 (p)
REVERT: B  153 MET cc_start: 0.8783 (mtp) cc_final: 0.8435 (mtp)
REVERT: B  310 GLN cc_start: 0.7643 (mt0) cc_final: 0.7292 (mp10)
REVERT: B  333 MET cc_start: 0.8903 (tpp) cc_final: 0.8285 (ttm)
REVERT: B  617 MET cc_start: 0.8271 (tpt) cc_final: 0.7995 (tpp)
REVERT: B  639 MET cc_start: 0.7123 (mmt) cc_final: 0.6228 (tmm)
REVERT: B  676 GLU cc_start: 0.8028 (tp30) cc_final: 0.7631 (tp30)
  outliers start: 17
  outliers final: 14
  residues processed: 168
  average time/residue: 0.1499
  time to fit residues: 34.5817
Evaluate side-chains
  164 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  183 MET
Chi-restraints excluded: chain A residue  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  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 2 optimal weight:    0.9990
   chunk 36 optimal weight:    0.1980
   chunk 7 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.105240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.084458 restraints weight = 15927.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.086429 restraints weight = 10318.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.087874 restraints weight = 7893.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6342  Z= 0.122
  Angle     :  0.606  11.023   8610  Z= 0.305
  Chirality :  0.037   0.190   1046
  Planarity :  0.003   0.029   1048
  Dihedral  :  3.793  18.632    862
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 27.80 %
    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:  1.36 (0.33), residues: 696
  helix:  1.93 (0.22), residues: 548
  sheet: -4.62 (0.58), residues: 20
  loop : -2.84 (0.52), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP B 184 
 HIS   0.002   0.000   HIS B 206 
 PHE   0.063   0.002   PHE A 221 
 TYR   0.016   0.001   TYR A 678 
 ARG   0.000   0.000   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03428 (  433)
  hydrogen bonds       : angle       3.26168 ( 1299)
  covalent geometry    : bond        0.00267 ( 6342)
  covalent geometry    : angle       0.60641 ( 8610)

********************** 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
  165 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.8737 (tmm) cc_final: 0.8319 (tmm)
REVERT: A  150 CYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8860 (p)
REVERT: A  262 ASP cc_start: 0.8541 (m-30) cc_final: 0.8275 (m-30)
REVERT: A  310 GLN cc_start: 0.7642 (mt0) cc_final: 0.7312 (mp10)
REVERT: A  333 MET cc_start: 0.8841 (tpp) cc_final: 0.8402 (ttm)
REVERT: A  508 LEU cc_start: 0.8525 (tp) cc_final: 0.8289 (tt)
REVERT: A  617 MET cc_start: 0.8191 (tpt) cc_final: 0.7691 (tpp)
REVERT: A  639 MET cc_start: 0.7079 (mmt) cc_final: 0.6242 (tmm)
REVERT: A  676 GLU cc_start: 0.7982 (tp30) cc_final: 0.7386 (tp30)
REVERT: B  109 LYS cc_start: 0.8208 (mttt) cc_final: 0.7495 (mtmm)
REVERT: B  123 MET cc_start: 0.8816 (tmm) cc_final: 0.8491 (tmm)
REVERT: B  150 CYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8778 (p)
REVERT: B  153 MET cc_start: 0.8643 (mtp) cc_final: 0.8311 (mtp)
REVERT: B  310 GLN cc_start: 0.7667 (mt0) cc_final: 0.7332 (mp10)
REVERT: B  333 MET cc_start: 0.8834 (tpp) cc_final: 0.8091 (ttm)
REVERT: B  508 LEU cc_start: 0.8592 (tp) cc_final: 0.8269 (tt)
REVERT: B  617 MET cc_start: 0.8304 (tpt) cc_final: 0.8040 (tpp)
REVERT: B  639 MET cc_start: 0.7054 (mmt) cc_final: 0.6402 (tmm)
REVERT: B  676 GLU cc_start: 0.7985 (tp30) cc_final: 0.7573 (tp30)
  outliers start: 17
  outliers final: 14
  residues processed: 157
  average time/residue: 0.1489
  time to fit residues: 32.1427
Evaluate side-chains
  162 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  183 MET
Chi-restraints excluded: chain A residue  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  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:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.105211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.084999 restraints weight = 15989.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.087108 restraints weight = 10258.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.088299 restraints weight = 7667.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.4557

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= 0.115
  Angle     :  0.592  11.117   8610  Z= 0.295
  Chirality :  0.036   0.166   1046
  Planarity :  0.003   0.030   1048
  Dihedral  :  3.772  18.294    862
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 28.12 %
    Favored  : 69.17 %
  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:  1.36 (0.33), residues: 696
  helix:  2.00 (0.22), residues: 546
  sheet: -4.56 (0.62), residues: 20
  loop : -3.15 (0.47), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP B 184 
 HIS   0.002   0.000   HIS B 206 
 PHE   0.050   0.002   PHE B 221 
 TYR   0.015   0.001   TYR A 678 
 ARG   0.000   0.000   ARG A 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  433)
  hydrogen bonds       : angle       3.34575 ( 1299)
  covalent geometry    : bond        0.00249 ( 6342)
  covalent geometry    : angle       0.59218 ( 8610)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2118.82 seconds
wall clock time: 38 minutes 9.66 seconds (2289.66 seconds total)