Starting phenix.real_space_refine
on Wed Mar  4 20:26:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7epa_31235/03_2026/7epa_31235.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7epa_31235/03_2026/7epa_31235.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7epa_31235/03_2026/7epa_31235.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7epa_31235/03_2026/7epa_31235.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7epa_31235/03_2026/7epa_31235.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7epa_31235/03_2026/7epa_31235.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.194 sd=   0.754
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6779 atoms to isotropic.
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      62      5.16       5
     C    6676      2.51       5
     N    1956      2.21       5
     O    1941      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10635
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 782, 5310
          Classifications: {'peptide': 782}
          Incomplete info: {'truncation_to_alanine': 214}
          Link IDs: {'PTRANS': 38, 'TRANS': 743}
          Chain breaks: 1
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 814
          Unresolved non-hydrogen angles: 1054
          Unresolved non-hydrogen dihedrals: 684
          Unresolved non-hydrogen chiralities: 76
          Planarities with less than four sites: {'GLU:plan': 22, 'ASP:plan': 10, 'GLN:plan1': 10, 'ARG:plan': 13, 'HIS:plan': 4, 'TYR:plan': 13, 'PHE:plan': 15, 'ASN:plan1': 7, 'TRP:plan': 4}
          Unresolved non-hydrogen planarities: 481
    Chain: "B"
      Number of atoms: 5325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 782, 5325
          Classifications: {'peptide': 782}
          Incomplete info: {'truncation_to_alanine': 212}
          Link IDs: {'PTRANS': 38, 'TRANS': 743}
          Chain breaks: 1
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 799
          Unresolved non-hydrogen angles: 1039
          Unresolved non-hydrogen dihedrals: 669
          Unresolved non-hydrogen chiralities: 80
          Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 22, 'ARG:plan': 12, 'HIS:plan': 4, 'TYR:plan': 13, 'PHE:plan': 15, 'GLN:plan1': 7, 'TRP:plan': 4, 'ASN:plan1': 5}
          Unresolved non-hydrogen planarities: 464
  Time building chain proxies: 2.81, per 1000 atoms: 0.26
  Number of scatterers: 10635
  At special positions: 0
  Unit cell: (118.9, 77.9, 188.6, 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      62     16.00
     O    1941      8.00
     N    1956      7.00
     C    6676      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=19, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 121 " - pdb=" SG  CYS B 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 518 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 355 " - pdb=" SG  CYS A 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 400 " - pdb=" SG  CYS A 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 500 " - pdb=" SG  CYS A 519 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 504 " - pdb=" SG  CYS A 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 525 " - pdb=" SG  CYS A 537 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 540 " - pdb=" SG  CYS A 553 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 632 " - pdb=" SG  CYS A 721 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 234 " - pdb=" SG  CYS B 518 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 355 " - pdb=" SG  CYS B 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 400 " - pdb=" SG  CYS B 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 500 " - pdb=" SG  CYS B 519 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 504 " - pdb=" SG  CYS B 522 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 525 " - pdb=" SG  CYS B 537 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 540 " - pdb=" SG  CYS B 553 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 632 " - pdb=" SG  CYS B 721 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 587.9 milliseconds
  

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2908

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      48.5% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 74
    Processing helix  chain 'A' and resid 95 through 110
    Processing helix  chain 'A' and resid 111 through 113
      No H-bonds generated for 'chain 'A' and resid 111 through 113'
    Processing helix  chain 'A' and resid 144 through 155
    Processing helix  chain 'A' and resid 169 through 173
      removed outlier: 3.919A  pdb=" N   LEU A 172 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 202
      removed outlier: 3.594A  pdb=" N   GLN A 191 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE A 202 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 3.536A  pdb=" N   ARG A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 259
      removed outlier: 3.990A  pdb=" N   PHE A 250 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 286
    Processing helix  chain 'A' and resid 301 through 305
      removed outlier: 3.587A  pdb=" N   ALA A 305 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.538A  pdb=" N   ALA A 310 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA A 311 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 307 through 311'
    Processing helix  chain 'A' and resid 324 through 333
      removed outlier: 3.567A  pdb=" N   SER A 333 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 353
      removed outlier: 4.523A  pdb=" N   GLU A 347 " --> pdb=" O   PRO A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 365
      removed outlier: 3.940A  pdb=" N   ALA A 364 " --> pdb=" O   ASP A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 400
    Processing helix  chain 'A' and resid 414 through 422
      removed outlier: 3.753A  pdb=" N   PHE A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 592
      removed outlier: 4.139A  pdb=" N   GLY A 570 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 595 through 600
      removed outlier: 3.549A  pdb=" N   ALA A 600 " --> pdb=" O   PRO A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 623
    Processing helix  chain 'A' and resid 628 through 656
    Processing helix  chain 'A' and resid 677 through 700
      removed outlier: 3.717A  pdb=" N   ALA A 681 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 748
      removed outlier: 3.778A  pdb=" N   GLY A 730 " --> pdb=" O   ALA A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 783
      Proline residue:  A 778  - end of helix
    Processing helix  chain 'A' and resid 788 through 820
      Proline residue:  A 812  - end of helix
    Processing helix  chain 'B' and resid 57 through 74
    Processing helix  chain 'B' and resid 95 through 110
    Processing helix  chain 'B' and resid 111 through 113
      No H-bonds generated for 'chain 'B' and resid 111 through 113'
    Processing helix  chain 'B' and resid 144 through 155
    Processing helix  chain 'B' and resid 169 through 173
      removed outlier: 3.865A  pdb=" N   LEU B 172 " --> pdb=" O   SER B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 202
      removed outlier: 3.552A  pdb=" N   GLN B 191 " --> pdb=" O   PRO B 187 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE B 202 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 231
      removed outlier: 3.550A  pdb=" N   ARG B 231 " --> pdb=" O   GLU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 259
      removed outlier: 4.094A  pdb=" N   PHE B 250 " --> pdb=" O   SER B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 286
    Processing helix  chain 'B' and resid 301 through 305
      removed outlier: 3.592A  pdb=" N   ALA B 305 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 311
      removed outlier: 3.555A  pdb=" N   ALA B 310 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ALA B 311 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 307 through 311'
    Processing helix  chain 'B' and resid 324 through 333
      removed outlier: 3.614A  pdb=" N   SER B 333 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 353
      removed outlier: 4.470A  pdb=" N   GLU B 347 " --> pdb=" O   PRO B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 400
    Processing helix  chain 'B' and resid 407 through 411
      removed outlier: 3.515A  pdb=" N   MET B 410 " --> pdb=" O   CYS B 407 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ARG B 411 " --> pdb=" O   ASP B 408 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 407 through 411'
    Processing helix  chain 'B' and resid 414 through 422
      removed outlier: 3.630A  pdb=" N   PHE B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 592
      removed outlier: 4.143A  pdb=" N   GLY B 570 " --> pdb=" O   ALA B 566 " (cutoff:3.500A)
      Proline residue:  B 571  - end of helix
    Processing helix  chain 'B' and resid 595 through 600
      removed outlier: 3.551A  pdb=" N   ALA B 600 " --> pdb=" O   PRO B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 623
    Processing helix  chain 'B' and resid 628 through 656
    Processing helix  chain 'B' and resid 677 through 700
      removed outlier: 3.758A  pdb=" N   ALA B 681 " --> pdb=" O   ALA B 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 726 through 747
      removed outlier: 3.701A  pdb=" N   GLY B 730 " --> pdb=" O   ALA B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 755 through 784
      Proline residue:  B 778  - end of helix
    Processing helix  chain 'B' and resid 788 through 820
      Proline residue:  B 812  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 6.537A  pdb=" N   LEU A  32 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   HIS A  87 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   LEU A  89 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   GLY A  36 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 8.750A  pdb=" N   ILE A 140 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   GLY A  35 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   VAL A 139 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 241
      removed outlier: 7.785A  pdb=" N   VAL A 207 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   SER A 238 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   THR A 209 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   LYS A 240 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ALA A 211 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ALA A 266 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE A 317 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLY A 472 " --> pdb=" O   ILE A 455 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   THR A 457 " --> pdb=" O   LYS A 470 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   LYS A 470 " --> pdb=" O   THR A 457 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   LEU A 459 " --> pdb=" O   TYR A 468 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   TYR A 468 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR A 473 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   THR A 479 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 428 through 429
      removed outlier: 4.444A  pdb=" N   PHE A 428 " --> pdb=" O   VAL A 441 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 512
    Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 28
      removed outlier: 6.601A  pdb=" N   LEU B  32 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   HIS B  87 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LEU B  34 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   LEU B  89 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   GLY B  36 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL B  33 " --> pdb=" O   ILE B 136 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY B 138 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 8.675A  pdb=" N   ILE B 163 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   VAL B 139 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241
      removed outlier: 3.539A  pdb=" N   GLU B 239 " --> pdb=" O   THR B 209 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   ALA B 266 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE B 317 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY B 472 " --> pdb=" O   ILE B 455 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   THR B 457 " --> pdb=" O   LYS B 470 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   LYS B 470 " --> pdb=" O   THR B 457 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   LEU B 459 " --> pdb=" O   TYR B 468 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   TYR B 468 " --> pdb=" O   LEU B 459 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   TYR B 473 " --> pdb=" O   THR B 479 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   THR B 479 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 428 through 429
      removed outlier: 4.506A  pdb=" N   PHE B 428 " --> pdb=" O   VAL B 441 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL B 441 " --> pdb=" O   PHE B 428 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 512

    571 hydrogen bonds defined for protein.
    1671 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: 2.06

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3684
        1.35 -     1.46: 2466
        1.46 -     1.58: 4617
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 10847
  Sorted by residual:
  bond pdb=" C   ARG A 411 "
       pdb=" N   PRO A 412 "
    ideal  model  delta    sigma   weight residual
    1.333  1.348 -0.015 1.01e-02 9.80e+03 2.13e+00
  bond pdb=" C   GLU A 502 "
       pdb=" N   PRO A 503 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.36e+00
  bond pdb=" C   GLU B 502 "
       pdb=" N   PRO B 503 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.31e+00
  bond pdb=" C   GLY A 116 "
       pdb=" O   GLY A 116 "
    ideal  model  delta    sigma   weight residual
    1.243  1.235  0.008 9.30e-03 1.16e+04 7.32e-01
  bond pdb=" CA  ASP B 421 "
       pdb=" CB  ASP B 421 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.013 1.69e-02 3.50e+03 6.03e-01
  ... (remaining 10842 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 14428
        1.28 -     2.56: 320
        2.56 -     3.85: 71
        3.85 -     5.13: 15
        5.13 -     6.41: 5
  Bond angle restraints: 14839
  Sorted by residual:
  angle pdb=" C   GLY B 130 "
        pdb=" N   ASP B 131 "
        pdb=" CA  ASP B 131 "
      ideal   model   delta    sigma   weight residual
     121.54  126.07   -4.53 1.91e+00 2.74e-01 5.62e+00
  angle pdb=" N   GLN B  42 "
        pdb=" CA  GLN B  42 "
        pdb=" C   GLN B  42 "
      ideal   model   delta    sigma   weight residual
     108.34  111.19   -2.85 1.31e+00 5.83e-01 4.72e+00
  angle pdb=" N   GLU B 502 "
        pdb=" CA  GLU B 502 "
        pdb=" C   GLU B 502 "
      ideal   model   delta    sigma   weight residual
     109.81  114.19   -4.38 2.21e+00 2.05e-01 3.94e+00
  angle pdb=" N   GLU A 502 "
        pdb=" CA  GLU A 502 "
        pdb=" C   GLU A 502 "
      ideal   model   delta    sigma   weight residual
     109.81  114.14   -4.33 2.21e+00 2.05e-01 3.84e+00
  angle pdb=" C   ALA A 230 "
        pdb=" N   ARG A 231 "
        pdb=" CA  ARG A 231 "
      ideal   model   delta    sigma   weight residual
     122.76  119.74    3.02 1.63e+00 3.76e-01 3.42e+00
  ... (remaining 14834 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 5987
       16.08 -    32.16: 367
       32.16 -    48.24: 91
       48.24 -    64.33: 13
       64.33 -    80.41: 2
  Dihedral angle restraints: 6460
    sinusoidal: 1958
      harmonic: 4502
  Sorted by residual:
  dihedral pdb=" CB  CYS A 234 "
           pdb=" SG  CYS A 234 "
           pdb=" SG  CYS A 518 "
           pdb=" CB  CYS A 518 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   14.04   78.96     1      1.00e+01 1.00e-02 7.76e+01
  dihedral pdb=" CB  CYS A 632 "
           pdb=" SG  CYS A 632 "
           pdb=" SG  CYS A 721 "
           pdb=" CB  CYS A 721 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.68  -64.32     1      1.00e+01 1.00e-02 5.44e+01
  dihedral pdb=" CB  CYS B 234 "
           pdb=" SG  CYS B 234 "
           pdb=" SG  CYS B 518 "
           pdb=" CB  CYS B 518 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   29.55   63.45     1      1.00e+01 1.00e-02 5.31e+01
  ... (remaining 6457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 964
       0.024 -    0.049: 476
       0.049 -    0.073: 172
       0.073 -    0.098: 76
       0.098 -    0.122: 42
  Chirality restraints: 1730
  Sorted by residual:
  chirality pdb=" CA  ILE B 317 "
            pdb=" N   ILE B 317 "
            pdb=" C   ILE B 317 "
            pdb=" CB  ILE B 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  chirality pdb=" CA  ILE B 140 "
            pdb=" N   ILE B 140 "
            pdb=" C   ILE B 140 "
            pdb=" CB  ILE B 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.59e-01
  chirality pdb=" CA  ILE B 315 "
            pdb=" N   ILE B 315 "
            pdb=" C   ILE B 315 "
            pdb=" CB  ILE B 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.56e-01
  ... (remaining 1727 not shown)

  Planarity restraints: 1976
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 523 "    0.027 5.00e-02 4.00e+02   4.08e-02 2.66e+00
        pdb=" N   PRO B 524 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 524 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 524 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 523 "   -0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO A 524 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 524 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 524 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 502 "    0.021 5.00e-02 4.00e+02   3.20e-02 1.64e+00
        pdb=" N   PRO A 503 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 503 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 503 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1973 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2872
        2.80 -     3.32: 9937
        3.32 -     3.85: 17382
        3.85 -     4.37: 17184
        4.37 -     4.90: 30790
  Nonbonded interactions: 78165
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 356 "
            pdb=" OE1 GLN B 359 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER A 294 "
            pdb=" OD1 ASP A 295 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OG  SER B 294 "
            pdb=" OD1 ASP B 295 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" NH1 ARG B 720 "
            pdb=" O   ASP B 786 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" N   GLY A  35 "
            pdb=" O   GLY A 138 "
     model   vdw
     2.349 3.120
  ... (remaining 78160 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 24 through 62 or (resid 63 through 64 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 65 through 88 or (resid 89 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 90 through 109 or (re \ 
sid 110 through 112 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 113 through 254 or (resid 255 through 256 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 257 through 300 or (resid 301 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 302 through 317 or (resid 318  \ 
and (name N or name CA or name C or name O or name CB )) or resid 319 through 34 \ 
5 or (resid 346 through 347 and (name N or name CA or name C or name O or name C \ 
B )) or resid 348 through 532 or (resid 533 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 534 through 538 or (resid 539 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 540 through 604 or (resid 605 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 606 through 644 or \ 
 (resid 645 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 
6 through 685 or (resid 686 through 688 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 689 through 820))
  selection = (chain 'B' and (resid 24 through 28 or (resid 29 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 30 through 41 or (resid 42 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 43 through 93 or (resid 94 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 95 through 196 or ( \ 
resid 197 and (name N or name CA or name C or name O or name CB )) or resid 198  \ 
through 199 or (resid 200 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 201 through 272 or (resid 273 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 274 through 285 or (resid 286 through 287 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 288 through 432 or (resi \ 
d 433 and (name N or name CA or name C or name O or name CB )) or resid 434 thro \ 
ugh 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 471 through 505 or (resid 506 through 507 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 508 through 525 or (resid 526 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 527 through 607 or (resid 60 \ 
8 through 610 and (name N or name CA or name C or name O or name CB )) or resid  \ 
611 through 719 or (resid 720 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 721 through 820))
}

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:             3.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.070
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
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      :  0.002   0.036  10866  Z= 0.099
  Angle     :  0.482   6.408  14877  Z= 0.273
  Chirality :  0.038   0.122   1730
  Planarity :  0.003   0.041   1976
  Dihedral  : 11.031  80.407   3495
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.19), residues: 1556
  helix:  0.45 (0.18), residues: 718
  sheet: -0.80 (0.40), residues: 166
  loop : -2.76 (0.20), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 714 
 TYR   0.005   0.001   TYR B 386 
 PHE   0.008   0.000   PHE B 189 
 TRP   0.003   0.000   TRP B 487 
 HIS   0.002   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00187 (10847)
  covalent geometry    : angle       0.48206 (14839)
  SS BOND              : bond        0.00140 (   19)
  SS BOND              : angle       0.46837 (   38)
  hydrogen bonds       : bond        0.10722 (  571)
  hydrogen bonds       : angle       3.98156 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: A   70 ASP cc_start: 0.7933 (t0) cc_final: 0.7656 (t0)
REVERT: A  137 THR cc_start: 0.9223 (m) cc_final: 0.9016 (p)
REVERT: A  159 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7299 (mm-40)
REVERT: A  180 TYR cc_start: 0.7840 (m-10) cc_final: 0.6813 (m-10)
REVERT: B   70 ASP cc_start: 0.8290 (t0) cc_final: 0.8082 (t0)
REVERT: B  162 GLN cc_start: 0.7825 (tt0) cc_final: 0.7623 (tm-30)
REVERT: B  269 PHE cc_start: 0.8476 (m-80) cc_final: 0.7720 (m-80)
REVERT: B  399 LEU cc_start: 0.8935 (tp) cc_final: 0.8659 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1160
  time to fit residues: 39.1816
Evaluate side-chains
  189 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    0.0980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:   40.0000
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.0060
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    0.3980
   overall best weight:    1.0198

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
** B 396 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 = 0.4041 r_free = 0.4041 target = 0.131422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.110537 restraints weight = 30682.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.113691 restraints weight = 16142.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.115737 restraints weight = 9718.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.117001 restraints weight = 6447.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.118017 restraints weight = 4690.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10866  Z= 0.132
  Angle     :  0.559   8.940  14877  Z= 0.278
  Chirality :  0.039   0.130   1730
  Planarity :  0.004   0.050   1976
  Dihedral  :  3.316  23.002   1677
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.60 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.21), residues: 1556
  helix:  1.79 (0.19), residues: 722
  sheet: -0.21 (0.46), residues: 144
  loop : -2.12 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 360 
 TYR   0.014   0.001   TYR A 180 
 PHE   0.014   0.001   PHE B 158 
 TRP   0.024   0.002   TRP B 291 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10847)
  covalent geometry    : angle       0.55829 (14839)
  SS BOND              : bond        0.00397 (   19)
  SS BOND              : angle       0.65967 (   38)
  hydrogen bonds       : bond        0.02566 (  571)
  hydrogen bonds       : angle       3.08288 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 204
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A   63 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8402 (mm-30)
REVERT: A   70 ASP cc_start: 0.7975 (t0) cc_final: 0.7645 (t0)
REVERT: A  165 TYR cc_start: 0.8766 (p90) cc_final: 0.8450 (p90)
REVERT: A  173 SER cc_start: 0.8792 (m) cc_final: 0.8407 (p)
REVERT: B   70 ASP cc_start: 0.8138 (t0) cc_final: 0.7867 (t0)
REVERT: B  165 TYR cc_start: 0.8642 (p90) cc_final: 0.8291 (p90)
REVERT: B  399 LEU cc_start: 0.9009 (tp) cc_final: 0.8702 (tp)
  outliers start: 17
  outliers final: 7
  residues processed: 207
  average time/residue: 0.1080
  time to fit residues: 31.0744
Evaluate side-chains
  187 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 180
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  291 TRP
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain B residue  270 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 66 optimal weight:    0.0980
   chunk 71 optimal weight:    0.0270
   chunk 138 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   chunk 86 optimal weight:    4.9990
   chunk 147 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0870
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.4420

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 GLN
B 526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.121743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.101030 restraints weight = 30461.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.104143 restraints weight = 15563.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.106172 restraints weight = 9215.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.107532 restraints weight = 6016.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.108372 restraints weight = 4250.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10866  Z= 0.169
  Angle     :  0.583   7.002  14877  Z= 0.299
  Chirality :  0.041   0.166   1730
  Planarity :  0.004   0.043   1976
  Dihedral  :  3.895  24.384   1677
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.86 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.22), residues: 1556
  helix:  2.12 (0.19), residues: 716
  sheet: -0.29 (0.45), residues: 148
  loop : -1.93 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 499 
 TYR   0.024   0.002   TYR B 386 
 PHE   0.018   0.002   PHE B 432 
 TRP   0.032   0.002   TRP B 291 
 HIS   0.003   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (10847)
  covalent geometry    : angle       0.58224 (14839)
  SS BOND              : bond        0.00612 (   19)
  SS BOND              : angle       0.78778 (   38)
  hydrogen bonds       : bond        0.03061 (  571)
  hydrogen bonds       : angle       3.44662 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8207 (mm-30)
REVERT: A   70 ASP cc_start: 0.8099 (t0) cc_final: 0.7788 (t0)
REVERT: A   99 LEU cc_start: 0.8356 (mt) cc_final: 0.8144 (mt)
REVERT: A  165 TYR cc_start: 0.8790 (p90) cc_final: 0.8569 (p90)
REVERT: A  173 SER cc_start: 0.8945 (m) cc_final: 0.8571 (p)
REVERT: A  195 MET cc_start: 0.8387 (mmm) cc_final: 0.8162 (mmm)
REVERT: A  351 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8695 (tp-100)
REVERT: A  421 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7397 (m-30)
REVERT: B   70 ASP cc_start: 0.8232 (t0) cc_final: 0.7976 (t0)
REVERT: B  165 TYR cc_start: 0.8649 (p90) cc_final: 0.8235 (p90)
  outliers start: 28
  outliers final: 20
  residues processed: 197
  average time/residue: 0.1080
  time to fit residues: 29.6090
Evaluate side-chains
  185 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  270 THR
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  326 ASP
Chi-restraints excluded: chain B residue  372 PHE
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 128 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 91 optimal weight:    0.7980
   chunk 72 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 414 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.121463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.100731 restraints weight = 30544.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.103876 restraints weight = 15608.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.105861 restraints weight = 9265.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.107234 restraints weight = 6081.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.108127 restraints weight = 4310.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10866  Z= 0.135
  Angle     :  0.567  10.243  14877  Z= 0.282
  Chirality :  0.040   0.157   1730
  Planarity :  0.004   0.049   1976
  Dihedral  :  3.764  23.590   1677
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.66 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.22), residues: 1556
  helix:  2.39 (0.19), residues: 714
  sheet: -0.51 (0.43), residues: 152
  loop : -1.88 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 368 
 TYR   0.017   0.001   TYR B 386 
 PHE   0.013   0.001   PHE B 158 
 TRP   0.027   0.001   TRP B 291 
 HIS   0.002   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10847)
  covalent geometry    : angle       0.56737 (14839)
  SS BOND              : bond        0.00269 (   19)
  SS BOND              : angle       0.56251 (   38)
  hydrogen bonds       : bond        0.02824 (  571)
  hydrogen bonds       : angle       3.35017 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8190 (mm-30)
REVERT: A   70 ASP cc_start: 0.8083 (t0) cc_final: 0.7712 (t0)
REVERT: A  156 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.7876 (ttm-80)
REVERT: A  165 TYR cc_start: 0.8706 (p90) cc_final: 0.8405 (p90)
REVERT: A  173 SER cc_start: 0.8909 (m) cc_final: 0.8548 (p)
REVERT: A  351 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8683 (tp-100)
REVERT: A  421 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7361 (m-30)
REVERT: A  499 ARG cc_start: 0.7312 (mmm160) cc_final: 0.7049 (mmm160)
REVERT: B   70 ASP cc_start: 0.8166 (t0) cc_final: 0.7883 (t0)
REVERT: B   94 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8141 (mmtm)
REVERT: B  414 ASN cc_start: 0.8027 (t0) cc_final: 0.7645 (t0)
  outliers start: 28
  outliers final: 19
  residues processed: 189
  average time/residue: 0.1045
  time to fit residues: 27.7867
Evaluate side-chains
  186 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  270 THR
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 63 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 153 optimal weight:   20.0000
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 68 optimal weight:    0.4980
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 396 HIS
** B 396 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 = 0.3743 r_free = 0.3743 target = 0.110236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.090250 restraints weight = 30341.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.093150 restraints weight = 14970.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.095010 restraints weight = 8680.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.096207 restraints weight = 5617.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.096942 restraints weight = 3952.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.5719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  10866  Z= 0.327
  Angle     :  0.761  10.770  14877  Z= 0.401
  Chirality :  0.045   0.233   1730
  Planarity :  0.006   0.100   1976
  Dihedral  :  5.132  25.550   1677
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 23.78 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.21), residues: 1556
  helix:  1.59 (0.19), residues: 708
  sheet: -0.85 (0.40), residues: 154
  loop : -2.12 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 433 
 TYR   0.021   0.002   TYR A 386 
 PHE   0.029   0.002   PHE A 158 
 TRP   0.034   0.002   TRP B 291 
 HIS   0.005   0.001   HIS B 393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00677 (10847)
  covalent geometry    : angle       0.76018 (14839)
  SS BOND              : bond        0.00430 (   19)
  SS BOND              : angle       1.01812 (   38)
  hydrogen bonds       : bond        0.04316 (  571)
  hydrogen bonds       : angle       4.53582 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 157
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8538 (mm)
REVERT: A   70 ASP cc_start: 0.8332 (t0) cc_final: 0.7952 (t0)
REVERT: A  245 MET cc_start: 0.8129 (pmm) cc_final: 0.7921 (ptp)
REVERT: A  396 HIS cc_start: 0.8538 (t-170) cc_final: 0.8297 (t-90)
REVERT: A  421 ASP cc_start: 0.7845 (m-30) cc_final: 0.7600 (m-30)
REVERT: A  499 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7236 (mmm160)
REVERT: B   70 ASP cc_start: 0.8349 (t0) cc_final: 0.8076 (t0)
REVERT: B   93 SER cc_start: 0.9124 (t) cc_final: 0.8822 (p)
REVERT: B   94 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8623 (mmmt)
REVERT: B  291 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.7420 (m-10)
REVERT: B  351 GLN cc_start: 0.8974 (tp40) cc_final: 0.8754 (tp-100)
  outliers start: 51
  outliers final: 23
  residues processed: 190
  average time/residue: 0.1070
  time to fit residues: 28.5875
Evaluate side-chains
  175 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  270 THR
Chi-restraints excluded: chain B residue  291 TRP
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  326 ASP
Chi-restraints excluded: chain B residue  372 PHE
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 60 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 134 optimal weight:    8.9990
   chunk 93 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 87 optimal weight:   30.0000
   chunk 100 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 396 HIS
B 414 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.114770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.094460 restraints weight = 30611.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.097476 restraints weight = 15086.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.099420 restraints weight = 8732.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.100659 restraints weight = 5642.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.101533 restraints weight = 3970.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.5492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10866  Z= 0.151
  Angle     :  0.640  13.201  14877  Z= 0.314
  Chirality :  0.042   0.170   1730
  Planarity :  0.004   0.033   1976
  Dihedral  :  4.369  23.003   1677
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 27.04 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.22), residues: 1556
  helix:  2.11 (0.20), residues: 708
  sheet: -0.78 (0.40), residues: 152
  loop : -1.94 (0.23), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 433 
 TYR   0.016   0.001   TYR B 386 
 PHE   0.019   0.001   PHE A 158 
 TRP   0.028   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (10847)
  covalent geometry    : angle       0.64010 (14839)
  SS BOND              : bond        0.00410 (   19)
  SS BOND              : angle       0.66497 (   38)
  hydrogen bonds       : bond        0.03328 (  571)
  hydrogen bonds       : angle       3.86509 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8131 (mm-30)
REVERT: A   70 ASP cc_start: 0.8147 (t0) cc_final: 0.7731 (t0)
REVERT: A  374 GLN cc_start: 0.8062 (pp30) cc_final: 0.7835 (pp30)
REVERT: A  396 HIS cc_start: 0.8502 (t-170) cc_final: 0.8276 (t-90)
REVERT: A  421 ASP cc_start: 0.7808 (m-30) cc_final: 0.7532 (m-30)
REVERT: A  499 ARG cc_start: 0.7470 (mmm160) cc_final: 0.7216 (mmm160)
REVERT: B   70 ASP cc_start: 0.8202 (t0) cc_final: 0.7902 (t0)
REVERT: B   94 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8464 (mmmt)
REVERT: B  154 LEU cc_start: 0.9166 (tp) cc_final: 0.8937 (tt)
REVERT: B  351 GLN cc_start: 0.8930 (tp40) cc_final: 0.8699 (tp-100)
  outliers start: 32
  outliers final: 19
  residues processed: 176
  average time/residue: 0.1061
  time to fit residues: 26.2653
Evaluate side-chains
  177 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   56 HIS
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  270 THR
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 134 optimal weight:   10.0000
   chunk 129 optimal weight:    4.9990
   chunk 133 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 123 optimal weight:    0.8980
   chunk 114 optimal weight:    3.9990
   chunk 67 optimal weight:    0.3980
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 396 HIS
B 414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.116501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.096287 restraints weight = 30270.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.099366 restraints weight = 14998.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.101343 restraints weight = 8672.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.102649 restraints weight = 5574.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.103502 restraints weight = 3886.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.5405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10866  Z= 0.128
  Angle     :  0.629  14.108  14877  Z= 0.305
  Chirality :  0.041   0.150   1730
  Planarity :  0.004   0.052   1976
  Dihedral  :  4.097  21.639   1677
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 28.09 %
    Favored  : 68.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.22), residues: 1556
  helix:  2.29 (0.20), residues: 706
  sheet: -0.65 (0.41), residues: 150
  loop : -1.81 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 264 
 TYR   0.016   0.001   TYR B 386 
 PHE   0.018   0.001   PHE B 269 
 TRP   0.021   0.001   TRP B 291 
 HIS   0.003   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10847)
  covalent geometry    : angle       0.62871 (14839)
  SS BOND              : bond        0.00259 (   19)
  SS BOND              : angle       0.74279 (   38)
  hydrogen bonds       : bond        0.03171 (  571)
  hydrogen bonds       : angle       3.73946 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8179 (mm-30)
REVERT: A   70 ASP cc_start: 0.8085 (t0) cc_final: 0.7662 (t0)
REVERT: A  140 ILE cc_start: 0.8780 (mp) cc_final: 0.8304 (pt)
REVERT: A  245 MET cc_start: 0.7905 (pmm) cc_final: 0.7637 (ptp)
REVERT: A  396 HIS cc_start: 0.8471 (t-170) cc_final: 0.8239 (t-90)
REVERT: A  421 ASP cc_start: 0.7772 (m-30) cc_final: 0.7473 (m-30)
REVERT: A  499 ARG cc_start: 0.7415 (mmm160) cc_final: 0.7151 (mmm160)
REVERT: A  766 MET cc_start: 0.5489 (ppp) cc_final: 0.5173 (ppp)
REVERT: B   70 ASP cc_start: 0.8163 (t0) cc_final: 0.7861 (t0)
REVERT: B   94 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8397 (mmmt)
REVERT: B  154 LEU cc_start: 0.9160 (tp) cc_final: 0.8956 (tt)
REVERT: B  351 GLN cc_start: 0.8897 (tp40) cc_final: 0.8691 (tp-100)
REVERT: B  414 ASN cc_start: 0.8122 (t0) cc_final: 0.7793 (t0)
  outliers start: 27
  outliers final: 18
  residues processed: 180
  average time/residue: 0.1042
  time to fit residues: 26.6841
Evaluate side-chains
  175 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 HIS
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  178 TYR
Chi-restraints excluded: chain B residue  234 CYS
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  270 THR
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 123 optimal weight:    0.4980
   chunk 149 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 79 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.118147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.098029 restraints weight = 30215.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.101105 restraints weight = 15017.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.103071 restraints weight = 8701.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.104382 restraints weight = 5614.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.105256 restraints weight = 3941.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.5310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10866  Z= 0.115
  Angle     :  0.625  14.341  14877  Z= 0.299
  Chirality :  0.041   0.151   1730
  Planarity :  0.004   0.049   1976
  Dihedral  :  3.916  21.406   1677
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 28.09 %
    Favored  : 68.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.22), residues: 1556
  helix:  2.41 (0.20), residues: 706
  sheet: -0.52 (0.41), residues: 150
  loop : -1.72 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 264 
 TYR   0.015   0.001   TYR A 386 
 PHE   0.019   0.001   PHE A 181 
 TRP   0.019   0.001   TRP B 291 
 HIS   0.003   0.000   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10847)
  covalent geometry    : angle       0.62505 (14839)
  SS BOND              : bond        0.00221 (   19)
  SS BOND              : angle       0.72448 (   38)
  hydrogen bonds       : bond        0.02944 (  571)
  hydrogen bonds       : angle       3.58501 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8270 (mm-30)
REVERT: A   70 ASP cc_start: 0.7987 (t0) cc_final: 0.7544 (t0)
REVERT: A  140 ILE cc_start: 0.8739 (mp) cc_final: 0.8289 (pt)
REVERT: A  421 ASP cc_start: 0.7725 (m-30) cc_final: 0.7434 (m-30)
REVERT: A  766 MET cc_start: 0.5382 (ppp) cc_final: 0.5053 (ppp)
REVERT: B   70 ASP cc_start: 0.8096 (t0) cc_final: 0.7781 (t0)
REVERT: B   94 LYS cc_start: 0.8591 (mmtp) cc_final: 0.8278 (mmmt)
REVERT: B  154 LEU cc_start: 0.9113 (tp) cc_final: 0.8881 (tt)
  outliers start: 30
  outliers final: 19
  residues processed: 184
  average time/residue: 0.1066
  time to fit residues: 27.6669
Evaluate side-chains
  179 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  178 TYR
Chi-restraints excluded: chain B residue  234 CYS
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  522 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 136 optimal weight:   10.0000
   chunk 154 optimal weight:    3.9990
   chunk 125 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 146 optimal weight:    5.9990
   chunk 60 optimal weight:   30.0000
   chunk 84 optimal weight:    9.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 755 ASN
B 191 GLN
B 351 GLN
B 396 HIS
B 414 ASN
B 755 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.110499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.090752 restraints weight = 30532.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.093721 restraints weight = 15028.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.095629 restraints weight = 8641.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.096834 restraints weight = 5526.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.097670 restraints weight = 3871.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.6152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  10866  Z= 0.275
  Angle     :  0.740  12.335  14877  Z= 0.378
  Chirality :  0.044   0.197   1730
  Planarity :  0.005   0.077   1976
  Dihedral  :  4.798  22.543   1677
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 28.44 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.22), residues: 1556
  helix:  1.93 (0.19), residues: 708
  sheet: -0.94 (0.40), residues: 152
  loop : -1.93 (0.23), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 368 
 TYR   0.016   0.002   TYR A 386 
 PHE   0.028   0.002   PHE A 158 
 TRP   0.019   0.002   TRP A 291 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 (10847)
  covalent geometry    : angle       0.73900 (14839)
  SS BOND              : bond        0.00355 (   19)
  SS BOND              : angle       0.93608 (   38)
  hydrogen bonds       : bond        0.04042 (  571)
  hydrogen bonds       : angle       4.29818 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8302 (mm-30)
REVERT: A   70 ASP cc_start: 0.8232 (t0) cc_final: 0.7809 (t0)
REVERT: A  175 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8915 (mmmt)
REVERT: A  421 ASP cc_start: 0.7863 (m-30) cc_final: 0.7610 (m-30)
REVERT: B   70 ASP cc_start: 0.8286 (t0) cc_final: 0.7986 (t0)
REVERT: B   93 SER cc_start: 0.9072 (t) cc_final: 0.8747 (p)
REVERT: B   94 LYS cc_start: 0.8866 (mmtp) cc_final: 0.8514 (mmmt)
REVERT: B  154 LEU cc_start: 0.9156 (tp) cc_final: 0.8915 (tt)
REVERT: B  291 TRP cc_start: 0.7764 (OUTLIER) cc_final: 0.7251 (m-10)
REVERT: B  414 ASN cc_start: 0.8305 (t0) cc_final: 0.8005 (t0)
  outliers start: 33
  outliers final: 22
  residues processed: 175
  average time/residue: 0.1084
  time to fit residues: 26.6344
Evaluate side-chains
  170 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  178 TYR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  291 TRP
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain B residue  410 MET
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 105 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 396 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.115161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.095158 restraints weight = 30463.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.098228 restraints weight = 14971.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.100172 restraints weight = 8615.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.101476 restraints weight = 5549.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.102252 restraints weight = 3878.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.5933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10866  Z= 0.132
  Angle     :  0.676  14.931  14877  Z= 0.325
  Chirality :  0.042   0.150   1730
  Planarity :  0.004   0.053   1976
  Dihedral  :  4.281  21.494   1677
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 30.54 %
    Favored  : 66.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.22), residues: 1556
  helix:  2.23 (0.19), residues: 706
  sheet: -0.87 (0.40), residues: 150
  loop : -1.74 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 499 
 TYR   0.017   0.001   TYR B 386 
 PHE   0.022   0.001   PHE A 189 
 TRP   0.018   0.001   TRP B 291 
 HIS   0.003   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10847)
  covalent geometry    : angle       0.67543 (14839)
  SS BOND              : bond        0.00278 (   19)
  SS BOND              : angle       0.72117 (   38)
  hydrogen bonds       : bond        0.03320 (  571)
  hydrogen bonds       : angle       3.82589 ( 1671)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7634 (mp10) cc_final: 0.7333 (mp10)
REVERT: A   63 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8321 (mm-30)
REVERT: A   70 ASP cc_start: 0.8050 (t0) cc_final: 0.7609 (t0)
REVERT: A  421 ASP cc_start: 0.7812 (m-30) cc_final: 0.7538 (m-30)
REVERT: A  766 MET cc_start: 0.5771 (ppp) cc_final: 0.5506 (ppp)
REVERT: B   70 ASP cc_start: 0.8166 (t0) cc_final: 0.7869 (t0)
REVERT: B   94 LYS cc_start: 0.8707 (mmtp) cc_final: 0.8386 (mmmt)
REVERT: B  154 LEU cc_start: 0.9161 (tp) cc_final: 0.8944 (tt)
REVERT: B  200 ARG cc_start: 0.7234 (ttm170) cc_final: 0.7007 (ttm-80)
REVERT: B  330 TYR cc_start: 0.8929 (t80) cc_final: 0.8681 (t80)
  outliers start: 22
  outliers final: 19
  residues processed: 180
  average time/residue: 0.1161
  time to fit residues: 28.7334
Evaluate side-chains
  179 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain A residue  544 TYR
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  178 TYR
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  522 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0370
   chunk 51 optimal weight:    0.9980
   chunk 83 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0050
   chunk 124 optimal weight:    0.6980
   chunk 155 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0170
   chunk 79 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0020
   overall best weight:    0.1118

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

Flipped N/Q/H residues before XYZ refinement:
B 191 GLN
B 396 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.120388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.100254 restraints weight = 30263.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.103457 restraints weight = 15100.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.105514 restraints weight = 8742.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.106759 restraints weight = 5606.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.107717 restraints weight = 3982.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.5569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10866  Z= 0.112
  Angle     :  0.656  15.072  14877  Z= 0.309
  Chirality :  0.041   0.160   1730
  Planarity :  0.004   0.054   1976
  Dihedral  :  3.893  21.552   1677
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 30.42 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.22), residues: 1556
  helix:  2.34 (0.19), residues: 708
  sheet: -0.40 (0.43), residues: 144
  loop : -1.64 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 499 
 TYR   0.017   0.001   TYR B 386 
 PHE   0.030   0.001   PHE A 189 
 TRP   0.015   0.001   TRP B 291 
 HIS   0.003   0.000   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10847)
  covalent geometry    : angle       0.65556 (14839)
  SS BOND              : bond        0.00202 (   19)
  SS BOND              : angle       0.63795 (   38)
  hydrogen bonds       : bond        0.02983 (  571)
  hydrogen bonds       : angle       3.56642 ( 1671)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1866.76 seconds
wall clock time: 32 minutes 46.66 seconds (1966.66 seconds total)