Starting phenix.real_space_refine
on Wed Mar  4 09:51:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tyk_26183/03_2026/7tyk_26183_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tyk_26183/03_2026/7tyk_26183.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tyk_26183/03_2026/7tyk_26183_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tyk_26183/03_2026/7tyk_26183_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tyk_26183/03_2026/7tyk_26183.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tyk_26183/03_2026/7tyk_26183.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     C    8034      2.51       5
     N    2260      2.21       5
     O    2326      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  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: 12698
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 809, 6349
          Classifications: {'peptide': 809}
          Link IDs: {'PTRANS': 44, 'TRANS': 764}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 6349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 809, 6349
          Classifications: {'peptide': 809}
          Link IDs: {'PTRANS': 44, 'TRANS': 764}
          Chain breaks: 4
  Time building chain proxies: 2.72, per 1000 atoms: 0.21
  Number of scatterers: 12698
  At special positions: 0
  Unit cell: (141.48, 113.4, 141.48, 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      78     16.00
     O    2326      8.00
     N    2260      7.00
     C    8034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=32, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 122 " - pdb=" SG  CYS A 150 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS A 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 188 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 190 " - pdb=" SG  CYS A 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 207 " - pdb=" SG  CYS A 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 223 " - pdb=" SG  CYS A 232 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 254 " - pdb=" SG  CYS A 274 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 302 " - pdb=" SG  CYS A 321 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 423 " - pdb=" SG  CYS A 456 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 631 " - pdb=" SG  CYS A 838 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 764 " - pdb=" SG  CYS A 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 122 " - pdb=" SG  CYS B 150 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 154 " - pdb=" SG  CYS B 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 165 " - pdb=" SG  CYS B 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 188 " - pdb=" SG  CYS B 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 190 " - pdb=" SG  CYS B 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 207 " - pdb=" SG  CYS B 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 223 " - pdb=" SG  CYS B 232 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 254 " - pdb=" SG  CYS B 274 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 278 " - pdb=" SG  CYS B 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 302 " - pdb=" SG  CYS B 321 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 423 " - pdb=" SG  CYS B 456 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 631 " - pdb=" SG  CYS B 838 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 764 " - pdb=" SG  CYS B 773 " 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: 0.95
  Conformation dependent library (CDL) restraints added in 458.0 milliseconds
  

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3008

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 32 sheets defined
      11.4% alpha, 28.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 18
      removed outlier: 3.770A  pdb=" N   GLN A  18 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 44
      removed outlier: 3.598A  pdb=" N   PHE A  42 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLY A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 139
      removed outlier: 3.592A  pdb=" N   ASN A 139 " --> pdb=" O   PRO A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 220
      removed outlier: 3.521A  pdb=" N   CYS A 220 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 258
    Processing helix  chain 'A' and resid 311 through 316
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 338 through 346
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 4.063A  pdb=" N   ILE A 427 " --> pdb=" O   CYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 626
    Processing helix  chain 'A' and resid 678 through 693
      removed outlier: 4.024A  pdb=" N   ASN A 693 " --> pdb=" O   ASN A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 848
      removed outlier: 3.858A  pdb=" N   PHE A 847 " --> pdb=" O   ARG A 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 18
      removed outlier: 3.769A  pdb=" N   GLN B  18 " --> pdb=" O   GLU B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 44
      removed outlier: 3.599A  pdb=" N   PHE B  42 " --> pdb=" O   THR B  38 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLY B  44 " --> pdb=" O   GLU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 139
      removed outlier: 3.593A  pdb=" N   ASN B 139 " --> pdb=" O   PRO B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 220
      removed outlier: 3.520A  pdb=" N   CYS B 220 " --> pdb=" O   PRO B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 258
    Processing helix  chain 'B' and resid 311 through 316
    Processing helix  chain 'B' and resid 317 through 319
      No H-bonds generated for 'chain 'B' and resid 317 through 319'
    Processing helix  chain 'B' and resid 338 through 346
    Processing helix  chain 'B' and resid 423 through 435
      removed outlier: 4.063A  pdb=" N   ILE B 427 " --> pdb=" O   CYS B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 626
    Processing helix  chain 'B' and resid 678 through 693
      removed outlier: 4.024A  pdb=" N   ASN B 693 " --> pdb=" O   ASN B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 841 through 848
      removed outlier: 3.858A  pdb=" N   PHE B 847 " --> pdb=" O   ARG B 843 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10
      removed outlier: 8.120A  pdb=" N   GLN A  30 " --> pdb=" O   PRO A   5 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU A   7 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   LEU A  32 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ILE A   9 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   MET A  34 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 10
      removed outlier: 8.120A  pdb=" N   GLN A  30 " --> pdb=" O   PRO A   5 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU A   7 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   LEU A  32 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ILE A   9 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   MET A  34 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   LEU A  57 " --> pdb=" O   HIS A  28 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   GLN A  30 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU A  59 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU A  32 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ARG A  61 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   PHE A  92 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU A  59 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   ARG A 114 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   VAL A  90 " --> pdb=" O   ARG A 114 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   GLU A 116 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   PHE A  92 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169
    Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228
    Processing sheet with id=AA5, first strand: chain 'A' and resid 241 through 243
    Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283
      removed outlier: 3.511A  pdb=" N   HIS A 292 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 309
      removed outlier: 7.137A  pdb=" N   CYS A 302 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   SER A 327 " --> pdb=" O   CYS A 302 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   VAL A 304 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 9.041A  pdb=" N   ILE A 329 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 9.185A  pdb=" N   THR A 306 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 309
      removed outlier: 7.137A  pdb=" N   CYS A 302 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   SER A 327 " --> pdb=" O   CYS A 302 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   VAL A 304 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 9.041A  pdb=" N   ILE A 329 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 9.185A  pdb=" N   THR A 306 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   LEU A 356 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   LEU A 391 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ILE A 358 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   TYR A 415 " --> pdb=" O   THR A 387 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   TYR A 389 " --> pdb=" O   TYR A 415 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   ALA A 417 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 459 through 460
      removed outlier: 6.100A  pdb=" N   ARG A 459 " --> pdb=" O   GLN A 566 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 463 through 468
      removed outlier: 6.632A  pdb=" N   ARG A 476 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ASN A 466 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   LEU A 474 " --> pdb=" O   ASN A 466 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   THR A 468 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ARG A 472 " --> pdb=" O   THR A 468 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 518 through 522
    Processing sheet with id=AB3, first strand: chain 'A' and resid 583 through 591
      removed outlier: 5.926A  pdb=" N   ASP A 584 " --> pdb=" O   LYS A 600 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LYS A 600 " --> pdb=" O   ASP A 584 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ASN A 590 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   HIS A 594 " --> pdb=" O   ASN A 590 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 737 through 741
      removed outlier: 3.670A  pdb=" N   TYR A 611 " --> pdb=" O   CYS A 764 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLU A 756 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 797 through 800
    Processing sheet with id=AB6, first strand: chain 'A' and resid 835 through 840
      removed outlier: 7.219A  pdb=" N   THR A 867 " --> pdb=" O   LEU A 821 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 835 through 840
    Processing sheet with id=AB8, first strand: chain 'B' and resid 5 through 10
      removed outlier: 8.121A  pdb=" N   GLN B  30 " --> pdb=" O   PRO B   5 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU B   7 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ILE B   9 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   MET B  34 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 5 through 10
      removed outlier: 8.121A  pdb=" N   GLN B  30 " --> pdb=" O   PRO B   5 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU B   7 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ILE B   9 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   MET B  34 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   LEU B  57 " --> pdb=" O   HIS B  28 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   GLN B  30 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU B  59 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ARG B  61 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   PHE B  92 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU B  59 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   ARG B 114 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   VAL B  90 " --> pdb=" O   ARG B 114 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   GLU B 116 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   PHE B  92 " --> pdb=" O   GLU B 116 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 167 through 169
    Processing sheet with id=AC2, first strand: chain 'B' and resid 226 through 228
    Processing sheet with id=AC3, first strand: chain 'B' and resid 241 through 243
    Processing sheet with id=AC4, first strand: chain 'B' and resid 282 through 283
      removed outlier: 3.511A  pdb=" N   HIS B 292 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 301 through 309
      removed outlier: 7.136A  pdb=" N   CYS B 302 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   SER B 327 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   VAL B 304 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 9.040A  pdb=" N   ILE B 329 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
      removed outlier: 9.186A  pdb=" N   THR B 306 " --> pdb=" O   ILE B 329 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 301 through 309
      removed outlier: 7.136A  pdb=" N   CYS B 302 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   SER B 327 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   VAL B 304 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 9.040A  pdb=" N   ILE B 329 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
      removed outlier: 9.186A  pdb=" N   THR B 306 " --> pdb=" O   ILE B 329 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   LEU B 356 " --> pdb=" O   TYR B 389 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   LEU B 391 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ILE B 358 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   TYR B 415 " --> pdb=" O   THR B 387 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   TYR B 389 " --> pdb=" O   TYR B 415 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   ALA B 417 " --> pdb=" O   TYR B 389 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   LEU B 391 " --> pdb=" O   ALA B 417 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 459 through 460
      removed outlier: 6.100A  pdb=" N   ARG B 459 " --> pdb=" O   GLN B 566 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7
    Processing sheet with id=AC8, first strand: chain 'B' and resid 463 through 468
      removed outlier: 6.631A  pdb=" N   ARG B 476 " --> pdb=" O   VAL B 464 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ASN B 466 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   LEU B 474 " --> pdb=" O   ASN B 466 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   THR B 468 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ARG B 472 " --> pdb=" O   THR B 468 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 518 through 522
    Processing sheet with id=AD1, first strand: chain 'B' and resid 583 through 591
      removed outlier: 5.925A  pdb=" N   ASP B 584 " --> pdb=" O   LYS B 600 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LYS B 600 " --> pdb=" O   ASP B 584 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ASN B 590 " --> pdb=" O   HIS B 594 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   HIS B 594 " --> pdb=" O   ASN B 590 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 737 through 741
      removed outlier: 3.671A  pdb=" N   TYR B 611 " --> pdb=" O   CYS B 764 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLU B 756 " --> pdb=" O   LEU B 619 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 797 through 800
    Processing sheet with id=AD4, first strand: chain 'B' and resid 835 through 840
      removed outlier: 7.219A  pdb=" N   THR B 867 " --> pdb=" O   LEU B 821 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 835 through 840

    282 hydrogen bonds defined for protein.
    714 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: 2.39

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        0.93 -     1.24: 1729
        1.24 -     1.55: 11175
        1.55 -     1.86: 94
        1.86 -     2.17: 0
        2.17 -     2.48: 2
  Bond restraints: 13000
  Sorted by residual:
  bond pdb=" CB  PRO A 136 "
       pdb=" CG  PRO A 136 "
    ideal  model  delta    sigma   weight residual
    1.492  2.479 -0.987 5.00e-02 4.00e+02 3.90e+02
  bond pdb=" CB  PRO B 136 "
       pdb=" CG  PRO B 136 "
    ideal  model  delta    sigma   weight residual
    1.492  2.479 -0.987 5.00e-02 4.00e+02 3.90e+02
  bond pdb=" CG  PRO B 136 "
       pdb=" CD  PRO B 136 "
    ideal  model  delta    sigma   weight residual
    1.503  0.930  0.573 3.40e-02 8.65e+02 2.84e+02
  bond pdb=" CG  PRO A 136 "
       pdb=" CD  PRO A 136 "
    ideal  model  delta    sigma   weight residual
    1.503  0.930  0.573 3.40e-02 8.65e+02 2.84e+02
  bond pdb=" CG  PRO B 482 "
       pdb=" CD  PRO B 482 "
    ideal  model  delta    sigma   weight residual
    1.503  1.143  0.360 3.40e-02 8.65e+02 1.12e+02
  ... (remaining 12995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    21.22: 17664
       21.22 -    42.44: 6
       42.44 -    63.65: 0
       63.65 -    84.87: 0
       84.87 -   106.09: 2
  Bond angle restraints: 17672
  Sorted by residual:
  angle pdb=" CB  PRO B 136 "
        pdb=" CG  PRO B 136 "
        pdb=" CD  PRO B 136 "
      ideal   model   delta    sigma   weight residual
     106.10    0.01  106.09 3.20e+00 9.77e-02 1.10e+03
  angle pdb=" CB  PRO A 136 "
        pdb=" CG  PRO A 136 "
        pdb=" CD  PRO A 136 "
      ideal   model   delta    sigma   weight residual
     106.10    0.03  106.07 3.20e+00 9.77e-02 1.10e+03
  angle pdb=" N   PRO A 482 "
        pdb=" CD  PRO A 482 "
        pdb=" CG  PRO A 482 "
      ideal   model   delta    sigma   weight residual
     103.20   77.23   25.97 1.50e+00 4.44e-01 3.00e+02
  angle pdb=" N   PRO B 482 "
        pdb=" CD  PRO B 482 "
        pdb=" CG  PRO B 482 "
      ideal   model   delta    sigma   weight residual
     103.20   77.26   25.94 1.50e+00 4.44e-01 2.99e+02
  angle pdb=" CA  PRO B 482 "
        pdb=" CB  PRO B 482 "
        pdb=" CG  PRO B 482 "
      ideal   model   delta    sigma   weight residual
     104.50   74.57   29.93 1.90e+00 2.77e-01 2.48e+02
  ... (remaining 17667 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.64: 7363
       29.64 -    59.28: 419
       59.28 -    88.92: 56
       88.92 -   118.56: 1
      118.56 -   148.20: 1
  Dihedral angle restraints: 7840
    sinusoidal: 3170
      harmonic: 4670
  Sorted by residual:
  dihedral pdb=" N   PRO B 136 "
           pdb=" CG  PRO B 136 "
           pdb=" CD  PRO B 136 "
           pdb=" CB  PRO B 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00  178.20 -148.20     1      1.50e+01 4.44e-03 7.89e+01
  dihedral pdb=" CB  CYS A 165 "
           pdb=" SG  CYS A 165 "
           pdb=" SG  CYS A 184 "
           pdb=" CB  CYS A 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.75   75.75     1      1.00e+01 1.00e-02 7.24e+01
  dihedral pdb=" CB  CYS B 165 "
           pdb=" SG  CYS B 165 "
           pdb=" SG  CYS B 184 "
           pdb=" CB  CYS B 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.71   75.71     1      1.00e+01 1.00e-02 7.23e+01
  ... (remaining 7837 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1289
       0.032 -    0.064: 443
       0.064 -    0.096: 120
       0.096 -    0.128: 106
       0.128 -    0.160: 10
  Chirality restraints: 1968
  Sorted by residual:
  chirality pdb=" CA  PRO A 136 "
            pdb=" N   PRO A 136 "
            pdb=" C   PRO A 136 "
            pdb=" CB  PRO A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.41e-01
  chirality pdb=" CA  PRO B 136 "
            pdb=" N   PRO B 136 "
            pdb=" C   PRO B 136 "
            pdb=" CB  PRO B 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  ILE B  91 "
            pdb=" N   ILE B  91 "
            pdb=" C   ILE B  91 "
            pdb=" CB  ILE B  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.96e-01
  ... (remaining 1965 not shown)

  Planarity restraints: 2296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 482 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.89e+00
        pdb=" C   PRO A 482 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   PRO A 482 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU A 483 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 482 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.82e+00
        pdb=" C   PRO B 482 "    0.045 2.00e-02 2.50e+03
        pdb=" O   PRO B 482 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU B 483 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 135 "    0.012 2.00e-02 2.50e+03   2.39e-02 5.71e+00
        pdb=" C   ALA B 135 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ALA B 135 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PRO B 136 "    0.014 2.00e-02 2.50e+03
  ... (remaining 2293 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 729
        2.73 -     3.27: 12103
        3.27 -     3.82: 19660
        3.82 -     4.36: 23600
        4.36 -     4.90: 41473
  Nonbonded interactions: 97565
  Sorted by model distance:
  nonbonded pdb=" O   HIS B 766 "
            pdb=" OG1 THR B 770 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O   HIS A 766 "
            pdb=" OG1 THR A 770 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O   LEU A 461 "
            pdb=" OG  SER A 567 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   SER A 265 "
            pdb=" NH2 ARG A 284 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   SER B 265 "
            pdb=" NH2 ARG B 284 "
     model   vdw
     2.264 3.120
  ... (remaining 97560 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     12.440
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
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      :  0.015   0.987  13032  Z= 0.376
  Angle     :  1.389 106.088  17736  Z= 0.582
  Chirality :  0.042   0.160   1968
  Planarity :  0.003   0.034   2296
  Dihedral  : 17.403 148.196   4736
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  8.51 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 23.37 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.13 %
  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: -1.65 (0.21), residues: 1598
  helix:  1.31 (0.50), residues: 132
  sheet: -0.35 (0.25), residues: 432
  loop : -1.86 (0.19), residues: 1034

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 284 
 TYR   0.008   0.001   TYR A  56 
 PHE   0.012   0.001   PHE B 548 
 TRP   0.009   0.001   TRP B 179 
 HIS   0.006   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.01508 (13000)
  covalent geometry    : angle       1.39102 (17672)
  SS BOND              : bond        0.00173 (   32)
  SS BOND              : angle       0.82381 (   64)
  hydrogen bonds       : bond        0.13828 (  270)
  hydrogen bonds       : angle       5.16037 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 3
  residues processed: 118
  average time/residue: 0.1138
  time to fit residues: 19.8436
Evaluate side-chains
  114 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 LYS
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain B residue  371 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.1980
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    3.2388

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

Flipped N/Q/H residues before XYZ refinement:
A 139 ASN
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 ASN
A 689 ASN
B 139 ASN
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 466 ASN
B 689 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.169099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135508 restraints weight = 16831.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.132499 restraints weight = 17133.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.134774 restraints weight = 17332.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.135476 restraints weight = 11806.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.135888 restraints weight = 11170.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  13032  Z= 0.260
  Angle     :  0.708  11.007  17736  Z= 0.363
  Chirality :  0.048   0.153   1968
  Planarity :  0.006   0.094   2296
  Dihedral  :  5.202  23.482   1782
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 10.70 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 21.04 %
    Favored  : 73.22 %
  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: -1.97 (0.21), residues: 1598
  helix:  0.83 (0.51), residues: 134
  sheet: -0.69 (0.26), residues: 422
  loop : -1.99 (0.19), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  69 
 TYR   0.023   0.002   TYR B 389 
 PHE   0.021   0.002   PHE B 548 
 TRP   0.009   0.001   TRP B 542 
 HIS   0.009   0.002   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 (13000)
  covalent geometry    : angle       0.70552 (17672)
  SS BOND              : bond        0.00332 (   32)
  SS BOND              : angle       1.26470 (   64)
  hydrogen bonds       : bond        0.03865 (  270)
  hydrogen bonds       : angle       4.84894 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 112
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 MET cc_start: 0.8309 (mmt) cc_final: 0.7955 (mmt)
REVERT: A  123 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.8023 (t-90)
REVERT: A  213 GLN cc_start: 0.7521 (mp10) cc_final: 0.7188 (mm110)
REVERT: A  371 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7990 (mmmm)
REVERT: A  392 ASP cc_start: 0.8456 (t0) cc_final: 0.8108 (t0)
REVERT: A  641 ASN cc_start: 0.8255 (t0) cc_final: 0.7740 (t0)
REVERT: A  766 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.5096 (m90)
REVERT: B   34 MET cc_start: 0.8303 (mmt) cc_final: 0.7945 (mmt)
REVERT: B  123 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8016 (t-90)
REVERT: B  192 HIS cc_start: 0.7268 (m90) cc_final: 0.6962 (m170)
REVERT: B  213 GLN cc_start: 0.7567 (mp10) cc_final: 0.7209 (mm110)
REVERT: B  371 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7988 (mmmm)
REVERT: B  641 ASN cc_start: 0.8252 (t0) cc_final: 0.7704 (t0)
REVERT: B  766 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.5026 (m90)
  outliers start: 79
  outliers final: 40
  residues processed: 185
  average time/residue: 0.1064
  time to fit residues: 28.4414
Evaluate side-chains
  142 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 98
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  122 CYS
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  437 ARG
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  629 ASP
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  766 HIS
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  122 CYS
Chi-restraints excluded: chain B residue  123 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  437 ARG
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  629 ASP
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  847 PHE
Chi-restraints excluded: chain B residue  879 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 121 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 131 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 132 optimal weight:    0.9990
   chunk 149 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
A 344 HIS
A 466 ASN
A 689 ASN
B 344 HIS
B 689 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.173478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.138956 restraints weight = 16747.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.138010 restraints weight = 12985.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.139773 restraints weight = 14037.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.140394 restraints weight = 10119.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.140614 restraints weight = 9686.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13032  Z= 0.109
  Angle     :  0.563   8.159  17736  Z= 0.288
  Chirality :  0.043   0.137   1968
  Planarity :  0.004   0.033   2296
  Dihedral  :  4.600  22.643   1772
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  7.82 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 23.66 %
    Favored  : 72.71 %
  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: -1.87 (0.21), residues: 1598
  helix:  0.83 (0.51), residues: 134
  sheet: -0.54 (0.26), residues: 422
  loop : -1.94 (0.19), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 224 
 TYR   0.010   0.001   TYR A  56 
 PHE   0.013   0.001   PHE A 548 
 TRP   0.009   0.001   TRP B 616 
 HIS   0.004   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (13000)
  covalent geometry    : angle       0.56114 (17672)
  SS BOND              : bond        0.00210 (   32)
  SS BOND              : angle       0.89689 (   64)
  hydrogen bonds       : bond        0.02900 (  270)
  hydrogen bonds       : angle       4.63880 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 120
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  289 ILE cc_start: 0.7615 (mm) cc_final: 0.7173 (mm)
REVERT: A  344 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6431 (t70)
REVERT: A  371 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7682 (mmmm)
REVERT: A  484 GLU cc_start: 0.7189 (tt0) cc_final: 0.6876 (tt0)
REVERT: A  520 LEU cc_start: 0.9003 (tt) cc_final: 0.8709 (tp)
REVERT: A  766 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.4936 (m90)
REVERT: B  289 ILE cc_start: 0.7631 (mm) cc_final: 0.7190 (mm)
REVERT: B  344 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6425 (t70)
REVERT: B  371 LYS cc_start: 0.8051 (mtmm) cc_final: 0.7684 (mmmm)
REVERT: B  520 LEU cc_start: 0.9016 (tt) cc_final: 0.8723 (tp)
REVERT: B  766 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.4820 (m90)
  outliers start: 50
  outliers final: 24
  residues processed: 168
  average time/residue: 0.1024
  time to fit residues: 25.5537
Evaluate side-chains
  130 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  344 HIS
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  766 HIS
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  344 HIS
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  819 LEU
Chi-restraints excluded: chain B residue  847 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 159 optimal weight:    0.0020
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   chunk 154 optimal weight:    4.9990
   overall best weight:    2.9594

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 HIS
A 689 ASN
A 766 HIS
B 183 HIS
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
B 689 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.164939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.131652 restraints weight = 16577.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.129498 restraints weight = 14940.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.131949 restraints weight = 14035.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.132335 restraints weight = 9678.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132663 restraints weight = 9819.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  13032  Z= 0.241
  Angle     :  0.653   6.629  17736  Z= 0.337
  Chirality :  0.046   0.152   1968
  Planarity :  0.005   0.038   2296
  Dihedral  :  5.089  23.824   1772
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.26 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 23.15 %
    Favored  : 72.28 %
  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: -2.04 (0.21), residues: 1598
  helix:  0.58 (0.50), residues: 134
  sheet: -0.70 (0.26), residues: 426
  loop : -2.03 (0.19), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  69 
 TYR   0.020   0.002   TYR B 389 
 PHE   0.018   0.002   PHE B 548 
 TRP   0.015   0.002   TRP A 179 
 HIS   0.008   0.001   HIS A 766 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 (13000)
  covalent geometry    : angle       0.64920 (17672)
  SS BOND              : bond        0.00362 (   32)
  SS BOND              : angle       1.29141 (   64)
  hydrogen bonds       : bond        0.03451 (  270)
  hydrogen bonds       : angle       4.78190 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 96
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A  213 GLN cc_start: 0.7743 (mp10) cc_final: 0.7332 (mm110)
REVERT: A  344 HIS cc_start: 0.6903 (OUTLIER) cc_final: 0.6423 (t70)
REVERT: A  371 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7933 (mmmm)
REVERT: A  641 ASN cc_start: 0.8273 (t0) cc_final: 0.7744 (t0)
REVERT: A  766 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.3901 (m-70)
REVERT: B  213 GLN cc_start: 0.7736 (mp10) cc_final: 0.7328 (mm110)
REVERT: B  344 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.6427 (t70)
REVERT: B  371 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7933 (mmmm)
REVERT: B  641 ASN cc_start: 0.8221 (t0) cc_final: 0.7712 (t0)
REVERT: B  684 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6673 (mt0)
REVERT: B  766 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.4964 (m90)
  outliers start: 63
  outliers final: 43
  residues processed: 156
  average time/residue: 0.1030
  time to fit residues: 23.9990
Evaluate side-chains
  140 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 92
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  122 CYS
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  344 HIS
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  408 THR
Chi-restraints excluded: chain A residue  423 CYS
Chi-restraints excluded: chain A residue  445 ILE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  766 HIS
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  122 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  344 HIS
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  408 THR
Chi-restraints excluded: chain B residue  423 CYS
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  684 GLN
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  847 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 128 optimal weight:    0.6980
   chunk 106 optimal weight:   10.0000
   chunk 153 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 108 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 118 optimal weight:    0.5980
   chunk 138 optimal weight:   10.0000
   chunk 86 optimal weight:    2.9990
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 HIS
A 628 ASN
A 689 ASN
A 766 HIS
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
B 628 ASN
B 689 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.165825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132436 restraints weight = 16721.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.131339 restraints weight = 15777.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.133129 restraints weight = 14443.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.133744 restraints weight = 9805.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.134099 restraints weight = 9981.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  13032  Z= 0.228
  Angle     :  0.645   6.472  17736  Z= 0.335
  Chirality :  0.046   0.161   1968
  Planarity :  0.005   0.040   2296
  Dihedral  :  5.195  24.003   1772
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.01 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 22.86 %
    Favored  : 71.55 %
  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: -2.09 (0.21), residues: 1598
  helix:  0.48 (0.49), residues: 134
  sheet: -0.69 (0.26), residues: 426
  loop : -2.07 (0.19), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  69 
 TYR   0.018   0.002   TYR A 389 
 PHE   0.017   0.002   PHE A 548 
 TRP   0.014   0.001   TRP A 179 
 HIS   0.006   0.001   HIS B 766 

Details of bonding type rmsd
  covalent geometry    : bond        0.00555 (13000)
  covalent geometry    : angle       0.64049 (17672)
  SS BOND              : bond        0.00400 (   32)
  SS BOND              : angle       1.38407 (   64)
  hydrogen bonds       : bond        0.03313 (  270)
  hydrogen bonds       : angle       4.89461 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 98
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  213 GLN cc_start: 0.7763 (mp10) cc_final: 0.7466 (mm110)
REVERT: A  371 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7915 (mmmm)
REVERT: A  641 ASN cc_start: 0.8386 (t0) cc_final: 0.7845 (t0)
REVERT: A  684 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6667 (mt0)
REVERT: B  213 GLN cc_start: 0.7760 (mp10) cc_final: 0.7462 (mm110)
REVERT: B  371 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7918 (mmmm)
REVERT: B  641 ASN cc_start: 0.8370 (t0) cc_final: 0.7837 (t0)
REVERT: B  766 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.4976 (m90)
  outliers start: 77
  outliers final: 48
  residues processed: 171
  average time/residue: 0.1064
  time to fit residues: 26.9554
Evaluate side-chains
  140 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 90
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  122 CYS
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  423 CYS
Chi-restraints excluded: chain A residue  437 ARG
Chi-restraints excluded: chain A residue  445 ILE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  628 ASN
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  684 GLN
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  122 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  408 THR
Chi-restraints excluded: chain B residue  423 CYS
Chi-restraints excluded: chain B residue  437 ARG
Chi-restraints excluded: chain B residue  445 ILE
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  847 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0020
   chunk 74 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 HIS
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 HIS
A 689 ASN
A 766 HIS
B 225 HIS
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
B 689 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.172218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.138700 restraints weight = 16729.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136646 restraints weight = 14703.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.138388 restraints weight = 15744.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.139539 restraints weight = 10798.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.140028 restraints weight = 9764.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13032  Z= 0.107
  Angle     :  0.561   6.909  17736  Z= 0.292
  Chirality :  0.043   0.136   1968
  Planarity :  0.004   0.034   2296
  Dihedral  :  4.805  23.486   1772
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.20 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 24.17 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.92 (0.21), residues: 1598
  helix:  0.75 (0.50), residues: 134
  sheet: -0.61 (0.26), residues: 426
  loop : -1.95 (0.19), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 177 
 TYR   0.013   0.001   TYR A 630 
 PHE   0.016   0.001   PHE B 290 
 TRP   0.009   0.001   TRP B 179 
 HIS   0.004   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (13000)
  covalent geometry    : angle       0.55877 (17672)
  SS BOND              : bond        0.00175 (   32)
  SS BOND              : angle       1.06813 (   64)
  hydrogen bonds       : bond        0.02721 (  270)
  hydrogen bonds       : angle       4.67614 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 105
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.7749 (mp10) cc_final: 0.7362 (mm110)
REVERT: A  344 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.6370 (t70)
REVERT: A  371 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7721 (mmmm)
REVERT: A  641 ASN cc_start: 0.8238 (t0) cc_final: 0.7829 (t0)
REVERT: A  684 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6596 (mt0)
REVERT: B  213 GLN cc_start: 0.7742 (mp10) cc_final: 0.7355 (mm110)
REVERT: B  344 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.6394 (t70)
REVERT: B  371 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7716 (mmmm)
REVERT: B  520 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8807 (tp)
REVERT: B  641 ASN cc_start: 0.8241 (t0) cc_final: 0.7847 (t0)
REVERT: B  684 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6590 (mt0)
REVERT: B  766 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.5021 (m90)
  outliers start: 61
  outliers final: 35
  residues processed: 161
  average time/residue: 0.0981
  time to fit residues: 23.6038
Evaluate side-chains
  137 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 96
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  122 CYS
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  344 HIS
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  423 CYS
Chi-restraints excluded: chain A residue  437 ARG
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  684 GLN
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  122 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  344 HIS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  423 CYS
Chi-restraints excluded: chain B residue  437 ARG
Chi-restraints excluded: chain B residue  520 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  684 GLN
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  819 LEU
Chi-restraints excluded: chain B residue  847 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 94 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0970
   chunk 155 optimal weight:    5.9990
   chunk 139 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 HIS
A 628 ASN
A 689 ASN
A 766 HIS
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
B 628 ASN
B 689 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.164199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.131897 restraints weight = 16597.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.131544 restraints weight = 15253.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.132858 restraints weight = 15365.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.133595 restraints weight = 10247.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.134230 restraints weight = 9559.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13032  Z= 0.204
  Angle     :  0.617   6.111  17736  Z= 0.319
  Chirality :  0.045   0.154   1968
  Planarity :  0.004   0.034   2296
  Dihedral  :  5.025  23.708   1772
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.58 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 23.95 %
    Favored  : 70.75 %
  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: -2.01 (0.21), residues: 1598
  helix:  0.65 (0.50), residues: 134
  sheet: -0.65 (0.26), residues: 426
  loop : -2.03 (0.19), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.016   0.002   TYR A 389 
 PHE   0.016   0.002   PHE B 548 
 TRP   0.012   0.001   TRP B 179 
 HIS   0.011   0.001   HIS B 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (13000)
  covalent geometry    : angle       0.61357 (17672)
  SS BOND              : bond        0.00274 (   32)
  SS BOND              : angle       1.21609 (   64)
  hydrogen bonds       : bond        0.03147 (  270)
  hydrogen bonds       : angle       4.73332 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 97
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.7732 (mp10) cc_final: 0.7500 (mm110)
REVERT: A  348 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8365 (mt)
REVERT: A  641 ASN cc_start: 0.8418 (t0) cc_final: 0.8095 (t0)
REVERT: A  684 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6663 (mt0)
REVERT: B  213 GLN cc_start: 0.7721 (mp10) cc_final: 0.7492 (mm110)
REVERT: B  520 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8831 (tp)
REVERT: B  641 ASN cc_start: 0.8414 (t0) cc_final: 0.8093 (t0)
REVERT: B  684 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6663 (mt0)
REVERT: B  766 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.4892 (m90)
  outliers start: 73
  outliers final: 50
  residues processed: 165
  average time/residue: 0.1098
  time to fit residues: 26.8752
Evaluate side-chains
  148 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 93
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  122 CYS
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  408 THR
Chi-restraints excluded: chain A residue  423 CYS
Chi-restraints excluded: chain A residue  437 ARG
Chi-restraints excluded: chain A residue  445 ILE
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  628 ASN
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  684 GLN
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  122 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  423 CYS
Chi-restraints excluded: chain B residue  437 ARG
Chi-restraints excluded: chain B residue  520 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  684 GLN
Chi-restraints excluded: chain B residue  690 PHE
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  792 ILE
Chi-restraints excluded: chain B residue  847 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 127 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0670
   chunk 68 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 114 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 139 optimal weight:    5.9990
   overall best weight:    1.1724

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 689 ASN
A 766 HIS
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 689 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.168523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.134434 restraints weight = 16405.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.135218 restraints weight = 12892.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.136473 restraints weight = 12232.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.137376 restraints weight = 9346.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.138095 restraints weight = 8717.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13032  Z= 0.121
  Angle     :  0.567   6.489  17736  Z= 0.293
  Chirality :  0.043   0.139   1968
  Planarity :  0.004   0.035   2296
  Dihedral  :  4.779  23.574   1772
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.95 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 24.75 %
    Favored  : 70.68 %
  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: -1.92 (0.21), residues: 1598
  helix:  0.79 (0.50), residues: 134
  sheet: -0.61 (0.26), residues: 426
  loop : -1.96 (0.19), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.017   0.001   TYR A 630 
 PHE   0.019   0.001   PHE A 290 
 TRP   0.013   0.001   TRP A 179 
 HIS   0.004   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (13000)
  covalent geometry    : angle       0.56463 (17672)
  SS BOND              : bond        0.00214 (   32)
  SS BOND              : angle       0.97906 (   64)
  hydrogen bonds       : bond        0.02724 (  270)
  hydrogen bonds       : angle       4.59620 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 97
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.7744 (mp10) cc_final: 0.7441 (mm110)
REVERT: A  641 ASN cc_start: 0.8317 (t0) cc_final: 0.7882 (t0)
REVERT: A  684 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6595 (mt0)
REVERT: B  213 GLN cc_start: 0.7726 (mp10) cc_final: 0.7426 (mm110)
REVERT: B  520 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8819 (tp)
REVERT: B  641 ASN cc_start: 0.8312 (t0) cc_final: 0.7884 (t0)
REVERT: B  684 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6599 (mt0)
REVERT: B  766 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.5035 (m90)
  outliers start: 63
  outliers final: 41
  residues processed: 155
  average time/residue: 0.1039
  time to fit residues: 24.1030
Evaluate side-chains
  133 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 88
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  423 CYS
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  628 ASN
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  684 GLN
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  423 CYS
Chi-restraints excluded: chain B residue  520 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  684 GLN
Chi-restraints excluded: chain B residue  690 PHE
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  847 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 135 optimal weight:    3.9990
   chunk 122 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 766 HIS
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 343 GLN ** 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 = 0.3952 r_free = 0.3952 target = 0.170662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.137124 restraints weight = 16606.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.135401 restraints weight = 14232.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.137361 restraints weight = 14304.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.138247 restraints weight = 9871.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.138769 restraints weight = 8993.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13032  Z= 0.108
  Angle     :  0.550   6.304  17736  Z= 0.284
  Chirality :  0.043   0.135   1968
  Planarity :  0.004   0.034   2296
  Dihedral  :  4.572  23.291   1772
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.95 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.25 %
    Favored  : 70.75 %
  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: -1.88 (0.21), residues: 1598
  helix:  0.87 (0.50), residues: 134
  sheet: -0.56 (0.26), residues: 428
  loop : -1.96 (0.19), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.009   0.001   TYR B  56 
 PHE   0.012   0.001   PHE A 548 
 TRP   0.016   0.001   TRP B 179 
 HIS   0.003   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (13000)
  covalent geometry    : angle       0.54808 (17672)
  SS BOND              : bond        0.00208 (   32)
  SS BOND              : angle       0.91945 (   64)
  hydrogen bonds       : bond        0.02568 (  270)
  hydrogen bonds       : angle       4.49086 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 96
  time to evaluate  : 0.542 
Fit side-chains
REVERT: A  154 CYS cc_start: 0.4772 (m) cc_final: 0.4435 (m)
REVERT: A  213 GLN cc_start: 0.7773 (mp10) cc_final: 0.7439 (mm110)
REVERT: A  641 ASN cc_start: 0.8296 (t0) cc_final: 0.7863 (t0)
REVERT: A  684 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6552 (mt0)
REVERT: B  154 CYS cc_start: 0.4770 (m) cc_final: 0.4431 (m)
REVERT: B  213 GLN cc_start: 0.7744 (mp10) cc_final: 0.7418 (mm110)
REVERT: B  641 ASN cc_start: 0.8302 (t0) cc_final: 0.7866 (t0)
REVERT: B  684 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6520 (mt0)
REVERT: B  766 HIS cc_start: 0.7116 (OUTLIER) cc_final: 0.4912 (m90)
  outliers start: 55
  outliers final: 42
  residues processed: 146
  average time/residue: 0.1037
  time to fit residues: 22.5695
Evaluate side-chains
  132 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 87
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  270 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  423 CYS
Chi-restraints excluded: chain A residue  437 ARG
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  684 GLN
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  122 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  270 HIS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  423 CYS
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  684 GLN
Chi-restraints excluded: chain B residue  690 PHE
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  847 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 114 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 124 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 120 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 628 ASN
A 766 HIS
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 628 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.171540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.138046 restraints weight = 16628.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.137510 restraints weight = 15082.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139540 restraints weight = 12878.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.139930 restraints weight = 9055.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.140404 restraints weight = 8382.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13032  Z= 0.103
  Angle     :  0.542   6.501  17736  Z= 0.280
  Chirality :  0.043   0.135   1968
  Planarity :  0.004   0.034   2296
  Dihedral  :  4.474  23.306   1772
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.64 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 26.05 %
    Favored  : 70.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.21), residues: 1598
  helix:  0.91 (0.50), residues: 134
  sheet: -0.56 (0.26), residues: 426
  loop : -1.91 (0.19), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 114 
 TYR   0.009   0.001   TYR A  56 
 PHE   0.017   0.001   PHE A 290 
 TRP   0.015   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (13000)
  covalent geometry    : angle       0.54010 (17672)
  SS BOND              : bond        0.00196 (   32)
  SS BOND              : angle       0.88107 (   64)
  hydrogen bonds       : bond        0.02522 (  270)
  hydrogen bonds       : angle       4.42478 (  714)

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

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

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3196 Ramachandran restraints generated.
    1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 95
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A  154 CYS cc_start: 0.4744 (m) cc_final: 0.4389 (m)
REVERT: A  641 ASN cc_start: 0.8307 (t0) cc_final: 0.7879 (t0)
REVERT: A  684 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6499 (mt0)
REVERT: B  154 CYS cc_start: 0.4741 (m) cc_final: 0.4397 (m)
REVERT: B  641 ASN cc_start: 0.8311 (t0) cc_final: 0.7867 (t0)
REVERT: B  684 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6502 (mt0)
REVERT: B  766 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.5009 (m90)
  outliers start: 46
  outliers final: 36
  residues processed: 139
  average time/residue: 0.0990
  time to fit residues: 20.5733
Evaluate side-chains
  129 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 90
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  423 CYS
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  628 ASN
Chi-restraints excluded: chain A residue  639 THR
Chi-restraints excluded: chain A residue  684 GLN
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue  847 PHE
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  395 ASN
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  423 CYS
Chi-restraints excluded: chain B residue  437 ARG
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  639 THR
Chi-restraints excluded: chain B residue  684 GLN
Chi-restraints excluded: chain B residue  766 HIS
Chi-restraints excluded: chain B residue  847 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 131 optimal weight:    5.9990
   chunk 137 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 102 optimal weight:    5.9990
   chunk 142 optimal weight:    0.0470
   chunk 2 optimal weight:    4.9990
   overall best weight:    2.2882

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 766 HIS
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 628 ASN ** 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 = 0.3958 r_free = 0.3958 target = 0.171237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137693 restraints weight = 16621.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.136843 restraints weight = 14192.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.138606 restraints weight = 13691.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139428 restraints weight = 9669.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.139938 restraints weight = 8827.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094  13032  Z= 0.243
  Angle     :  1.012  59.167  17736  Z= 0.601
  Chirality :  0.047   0.527   1968
  Planarity :  0.004   0.034   2296
  Dihedral  :  4.463  23.258   1772
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.76 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 26.20 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.13 %
  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: -1.84 (0.21), residues: 1598
  helix:  0.88 (0.49), residues: 134
  sheet: -0.56 (0.26), residues: 426
  loop : -1.91 (0.19), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 114 
 TYR   0.009   0.001   TYR A  56 
 PHE   0.014   0.001   PHE B 548 
 TRP   0.013   0.001   TRP A 179 
 HIS   0.003   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (13000)
  covalent geometry    : angle       1.01216 (17672)
  SS BOND              : bond        0.00249 (   32)
  SS BOND              : angle       0.88447 (   64)
  hydrogen bonds       : bond        0.02563 (  270)
  hydrogen bonds       : angle       4.42414 (  714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1842.58 seconds
wall clock time: 32 minutes 28.10 seconds (1948.10 seconds total)