Starting phenix.real_space_refine
on Thu Feb  5 04:00:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m7x_63696/02_2026/9m7x_63696.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m7x_63696/02_2026/9m7x_63696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m7x_63696/02_2026/9m7x_63696.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m7x_63696/02_2026/9m7x_63696.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m7x_63696/02_2026/9m7x_63696.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m7x_63696/02_2026/9m7x_63696.cif"
  }
  resolution = 3.76
  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
-------------------------------------------------------------------------------
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=   0.006 sd=   0.057
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      46      5.16       5
     C    9407      2.51       5
     N    2557      2.21       5
     O    2842      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14852
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 4956
          Classifications: {'peptide': 616}
          Link IDs: {'PTRANS': 18, 'TRANS': 597}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 615, 4948
          Classifications: {'peptide': 615}
          Link IDs: {'PTRANS': 18, 'TRANS': 596}
    Chain: "C"
      Number of atoms: 4948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 615, 4948
          Classifications: {'peptide': 615}
          Link IDs: {'PTRANS': 18, 'TRANS': 596}
          Chain breaks: 1
  Time building chain proxies: 2.64, per 1000 atoms: 0.18
  Number of scatterers: 14852
  At special positions: 0
  Unit cell: (108, 132, 163.2, 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      46     16.00
     O    2842      8.00
     N    2557      7.00
     C    9407      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 413.9 milliseconds
  

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3398

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 29 sheets defined
      22.8% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 44
      removed outlier: 3.515A  pdb=" N   THR A  43 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 67
      removed outlier: 3.507A  pdb=" N   ASP A  64 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   VAL A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 90
      removed outlier: 3.756A  pdb=" N   VAL A  88 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLY A  90 " --> pdb=" O   ASN A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 102
      removed outlier: 3.829A  pdb=" N   LYS A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 135
      removed outlier: 4.140A  pdb=" N   ARG A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 128 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 144
    Processing helix  chain 'A' and resid 284 through 289
    Processing helix  chain 'A' and resid 413 through 423
      removed outlier: 3.952A  pdb=" N   GLY A 423 " --> pdb=" O   ILE A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 449
      removed outlier: 3.651A  pdb=" N   LEU A 449 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 465
      removed outlier: 3.757A  pdb=" N   LEU A 465 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
    Processing helix  chain 'A' and resid 564 through 568
      removed outlier: 3.633A  pdb=" N   HIS A 568 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 564 through 568'
    Processing helix  chain 'B' and resid 10 through 44
      removed outlier: 3.680A  pdb=" N   ALA B  15 " --> pdb=" O   ASN B  11 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS B  22 " --> pdb=" O   ASN B  18 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASN B  23 " --> pdb=" O   GLY B  19 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR B  43 " --> pdb=" O   ASN B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 67
      removed outlier: 3.985A  pdb=" N   ASP B  64 " --> pdb=" O   ASP B  60 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   VAL B  65 " --> pdb=" O   LYS B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 3.723A  pdb=" N   SER B  85 " --> pdb=" O   CYS B  81 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN B  86 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 102
    Processing helix  chain 'B' and resid 113 through 138
      removed outlier: 3.763A  pdb=" N   ARG B 117 " --> pdb=" O   THR B 113 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ALA B 128 " --> pdb=" O   ARG B 124 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLU B 137 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 144
    Processing helix  chain 'B' and resid 284 through 289
    Processing helix  chain 'B' and resid 301 through 305
      removed outlier: 3.508A  pdb=" N   GLU B 304 " --> pdb=" O   PRO B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 423
      removed outlier: 3.940A  pdb=" N   GLY B 423 " --> pdb=" O   ILE B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 449
    Processing helix  chain 'B' and resid 458 through 465
      removed outlier: 3.525A  pdb=" N   LEU B 464 " --> pdb=" O   SER B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 473
    Processing helix  chain 'B' and resid 563 through 568
      removed outlier: 3.797A  pdb=" N   THR B 566 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 44
      removed outlier: 3.844A  pdb=" N   PHE C  16 " --> pdb=" O   ARG C  12 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG C  17 " --> pdb=" O   GLU C  13 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ASN C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER C  32 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 89
    Processing helix  chain 'C' and resid 94 through 103
      removed outlier: 3.558A  pdb=" N   GLU C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER C 102 " --> pdb=" O   GLU C  98 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG C 103 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 138
      removed outlier: 3.601A  pdb=" N   ARG C 117 " --> pdb=" O   THR C 113 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU C 132 " --> pdb=" O   ALA C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 144
    Processing helix  chain 'C' and resid 242 through 246
      removed outlier: 3.592A  pdb=" N   LEU C 245 " --> pdb=" O   ASP C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 289
    Processing helix  chain 'C' and resid 301 through 305
      removed outlier: 3.557A  pdb=" N   GLU C 304 " --> pdb=" O   PRO C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 370
    Processing helix  chain 'C' and resid 413 through 423
      removed outlier: 3.849A  pdb=" N   GLY C 423 " --> pdb=" O   ILE C 419 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 465
      removed outlier: 3.626A  pdb=" N   LEU C 464 " --> pdb=" O   SER C 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 469 through 473
    Processing helix  chain 'C' and resid 538 through 543
      removed outlier: 3.583A  pdb=" N   TYR C 542 " --> pdb=" O   ASP C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 560 through 560
      No H-bonds generated for 'chain 'C' and resid 560 through 560'
    Processing helix  chain 'C' and resid 564 through 567
      No H-bonds generated for 'chain 'C' and resid 564 through 567'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 9
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.612A  pdb=" N   HIS A  49 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   TYR C  57 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 72
    Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 150
      removed outlier: 6.818A  pdb=" N   ILE A 404 " --> pdb=" O   TRP A 149 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A 403 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL A 387 " --> pdb=" O   THR A 380 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR A 380 " --> pdb=" O   VAL A 387 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLY A 376 " --> pdb=" O   GLY A 391 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 165
      removed outlier: 6.692A  pdb=" N   THR A 175 " --> pdb=" O   GLN A 161 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   PHE A 163 " --> pdb=" O   TYR A 173 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TYR A 173 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY A 198 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 216
      removed outlier: 3.658A  pdb=" N   GLY A 212 " --> pdb=" O   TRP A 223 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   TRP A 223 " --> pdb=" O   GLY A 212 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE A 233 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 263
      removed outlier: 4.285A  pdb=" N   ILE A 278 " --> pdb=" O   ARG A 274 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 317
      removed outlier: 6.622A  pdb=" N   VAL A 337 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   THR A 349 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   VAL A 339 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 357
    Processing sheet with id=AB1, first strand: chain 'A' and resid 437 through 438
      removed outlier: 6.763A  pdb=" N   HIS A 437 " --> pdb=" O   TYR A 456 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 490 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 437 through 438
      removed outlier: 6.763A  pdb=" N   HIS A 437 " --> pdb=" O   TYR A 456 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 490 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 530
      removed outlier: 3.913A  pdb=" N   GLN A 530 " --> pdb=" O   VAL B 526 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL B 526 " --> pdb=" O   GLN A 530 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR B 527 " --> pdb=" O   LYS B 505 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   LYS B 505 " --> pdb=" O   TYR B 527 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL B 490 " --> pdb=" O   ILE B 510 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL B 493 " --> pdb=" O   ASP B 480 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   HIS B 437 " --> pdb=" O   TYR B 456 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 529 through 530
      removed outlier: 3.913A  pdb=" N   GLN A 530 " --> pdb=" O   VAL B 526 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL B 526 " --> pdb=" O   GLN A 530 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR B 527 " --> pdb=" O   LYS B 505 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   LYS B 505 " --> pdb=" O   TYR B 527 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 578 through 585
      removed outlier: 3.826A  pdb=" N   PHE A 578 " --> pdb=" O   THR A 595 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   THR A 595 " --> pdb=" O   PHE A 578 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ARG A 591 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   TYR A 584 " --> pdb=" O   GLU A 589 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   GLU A 589 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE A 590 " --> pdb=" O   VAL A 609 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 72
    Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 151
      removed outlier: 7.196A  pdb=" N   ILE B 404 " --> pdb=" O   TRP B 149 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   GLU B 151 " --> pdb=" O   HIS B 402 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   HIS B 402 " --> pdb=" O   GLU B 151 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY B 391 " --> pdb=" O   GLY B 376 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   GLY B 376 " --> pdb=" O   GLY B 391 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   SER B 393 " --> pdb=" O   PRO B 374 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   GLY B 395 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   SER B 372 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 160 through 165
      removed outlier: 7.897A  pdb=" N   GLN B 160 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   SER B 177 " --> pdb=" O   GLN B 160 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   TYR B 162 " --> pdb=" O   THR B 175 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B 172 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY B 198 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 212 through 216
    Processing sheet with id=AC1, first strand: chain 'B' and resid 259 through 263
      removed outlier: 3.582A  pdb=" N   GLU B 280 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG B 274 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   ILE B 278 " --> pdb=" O   ARG B 274 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE B 279 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 315 through 317
      removed outlier: 3.551A  pdb=" N   ALA B 316 " --> pdb=" O   TYR B 323 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   VAL B 337 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   THR B 349 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   VAL B 339 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 529 through 530
    Processing sheet with id=AC4, first strand: chain 'B' and resid 578 through 584
      removed outlier: 6.562A  pdb=" N   ARG B 591 " --> pdb=" O   SER B 582 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN B 592 " --> pdb=" O   ARG B 607 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 147 through 150
      removed outlier: 3.514A  pdb=" N   TRP C 149 " --> pdb=" O   ILE C 404 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   ILE C 404 " --> pdb=" O   TRP C 149 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   GLY C 376 " --> pdb=" O   GLY C 391 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   SER C 393 " --> pdb=" O   PRO C 374 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   GLY C 395 " --> pdb=" O   SER C 372 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   SER C 372 " --> pdb=" O   GLY C 395 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 160 through 165
      removed outlier: 6.663A  pdb=" N   THR C 175 " --> pdb=" O   GLN C 161 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   PHE C 163 " --> pdb=" O   TYR C 173 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   TYR C 173 " --> pdb=" O   PHE C 163 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLN C 174 " --> pdb=" O   ASN C 188 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   PHE C 185 " --> pdb=" O   HIS C 201 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   HIS C 201 " --> pdb=" O   PHE C 185 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ILE C 187 " --> pdb=" O   THR C 199 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR C 199 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   GLU C 189 " --> pdb=" O   LEU C 197 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 212 through 216
    Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 263
      removed outlier: 3.578A  pdb=" N   GLU C 280 " --> pdb=" O   PHE C 272 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG C 274 " --> pdb=" O   ILE C 278 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ILE C 278 " --> pdb=" O   ARG C 274 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE C 279 " --> pdb=" O   VAL C 298 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 313 through 317
      removed outlier: 5.024A  pdb=" N   GLY C 314 " --> pdb=" O   MET C 325 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   VAL C 337 " --> pdb=" O   THR C 349 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   THR C 349 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   VAL C 339 " --> pdb=" O   LEU C 347 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 453 through 456
      removed outlier: 4.221A  pdb=" N   GLY C 453 " --> pdb=" O   ASN C 481 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL C 493 " --> pdb=" O   ASP C 480 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 580 through 584
      removed outlier: 6.246A  pdb=" N   ARG C 591 " --> pdb=" O   SER C 582 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   PHE C 590 " --> pdb=" O   VAL C 609 " (cutoff:3.500A)

    494 hydrogen bonds defined for protein.
    1314 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: 2.18

  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:
        1.20 -     1.51: 10270
        1.51 -     1.83: 4916
        1.83 -     2.14: 0
        2.14 -     2.46: 2
        2.46 -     2.78: 1
  Bond restraints: 15189
  Sorted by residual:
  bond pdb=" C   GLU B 560 "
       pdb=" N   ASN B 563 "
    ideal  model  delta    sigma   weight residual
    1.335  2.778 -1.443 1.36e-02 5.41e+03 1.13e+04
  bond pdb=" C   PRO B 552 "
       pdb=" N   LYS B 554 "
    ideal  model  delta    sigma   weight residual
    1.330  2.433 -1.103 1.20e-02 6.94e+03 8.46e+03
  bond pdb=" C   PRO C 552 "
       pdb=" N   LYS C 554 "
    ideal  model  delta    sigma   weight residual
    1.330  2.381 -1.051 1.45e-02 4.76e+03 5.26e+03
  bond pdb=" CA  LEU C 564 "
       pdb=" C   LEU C 564 "
    ideal  model  delta    sigma   weight residual
    1.522  1.412  0.111 1.36e-02 5.41e+03 6.62e+01
  bond pdb=" CA  TYR A 556 "
       pdb=" C   TYR A 556 "
    ideal  model  delta    sigma   weight residual
    1.530  1.448  0.082 1.11e-02 8.12e+03 5.44e+01
  ... (remaining 15184 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.12: 20332
        5.12 -    10.25: 179
       10.25 -    15.37: 20
       15.37 -    20.49: 3
       20.49 -    25.62: 2
  Bond angle restraints: 20536
  Sorted by residual:
  angle pdb=" O   PRO B 552 "
        pdb=" C   PRO B 552 "
        pdb=" N   LYS B 554 "
      ideal   model   delta    sigma   weight residual
     122.64   97.02   25.62 1.35e+00 5.49e-01 3.60e+02
  angle pdb=" C   GLU B 560 "
        pdb=" N   ASN B 563 "
        pdb=" CA  ASN B 563 "
      ideal   model   delta    sigma   weight residual
     120.29  142.94  -22.65 1.42e+00 4.96e-01 2.54e+02
  angle pdb=" O   PRO C 552 "
        pdb=" C   PRO C 552 "
        pdb=" N   LYS C 554 "
      ideal   model   delta    sigma   weight residual
     122.64  105.29   17.35 1.35e+00 5.49e-01 1.65e+02
  angle pdb=" N   ALA A 367 "
        pdb=" CA  ALA A 367 "
        pdb=" C   ALA A 367 "
      ideal   model   delta    sigma   weight residual
     111.07  124.23  -13.16 1.07e+00 8.73e-01 1.51e+02
  angle pdb=" N   VAL B 470 "
        pdb=" CA  VAL B 470 "
        pdb=" C   VAL B 470 "
      ideal   model   delta    sigma   weight residual
     110.62  122.22  -11.60 1.02e+00 9.61e-01 1.29e+02
  ... (remaining 20531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 8100
       17.77 -    35.54: 743
       35.54 -    53.31: 105
       53.31 -    71.08: 25
       71.08 -    88.85: 7
  Dihedral angle restraints: 8980
    sinusoidal: 3657
      harmonic: 5323
  Sorted by residual:
  dihedral pdb=" C   SER A 599 "
           pdb=" N   SER A 599 "
           pdb=" CA  SER A 599 "
           pdb=" CB  SER A 599 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.67   22.07     0      2.50e+00 1.60e-01 7.79e+01
  dihedral pdb=" N   SER A 599 "
           pdb=" C   SER A 599 "
           pdb=" CA  SER A 599 "
           pdb=" CB  SER A 599 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  143.66  -20.86     0      2.50e+00 1.60e-01 6.96e+01
  dihedral pdb=" CA  PRO B 552 "
           pdb=" C   PRO B 552 "
           pdb=" N   LYS B 554 "
           pdb=" CA  LYS B 554 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -141.92  -38.08     0      5.00e+00 4.00e-02 5.80e+01
  ... (remaining 8977 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.197: 2131
       0.197 -    0.393: 46
       0.393 -    0.590: 14
       0.590 -    0.787: 2
       0.787 -    0.984: 1
  Chirality restraints: 2194
  Sorted by residual:
  chirality pdb=" CA  SER A 599 "
            pdb=" N   SER A 599 "
            pdb=" C   SER A 599 "
            pdb=" CB  SER A 599 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.53    0.98 2.00e-01 2.50e+01 2.42e+01
  chirality pdb=" CA  TYR C 366 "
            pdb=" N   TYR C 366 "
            pdb=" C   TYR C 366 "
            pdb=" CB  TYR C 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.76    0.75 2.00e-01 2.50e+01 1.40e+01
  chirality pdb=" CA  HIS A 371 "
            pdb=" N   HIS A 371 "
            pdb=" C   HIS A 371 "
            pdb=" CB  HIS A 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.89    0.63 2.00e-01 2.50e+01 9.78e+00
  ... (remaining 2191 not shown)

  Planarity restraints: 2666
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 560 "    0.086 2.00e-02 2.50e+03   1.57e-01 2.45e+02
        pdb=" C   GLU B 560 "   -0.265 2.00e-02 2.50e+03
        pdb=" O   GLU B 560 "    0.135 2.00e-02 2.50e+03
        pdb=" N   ASN B 563 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 552 "    0.068 2.00e-02 2.50e+03   9.28e-02 8.62e+01
        pdb=" C   PRO B 552 "   -0.160 2.00e-02 2.50e+03
        pdb=" O   PRO B 552 "    0.056 2.00e-02 2.50e+03
        pdb=" N   LYS B 554 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C 552 "    0.047 2.00e-02 2.50e+03   6.86e-02 4.71e+01
        pdb=" C   PRO C 552 "   -0.118 2.00e-02 2.50e+03
        pdb=" O   PRO C 552 "    0.045 2.00e-02 2.50e+03
        pdb=" N   LYS C 554 "    0.026 2.00e-02 2.50e+03
  ... (remaining 2663 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2635
        2.76 -     3.29: 13762
        3.29 -     3.83: 23177
        3.83 -     4.36: 26649
        4.36 -     4.90: 45980
  Nonbonded interactions: 112203
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 606 "
            pdb=" OD1 ASN C 597 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OD2 ASP A 242 "
            pdb=" OG1 THR A 244 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG  SER C 326 "
            pdb=" N   LYS C 336 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OG  SER A 326 "
            pdb=" N   LYS A 336 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" OE2 GLU B  14 "
            pdb=" ND2 ASN B  18 "
     model   vdw
     2.261 3.120
  ... (remaining 112198 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 552 or resid 554 through 619))
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.180
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.710
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
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      :  0.019   1.443  15189  Z= 1.396
  Angle     :  1.213  25.616  20536  Z= 0.780
  Chirality :  0.083   0.984   2194
  Planarity :  0.008   0.157   2666
  Dihedral  : 13.605  88.853   5582
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  1.37 %
    Allowed  :  5.90 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  :  2.36 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.59 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.19), residues: 1830
  helix:  1.50 (0.28), residues: 341
  sheet:  0.01 (0.24), residues: 481
  loop : -1.83 (0.18), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 431 
 TYR   0.021   0.002   TYR A 556 
 PHE   0.026   0.002   PHE A 578 
 TRP   0.016   0.002   TRP C 617 
 HIS   0.006   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.01888 (15189)
  covalent geometry    : angle       1.21337 (20536)
  hydrogen bonds       : bond        0.24698 (  479)
  hydrogen bonds       : angle       8.86869 ( 1314)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 185
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  492 GLN cc_start: 0.8120 (tt0) cc_final: 0.7393 (tm-30)
REVERT: A  509 MET cc_start: 0.8428 (mmm) cc_final: 0.8008 (mmm)
REVERT: B  220 MET cc_start: 0.6856 (ttm) cc_final: 0.6441 (ttp)
REVERT: B  371 HIS cc_start: 0.7830 (t70) cc_final: 0.7445 (t70)
REVERT: B  557 MET cc_start: 0.7566 (mmm) cc_final: 0.7122 (mmm)
REVERT: B  601 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7853 (tpm170)
REVERT: C  250 MET cc_start: 0.8185 (mmm) cc_final: 0.7680 (mmm)
REVERT: C  281 LEU cc_start: 0.8882 (tp) cc_final: 0.8625 (tt)
  outliers start: 45
  outliers final: 13
  residues processed: 223
  average time/residue: 0.1101
  time to fit residues: 36.2821
Evaluate side-chains
  120 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  601 ARG
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  483 PRO
Chi-restraints excluded: chain C residue  560 GLU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  571 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    3.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 174 GLN
A 401 HIS
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 169 ASN
B 288 ASN
B 458 GLN
B 592 GLN
C 370 ASN
C 486 GLN
** C 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.070135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.057254 restraints weight = 65610.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.058966 restraints weight = 32079.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.060097 restraints weight = 19583.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.060860 restraints weight = 13806.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.061385 restraints weight = 10704.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15189  Z= 0.161
  Angle     :  0.703   8.696  20536  Z= 0.375
  Chirality :  0.045   0.280   2194
  Planarity :  0.005   0.054   2666
  Dihedral  :  6.955  59.769   2049
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  :  5.56 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  7.57 %
    Favored  : 90.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.19), residues: 1836
  helix:  2.09 (0.29), residues: 328
  sheet:  0.16 (0.24), residues: 488
  loop : -1.84 (0.17), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 491 
 TYR   0.024   0.001   TYR A 556 
 PHE   0.023   0.002   PHE A 590 
 TRP   0.014   0.002   TRP A 478 
 HIS   0.004   0.001   HIS C 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (15189)
  covalent geometry    : angle       0.70303 (20536)
  hydrogen bonds       : bond        0.06263 (  479)
  hydrogen bonds       : angle       6.25823 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8723 (tpt) cc_final: 0.8306 (tpt)
REVERT: A  340 TYR cc_start: 0.8521 (m-80) cc_final: 0.8304 (m-80)
REVERT: A  492 GLN cc_start: 0.8351 (tt0) cc_final: 0.7154 (tm-30)
REVERT: A  509 MET cc_start: 0.8461 (mmm) cc_final: 0.8208 (mmm)
REVERT: B  371 HIS cc_start: 0.7907 (t70) cc_final: 0.7470 (t70)
REVERT: B  601 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7571 (tpm170)
REVERT: C  250 MET cc_start: 0.8256 (mmm) cc_final: 0.7846 (mmm)
REVERT: C  325 MET cc_start: 0.8429 (ttp) cc_final: 0.8111 (ttp)
REVERT: C  443 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7987 (mt)
  outliers start: 27
  outliers final: 12
  residues processed: 136
  average time/residue: 0.1046
  time to fit residues: 21.4908
Evaluate side-chains
  99 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  601 ARG
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  571 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 39 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 99 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 135 optimal weight:    7.9990
   chunk 125 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0970
   overall best weight:    4.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 174 GLN
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 157 ASN
** C 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.068834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.055882 restraints weight = 66420.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.057562 restraints weight = 32405.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.058676 restraints weight = 19804.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.059430 restraints weight = 13933.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.059950 restraints weight = 10817.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15189  Z= 0.171
  Angle     :  0.665   8.405  20536  Z= 0.353
  Chirality :  0.044   0.185   2194
  Planarity :  0.005   0.055   2666
  Dihedral  :  6.147  53.988   2035
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  6.48 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  8.68 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.19), residues: 1836
  helix:  2.38 (0.29), residues: 321
  sheet:  0.22 (0.24), residues: 491
  loop : -1.70 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 491 
 TYR   0.012   0.001   TYR C  76 
 PHE   0.021   0.001   PHE A 590 
 TRP   0.013   0.002   TRP B 324 
 HIS   0.005   0.001   HIS C 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (15189)
  covalent geometry    : angle       0.66538 (20536)
  hydrogen bonds       : bond        0.05780 (  479)
  hydrogen bonds       : angle       5.62061 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8822 (tpt) cc_final: 0.8567 (tpt)
REVERT: A  250 MET cc_start: 0.7438 (mpp) cc_final: 0.7165 (mpp)
REVERT: A  492 GLN cc_start: 0.8281 (tt0) cc_final: 0.7171 (tm-30)
REVERT: A  509 MET cc_start: 0.8396 (mmm) cc_final: 0.8190 (mmm)
REVERT: B  371 HIS cc_start: 0.8150 (t70) cc_final: 0.7782 (t70)
REVERT: B  601 ARG cc_start: 0.8698 (mpt-90) cc_final: 0.7629 (tpt90)
REVERT: C  250 MET cc_start: 0.7940 (mmm) cc_final: 0.7558 (mmm)
REVERT: C  266 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9055 (ptpp)
REVERT: C  325 MET cc_start: 0.8492 (ttp) cc_final: 0.8239 (ttp)
REVERT: C  565 PHE cc_start: 0.5308 (OUTLIER) cc_final: 0.4886 (t80)
  outliers start: 37
  outliers final: 17
  residues processed: 129
  average time/residue: 0.0957
  time to fit residues: 19.1484
Evaluate side-chains
  102 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  266 LYS
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  571 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 167 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 90 optimal weight:   30.0000
   chunk 136 optimal weight:    1.9990
   chunk 59 optimal weight:   20.0000
   chunk 34 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 151 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 401 HIS
B 597 ASN
** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.067235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.054393 restraints weight = 66676.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.056039 restraints weight = 32217.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.057122 restraints weight = 19612.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.057847 restraints weight = 13823.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.058327 restraints weight = 10776.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15189  Z= 0.193
  Angle     :  0.676  13.793  20536  Z= 0.355
  Chirality :  0.044   0.274   2194
  Planarity :  0.005   0.053   2666
  Dihedral  :  5.857  52.306   2029
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  7.03 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 10.17 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.20), residues: 1836
  helix:  2.25 (0.29), residues: 323
  sheet:  0.07 (0.24), residues: 497
  loop : -1.63 (0.19), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 491 
 TYR   0.014   0.002   TYR C  76 
 PHE   0.018   0.002   PHE A 590 
 TRP   0.016   0.002   TRP B 324 
 HIS   0.005   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (15189)
  covalent geometry    : angle       0.67570 (20536)
  hydrogen bonds       : bond        0.05925 (  479)
  hydrogen bonds       : angle       5.44390 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   31 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9239 (m-10)
REVERT: A   40 SER cc_start: 0.9238 (t) cc_final: 0.8988 (p)
REVERT: B  309 TYR cc_start: 0.8088 (m-10) cc_final: 0.7810 (m-10)
REVERT: B  371 HIS cc_start: 0.8199 (t70) cc_final: 0.7872 (t70)
REVERT: B  601 ARG cc_start: 0.8631 (mpt-90) cc_final: 0.7521 (tpm170)
REVERT: C   55 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8985 (mp)
REVERT: C  250 MET cc_start: 0.7891 (mmm) cc_final: 0.7619 (mmm)
REVERT: C  503 MET cc_start: 0.6092 (mtp) cc_final: 0.5454 (mtp)
REVERT: C  565 PHE cc_start: 0.5406 (OUTLIER) cc_final: 0.4832 (t80)
  outliers start: 38
  outliers final: 23
  residues processed: 117
  average time/residue: 0.0937
  time to fit residues: 17.3950
Evaluate side-chains
  106 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 PHE
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  556 TYR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  571 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   chunk 161 optimal weight:   10.0000
   chunk 105 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 139 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 152 optimal weight:   10.0000
   chunk 154 optimal weight:    9.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 174 GLN
** C 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.066936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.054231 restraints weight = 66868.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.055832 restraints weight = 32796.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.056886 restraints weight = 20172.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.057614 restraints weight = 14279.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.058103 restraints weight = 11125.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15189  Z= 0.186
  Angle     :  0.652   9.408  20536  Z= 0.343
  Chirality :  0.043   0.171   2194
  Planarity :  0.005   0.053   2666
  Dihedral  :  5.749  53.094   2027
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  7.14 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 11.23 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.20), residues: 1836
  helix:  2.33 (0.29), residues: 321
  sheet:  0.15 (0.24), residues: 498
  loop : -1.63 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 491 
 TYR   0.013   0.001   TYR A 416 
 PHE   0.018   0.001   PHE B 590 
 TRP   0.016   0.002   TRP B 324 
 HIS   0.005   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (15189)
  covalent geometry    : angle       0.65194 (20536)
  hydrogen bonds       : bond        0.05760 (  479)
  hydrogen bonds       : angle       5.36614 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 90
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A   31 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9175 (m-10)
REVERT: A   40 SER cc_start: 0.9239 (t) cc_final: 0.8971 (p)
REVERT: B  371 HIS cc_start: 0.8130 (t70) cc_final: 0.7596 (t-170)
REVERT: B  601 ARG cc_start: 0.8623 (mpt-90) cc_final: 0.7466 (tpm170)
REVERT: C  565 PHE cc_start: 0.5387 (OUTLIER) cc_final: 0.4750 (t80)
  outliers start: 43
  outliers final: 26
  residues processed: 123
  average time/residue: 0.0990
  time to fit residues: 18.6964
Evaluate side-chains
  106 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 PHE
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  556 TYR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  530 GLN
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  571 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 131 optimal weight:    9.9990
   chunk 114 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 107 optimal weight:    0.6980
   chunk 182 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 174 GLN
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 597 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 = 0.3419 r_free = 0.3419 target = 0.068084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.055368 restraints weight = 65693.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.057015 restraints weight = 31804.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.058126 restraints weight = 19368.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.058871 restraints weight = 13587.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.059357 restraints weight = 10514.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15189  Z= 0.131
  Angle     :  0.616   8.996  20536  Z= 0.323
  Chirality :  0.042   0.162   2194
  Planarity :  0.005   0.062   2666
  Dihedral  :  5.510  53.021   2027
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  6.21 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.41 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.20), residues: 1836
  helix:  2.48 (0.29), residues: 330
  sheet:  0.27 (0.24), residues: 483
  loop : -1.62 (0.19), residues: 1023

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG C 491 
 TYR   0.016   0.001   TYR C 556 
 PHE   0.018   0.001   PHE B 590 
 TRP   0.016   0.001   TRP B 324 
 HIS   0.005   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (15189)
  covalent geometry    : angle       0.61632 (20536)
  hydrogen bonds       : bond        0.05067 (  479)
  hydrogen bonds       : angle       5.08270 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 91
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A   31 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.9176 (m-10)
REVERT: B  250 MET cc_start: 0.9267 (tmm) cc_final: 0.8485 (tmm)
REVERT: B  371 HIS cc_start: 0.8120 (t70) cc_final: 0.7763 (t70)
REVERT: B  591 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6647 (mpt180)
REVERT: B  601 ARG cc_start: 0.8620 (mpt-90) cc_final: 0.7488 (tpm170)
REVERT: B  608 MET cc_start: 0.6682 (tpp) cc_final: 0.5795 (tpp)
REVERT: C  565 PHE cc_start: 0.5290 (OUTLIER) cc_final: 0.4682 (t80)
  outliers start: 37
  outliers final: 26
  residues processed: 121
  average time/residue: 0.0949
  time to fit residues: 17.8364
Evaluate side-chains
  108 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 PHE
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  556 TYR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  530 GLN
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  537 ILE
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  571 LYS
Chi-restraints excluded: chain C residue  579 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 144 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   chunk 175 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 99 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 168 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 597 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 = 0.3395 r_free = 0.3395 target = 0.067038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.054272 restraints weight = 66112.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.055914 restraints weight = 32056.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.056990 restraints weight = 19533.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.057721 restraints weight = 13745.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.058180 restraints weight = 10666.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15189  Z= 0.168
  Angle     :  0.630   9.153  20536  Z= 0.331
  Chirality :  0.043   0.167   2194
  Planarity :  0.005   0.060   2666
  Dihedral  :  5.542  54.119   2027
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  7.03 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.34 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.20), residues: 1836
  helix:  2.46 (0.29), residues: 328
  sheet:  0.20 (0.24), residues: 490
  loop : -1.62 (0.19), residues: 1018

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 491 
 TYR   0.012   0.001   TYR A 416 
 PHE   0.019   0.001   PHE A 590 
 TRP   0.017   0.001   TRP B 324 
 HIS   0.004   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (15189)
  covalent geometry    : angle       0.62995 (20536)
  hydrogen bonds       : bond        0.05338 (  479)
  hydrogen bonds       : angle       5.12842 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 84
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   31 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.9119 (m-10)
REVERT: A   38 MET cc_start: 0.8851 (tpt) cc_final: 0.8442 (tpt)
REVERT: B   80 GLU cc_start: 0.8987 (tp30) cc_final: 0.8786 (tp30)
REVERT: B  250 MET cc_start: 0.9200 (tmm) cc_final: 0.8284 (tmm)
REVERT: B  371 HIS cc_start: 0.8040 (t70) cc_final: 0.7645 (t70)
REVERT: B  601 ARG cc_start: 0.8664 (mpt-90) cc_final: 0.7598 (tpm170)
REVERT: C  565 PHE cc_start: 0.5284 (OUTLIER) cc_final: 0.4681 (t80)
  outliers start: 40
  outliers final: 30
  residues processed: 116
  average time/residue: 0.0926
  time to fit residues: 17.0478
Evaluate side-chains
  112 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 PHE
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  556 TYR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  530 GLN
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  571 LYS
Chi-restraints excluded: chain C residue  579 TYR
Chi-restraints excluded: chain C residue  606 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 43 optimal weight:    0.4980
   chunk 35 optimal weight:    3.9990
   chunk 122 optimal weight:    0.0980
   chunk 128 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 136 optimal weight:    9.9990
   chunk 174 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
B 111 HIS
B 401 HIS
C  86 ASN
** C 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.069152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.056454 restraints weight = 65258.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.058174 restraints weight = 31420.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.059292 restraints weight = 18976.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.060042 restraints weight = 13215.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.060528 restraints weight = 10207.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  15189  Z= 0.109
  Angle     :  0.591  10.048  20536  Z= 0.309
  Chirality :  0.041   0.158   2194
  Planarity :  0.005   0.056   2666
  Dihedral  :  5.215  52.910   2027
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.45 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.02 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.20), residues: 1836
  helix:  2.69 (0.29), residues: 329
  sheet:  0.38 (0.24), residues: 479
  loop : -1.46 (0.19), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 491 
 TYR   0.014   0.001   TYR B 309 
 PHE   0.018   0.001   PHE B 590 
 TRP   0.018   0.001   TRP B 324 
 HIS   0.005   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (15189)
  covalent geometry    : angle       0.59117 (20536)
  hydrogen bonds       : bond        0.04280 (  479)
  hydrogen bonds       : angle       4.84318 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 94
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.9118 (m-10)
REVERT: A   38 MET cc_start: 0.8844 (tpt) cc_final: 0.8568 (tpt)
REVERT: A  222 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8360 (mtm)
REVERT: A  340 TYR cc_start: 0.8319 (m-80) cc_final: 0.8077 (m-10)
REVERT: A  553 MET cc_start: 0.8172 (mpp) cc_final: 0.7694 (mpp)
REVERT: A  555 MET cc_start: 0.8577 (tpt) cc_final: 0.8351 (tpt)
REVERT: B  250 MET cc_start: 0.9351 (tmm) cc_final: 0.8571 (tmm)
REVERT: B  371 HIS cc_start: 0.7967 (t70) cc_final: 0.7570 (t-170)
REVERT: B  601 ARG cc_start: 0.8696 (mpt-90) cc_final: 0.7643 (tpm170)
REVERT: C  557 MET cc_start: 0.6411 (ptp) cc_final: 0.5709 (pmm)
REVERT: C  565 PHE cc_start: 0.5086 (OUTLIER) cc_final: 0.4518 (t80)
  outliers start: 33
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0939
  time to fit residues: 17.7022
Evaluate side-chains
  106 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 PHE
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  556 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  571 LYS
Chi-restraints excluded: chain C residue  579 TYR
Chi-restraints excluded: chain C residue  604 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 168 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 76 optimal weight:    7.9990
   chunk 55 optimal weight:   20.0000
   chunk 172 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 148 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    5.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.066641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.053892 restraints weight = 66304.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.055521 restraints weight = 32130.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.056613 restraints weight = 19574.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.057323 restraints weight = 13744.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.057825 restraints weight = 10697.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15189  Z= 0.194
  Angle     :  0.659   8.542  20536  Z= 0.343
  Chirality :  0.043   0.169   2194
  Planarity :  0.005   0.064   2666
  Dihedral  :  5.504  55.085   2027
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  7.30 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.27 %
    Favored  : 83.75 %
  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: -0.48 (0.20), residues: 1836
  helix:  2.31 (0.30), residues: 331
  sheet:  0.10 (0.24), residues: 495
  loop : -1.52 (0.19), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C 491 
 TYR   0.015   0.001   TYR A 416 
 PHE   0.019   0.001   PHE B 590 
 TRP   0.018   0.002   TRP B 324 
 HIS   0.004   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (15189)
  covalent geometry    : angle       0.65907 (20536)
  hydrogen bonds       : bond        0.05531 (  479)
  hydrogen bonds       : angle       5.14831 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.9127 (m-10)
REVERT: A  340 TYR cc_start: 0.8492 (m-80) cc_final: 0.8275 (m-10)
REVERT: B  250 MET cc_start: 0.9127 (tmm) cc_final: 0.8111 (tmm)
REVERT: B  371 HIS cc_start: 0.7966 (t70) cc_final: 0.7520 (t-170)
REVERT: B  503 MET cc_start: 0.8318 (mmm) cc_final: 0.8012 (mtt)
REVERT: B  601 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7929 (mmm160)
REVERT: C  557 MET cc_start: 0.6328 (ptp) cc_final: 0.5641 (pmm)
REVERT: C  565 PHE cc_start: 0.5216 (OUTLIER) cc_final: 0.4573 (t80)
  outliers start: 32
  outliers final: 25
  residues processed: 108
  average time/residue: 0.0919
  time to fit residues: 15.9180
Evaluate side-chains
  106 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 PHE
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  556 TYR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  530 GLN
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  601 ARG
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  570 VAL
Chi-restraints excluded: chain C residue  571 LYS
Chi-restraints excluded: chain C residue  578 PHE
Chi-restraints excluded: chain C residue  579 TYR
Chi-restraints excluded: chain C residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 112 optimal weight:   20.0000
   chunk 166 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 110 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  41 HIS
C  42 GLN
** C 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.066800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.054091 restraints weight = 66090.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.055733 restraints weight = 31987.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.056802 restraints weight = 19435.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.057535 restraints weight = 13640.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.058031 restraints weight = 10564.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15189  Z= 0.172
  Angle     :  0.645  10.510  20536  Z= 0.336
  Chirality :  0.043   0.166   2194
  Planarity :  0.005   0.057   2666
  Dihedral  :  5.513  56.522   2027
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.70 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.76 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.20), residues: 1836
  helix:  2.26 (0.30), residues: 330
  sheet:  0.10 (0.24), residues: 489
  loop : -1.54 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 491 
 TYR   0.012   0.001   TYR A 416 
 PHE   0.019   0.001   PHE A 590 
 TRP   0.020   0.002   TRP B 324 
 HIS   0.004   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (15189)
  covalent geometry    : angle       0.64543 (20536)
  hydrogen bonds       : bond        0.05326 (  479)
  hydrogen bonds       : angle       5.07836 ( 1314)

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

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

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3672 Ramachandran restraints generated.
    1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.573 
Fit side-chains
REVERT: A   31 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9120 (m-10)
REVERT: A  340 TYR cc_start: 0.8465 (m-80) cc_final: 0.8247 (m-10)
REVERT: A  553 MET cc_start: 0.7870 (mpp) cc_final: 0.7442 (mpp)
REVERT: B  371 HIS cc_start: 0.7883 (t70) cc_final: 0.7449 (t-170)
REVERT: B  503 MET cc_start: 0.8314 (mmm) cc_final: 0.7727 (mtt)
REVERT: B  601 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7824 (mmm160)
REVERT: C  557 MET cc_start: 0.5926 (ptp) cc_final: 0.5095 (pmm)
REVERT: C  565 PHE cc_start: 0.5206 (OUTLIER) cc_final: 0.4535 (t80)
  outliers start: 32
  outliers final: 27
  residues processed: 104
  average time/residue: 0.0937
  time to fit residues: 15.5107
Evaluate side-chains
  108 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 PHE
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  556 TYR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  530 GLN
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  601 ARG
Chi-restraints excluded: chain C residue   60 ASP
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  239 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  565 PHE
Chi-restraints excluded: chain C residue  570 VAL
Chi-restraints excluded: chain C residue  571 LYS
Chi-restraints excluded: chain C residue  578 PHE
Chi-restraints excluded: chain C residue  579 TYR
Chi-restraints excluded: chain C residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 125 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 90 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 109 optimal weight:   10.0000
   chunk 162 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 103 optimal weight:   30.0000
   chunk 111 optimal weight:    6.9990
   overall best weight:    4.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.067126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.054449 restraints weight = 65678.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.056100 restraints weight = 31831.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.057181 restraints weight = 19352.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.057923 restraints weight = 13557.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.058428 restraints weight = 10466.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15189  Z= 0.150
  Angle     :  0.640  13.661  20536  Z= 0.330
  Chirality :  0.042   0.163   2194
  Planarity :  0.005   0.057   2666
  Dihedral  :  5.453  54.349   2027
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  6.64 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.64 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.20), residues: 1836
  helix:  2.29 (0.30), residues: 330
  sheet:  0.16 (0.24), residues: 484
  loop : -1.54 (0.19), residues: 1022

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 491 
 TYR   0.012   0.001   TYR C 579 
 PHE   0.019   0.001   PHE B 590 
 TRP   0.019   0.002   TRP B 324 
 HIS   0.004   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (15189)
  covalent geometry    : angle       0.64033 (20536)
  hydrogen bonds       : bond        0.05143 (  479)
  hydrogen bonds       : angle       5.04701 ( 1314)

===============================================================================
Job complete
usr+sys time: 1872.42 seconds
wall clock time: 33 minutes 25.31 seconds (2005.31 seconds total)